Contacts of the strand formed by residues 570 - 590 (chain A) in PDB entry 1QFG


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with SER 570 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516A  GLN*     6.0     0.2    -      -       -      -
    517A  VAL      5.5     0.2    +      -       -      -
    518A  GLY*     4.6     1.4    -      -       -      -
    519A  LYS*     4.7     2.3    +      -       -      +
    524A  PHE*     3.5    31.5    -      -       -      -
    560A  LEU*     4.2    18.4    -      -       -      +
    561A  MET      3.1    17.0    +      -       -      -
    562A  ALA*     4.8     0.8    -      -       -      +
    569A  PHE*     1.3    84.9    -      -       -      +
    571A  VAL*     1.3    73.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 571 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    519A  LYS*     6.5     1.3    -      -       +      -
    524A  PHE*     4.2     4.7    -      -       -      -
    560A  LEU*     3.5     6.2    -      -       -      -
    561A  MET*     2.7    48.0    +      -       +      +
    563A  ASP*     4.1    19.1    -      -       -      +
    564A  PRO*     4.0    27.8    -      -       +      -
    570A  SER*     1.3    80.5    -      -       -      +
    572A  GLU*     1.3    71.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 572 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    524A  PHE*     3.8    14.0    -      -       +      -
    525A  ALA*     3.5    27.9    +      -       -      +
    558A  ASN*     3.1    25.5    +      -       -      +
    559A  ASN      4.1     2.5    -      -       -      +
    560A  LEU*     3.7    18.4    -      -       +      -
    561A  MET*     3.2    19.1    -      -       -      +
    571A  VAL*     1.3    79.1    -      -       -      +
    573A  GLY*     1.3    68.9    +      -       -      +
    574A  GLY      3.1     4.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 573 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    558A  ASN*     2.9    18.9    +      -       -      +
    561A  MET*     4.2     3.8    -      -       -      -
    572A  GLU*     1.3    80.2    -      -       -      +
    574A  GLY*     1.3    66.3    +      -       -      +
    575A  GLU*     3.8     2.4    +      -       -      +
    608A  THR*     3.9    14.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 574 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    558A  ASN      2.8    11.8    +      -       -      -
    559A  ASN*     2.7    44.3    +      -       -      -
    561A  MET*     3.7    14.3    -      -       -      -
    572A  GLU      3.1     3.8    +      -       -      -
    573A  GLY*     1.3    80.0    -      -       -      +
    575A  GLU*     1.3    59.5    +      -       -      +
    608A  THR*     3.4    12.8    -      -       -      -
    609A  ASP*     5.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 575 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555A  THR*     4.1    14.5    +      -       +      +
    556A  LYS      3.4    13.2    -      -       -      +
    557A  THR*     3.6    23.2    -      -       +      +
    559A  ASN*     4.1     2.3    -      -       -      +
    573A  GLY      4.5     1.9    -      -       -      +
    574A  GLY*     1.3    74.7    -      -       -      +
    576A  ILE*     1.3    66.5    +      -       -      +
    577A  ARG*     6.1     0.6    -      -       +      +
    606A  TYR*     3.8     0.9    -      -       -      -
    607A  THR*     2.8    44.6    +      -       +      +
    608A  THR*     2.9    32.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 576 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  PHE*     3.6    34.6    -      -       +      -
    554A  LEU      4.0     0.5    -      -       -      +
    555A  THR*     3.6     3.5    +      -       -      +
    556A  LYS*     2.9    38.8    +      -       +      +
    559A  ASN*     3.1    38.3    -      -       -      +
    575A  GLU*     1.3    76.3    -      -       -      +
    577A  ARG*     1.3    70.4    +      -       -      +
    604A  ALA*     5.2     1.8    -      -       +      -
    605A  GLU      3.4    11.9    -      -       -      +
    606A  TYR*     3.5    36.8    -      -       +      +
    617A  PRO*     4.8    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 577 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553A  ASN*     3.7    14.3    +      -       -      +
