Contacts of the strand formed by residues 545 - 562 (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 ILE 545 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  THR*     4.0     0.2    -      -       -      +
     31A  ARG*     3.0    21.8    +      -       -      +
    538A  TYR*     2.9    41.1    -      -       +      +
    540A  PRO*     2.9    29.3    -      -       +      +
    543A  ARG*     3.0    24.9    +      -       +      +
    544A  PRO*     1.3    89.3    -      -       +      +
    546A  VAL*     1.3    68.2    +      -       -      +
    547A  VAL*     5.5     3.8    -      -       +      -
    586A  LYS      3.3     6.3    -      -       -      +
    587A  ALA*     3.7    18.4    -      -       +      -
    588A  ALA      4.9     3.8    -      -       -      +
    589A  LEU*     6.1     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 546 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  THR*     3.4    29.4    -      -       +      +
     30A  ALA      6.1     0.7    -      -       -      +
     31A  ARG*     4.8     7.4    -      -       +      +
     43A  ILE*     4.1    19.7    -      -       +      -
    538A  TYR      3.4     3.8    -      -       -      -
    539A  VAL*     4.0    27.1    -      -       +      -
    545A  ILE*     1.3    81.7    -      -       -      +
    547A  VAL*     1.3    71.5    +      -       -      +
    548A  THR*     6.1     2.2    -      -       -      -
    584A  GLU      5.4     0.2    -      -       -      -
    585A  ALA*     3.4     1.1    -      -       -      -
    586A  LYS*     2.8    49.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 547 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536A  VAL      4.1     0.5    -      -       -      +
    537A  LYS*     3.6     1.0    -      -       -      -
    538A  TYR*     2.7    61.5    +      -       +      +
    539A  VAL*     5.2     0.2    -      -       -      +
    545A  ILE*     5.5     3.4    -      -       +      -
    546A  VAL*     1.3    87.3    -      -       -      +
    548A  THR*     1.3    69.0    +      -       -      +
    583A  ILE*     5.5     4.3    -      -       +      -
    584A  GLU      3.4     9.2    -      -       -      +
    585A  ALA*     3.9    16.2    -      -       +      -
    586A  LYS      5.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 548 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  SER*     5.3     2.3    +      -       -      -
     74A  PRO*     5.2     3.6    -      -       +      -
    133A  ARG*     5.8     3.1    -      -       -      +
    504A  TYR*     4.6     2.8    +      -       -      -
    536A  VAL      3.5     5.3    +      -       -      -
    537A  LYS*     3.7    27.7    -      -       -      +
    546A  VAL*     6.1     2.7    -      -       -      -
    547A  VAL*     1.3    82.4    -      -       -      +
    549A  GLY*     1.3    67.7    +      -       -      +
    550A  ALA*     5.1     1.0    -      -       -      +
    582A  GLU      5.2     0.9    -      -       -      +
    583A  ILE*     3.3     9.3    -      -       -      +
    584A  GLU*     2.9    56.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 549 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    504A  TYR*     3.9     3.3    +      -       -      -
    535A  GLY*     3.3     2.3    -      -       -      -
    536A  VAL*     2.9    34.7    +      -       -      +
    548A  THR*     1.3    79.6    +      -       -      +
    550A  ALA*     1.3    65.1    +      -       -      +
    582A  GLU      3.3     9.4    -      -       -      -
    583A  ILE*     4.2     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 550 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  SER*     3.8    10.3    -      -       -      +
     93A  ARG*     5.2     0.4    -      -       -      +
    504A  TYR*     3.2    21.1    -      -       -      +
    533A  GLU*     3.7    16.4    -      -       -      +
    534A  VAL      3.5     7.4    -      -       -      +
    535A  GLY*     4.0     1.3    -      -       -      -
    548A  THR*     5.1     1.6    -      -       -      +
    549A  GLY*     1.3    77.3    -      -       -      +
    551A  VAL*     1.3    63.2    +      -       -      +
    552A  TYR*     5.2     1.3    -      -       -      -
    581A  VAL*     3.3     8.1    -      -       