    554A  LEU      3.5     6.3    -      -       -      +
    555A  THR*     4.0    11.9    -      -       -      +
    575A  GLU*     6.1     0.7    -      -       +      +
    576A  ILE*     1.3    76.9    -      -       -      +
    578A  ALA*     1.3    67.5    +      -       -      +
    579A  ARG*     3.1    56.1    -      -       +      +
    603A  ASP*     3.7     2.7    +      -       -      +
    604A  ALA*     3.1     1.9    -      -       -      -
    605A  GLU*     2.4    78.2    +      -       +      +
    607A  THR*     4.2    16.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 578 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  ARG      3.7    23.1    -      -       -      +
     95A  PHE*     3.8    15.7    -      -       +      -
    552A  TYR*     3.3    16.7    -      -       +      +
    554A  LEU*     2.7    39.2    +      -       +      +
    577A  ARG*     1.3    76.8    -      -       -      +
    579A  ARG*     1.3    60.0    +      -       -      +
    602A  THR*     4.7     2.9    -      -       +      -
    603A  ASP      3.3     7.0    -      -       -      +
    604A  ALA*     4.0    10.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 579 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552A  TYR*     3.2    11.4    -      -       -      +
    553A  ASN*     3.8    14.1    -      -       -      +
    577A  ARG*     3.1    49.0    -      -       -      +
    578A  ALA*     1.3    75.4    -      -       -      +
    580A  GLY*     1.3    58.8    +      -       -      +
    601A  TYR*     4.9     7.8    +      -       +      -
    602A  THR*     3.9     1.0    -      -       -      -
    603A  ASP*     2.3    83.4    +      -       +      +
    605A  GLU*     4.6     3.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 580 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  VAL*     3.0    10.3    -      -       -      +
    552A  TYR*     3.0    52.6    +      -       -      -
    579A  ARG*     1.3    75.3    -      -       -      +
    581A  VAL*     1.3    65.7    +      -       -      +
    601A  TYR*     3.0    16.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 581 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549A  GLY*     6.3     0.2    -      -       -      -
    550A  ALA      3.3    12.8    -      -       -      +
    551A  VAL*     4.4    13.5    -      -       +      -
    552A  TYR*     4.1     0.2    -      -       -      -
    580A  GLY*     1.3    79.9    -      -       -      +
    582A  GLU*     1.3    74.7    +      -       -      +
    583A  ILE*     4.7    10.8    -      -       +      -
    599A  TYR*     3.7     7.0    -      -       +      +
    600A  THR*     3.3     3.8    -      -       -      -
    601A  TYR*     2.7    58.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 582 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  SER*     3.6     4.9    +      -       -      -
     74A  PRO*     3.6    15.9    -      -       +      -
     75A  GLY*     3.6     8.8    -      -       -      +
     93A  ARG*     2.5    56.3    +      -       -      +
    133A  ARG*     3.3    25.2    +      -       -      +
    548A  THR*     4.5     1.7    -      -       -      +
    549A  GLY*     3.3     2.9    -      -       -      -
    550A  ALA*     2.8    38.8    +      -       +      +
    552A  TYR*     3.7     8.1    +      -       +      -
    581A  VAL*     1.3    81.6    -      -       -      +
    583A  ILE*     1.3    65.1    +      -       -      +
    599A  TYR      3.4     3.4    -      -       -      -
    600A  THR*     3.9    16.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 583 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  PRO*     4.0     2.4    -      -       -      +
    547A  VAL*     5.5     4.5    -      -       +      -
    548A  THR      3.3    12.8    -      -       -      +
    549A  GLY*     4.3     5.2    -      -       -      -
    581A  VAL*     4.7    10.3    -      -       +      -
    582A  GLU*     1.3    79.6    -      -       -      +
    584A  GLU*     1.3    68.8    -      -       -      +
    585A  ALA*     5.1     4.9    -      -       +      -
    597A  GLY      5.5     0.2    -      -       -      +
    598A  SER*     3.1    10.1    -      -       -      -
    599A  TYR*     2.8    63.5    +      -       +      +
   1101A  DDQ      5.9     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 584 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE      4.8     1.9    -      -       -      +
     51A  SER*     2.6    33.7    +      -       -      -
     52A  VAL      5.3     2.9    +      -       -      +
     72A  TYR      4.1     8.6    -      -       -      +
     73A  THR*     4.3     8.0    +      -       -      -
     74A  PRO*     3.4    23.3    -      -       +      +
    133A  ARG*     4.1     0.7    +      -       -      -
    546A  VAL      5.4     0.2    -      -       -      -
    547A  VAL*     3.4     3.2    -      -       -      +
    548A  THR*     2.9    50.3    +      -       +      +
    583A  ILE*     1.3    74.1    -      -       -      +
    585A  ALA*     1.3    71.0    +      -       -      +
    586A  LYS*     3.5    28.2    -      -       +      +
    596A  VAL*     5.4     0.7    -      -       -      +
    597A  GLY      3.5    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 585 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    546A  VAL      3.4     6.3    -      -       -      -
    547A  VAL*     3.9    18.4    -      -       +      -
    583A  ILE*     5.1     6.7    -      -       +      -
    584A  GLU*     1.3    80.9    -      -       -      +
    586A  LYS*     1.3    63.9    +      -       -      +
    595A  VAL*     4.6     2.0    -      -       -      +
    596A  VAL*     3.1     2.3    -      -       -      -
    597A  GLY*     2.6    42.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 586 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  THR*     4.7    18.4    +      -       +      +
     30A  ALA*     3.7    24.0    +      -       -      +
     52A  VAL*     3.5    24.1    +      -       -      +
     57A  GLU*     4.1    16.9    +      -       -      -
    545A  ILE*     3.3     1.0    -      -       -      -
    546A  VAL*     2.8    52.4    +      -       +      +
    547A  VAL*     5.1     0.4    -      -       -      +
    584A  GLU*     3.5    24.9    -      -       +      +
    585A  ALA*     1.3    75.2    -      -       -      +
    587A  ALA*     1.3    62.7    +      -       -      +
    595A  VAL*     3.2     7.4    -      -       -      +
    596A  VAL*     2.8    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 587 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  THR*     4.9     4.8    +      -       -      -
    544A  PRO      3.3     6.5    -      -       -      -
    545A  ILE*     3.7    23.3    -      -       +      -
    547A  VAL*     6.3     1.3    -      -       +      -
    586A  LYS*     1.3    76.3    -      -       -      +
    588A  ALA*     1.3    66.6    +      -       -      +
    589A  LEU*     3.6    14.5    +      -       +      +
    594A  ASN*     3.7     2.2    -      -       -      +
    595A  VAL*     2.7    42.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 588 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  GLY      5.3     0.2    -      -       -      -
     24A  PRO*     3.4    18.2    -      -       +      -
     27A  THR*     4.8     2.0    +      -       -      +
    544A  PRO*     3.0    37.0    +      -       +      +
    545A  ILE*     4.9     3.8    -      -       -      +
    587A  ALA*     1.3    73.4    -      -       -      +
    589A  LEU*     1.3    67.4    +      -       -      +
    590A  SER      3.5     8.7    -      -       -      +
    591A  ALA*     6.1     0.4    -      -       -      -
    594A  ASN*     3.2    22.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 589 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    545A  ILE*     6.1     0.4    -      -       +      -
    587A  ALA*     3.6    20.1    +      -       +      +
    588A  ALA*     1.3    81.6    -      -       -      +
    590A  SER*     1.3    59.8    +      -       -      +
    593A  VAL*     2.6    40.0    +      -       +      -
    595A  VAL*     4.5    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 590 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588A  ALA*     3.5     8.8    -      -       -      +
    589A  LEU*     1.3    77.2    +      -       -      +
    591A  ALA*     1.3    60.1    +      -       -      +
    592A  SER*     2.9    17.7    +      -       -      -
    593A  VAL*     3.1    36.6    +      -       -      +
    594A  ASN*     4.9     1.0    -      -       -      +
    631A  TYR*     5.2     0.5    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il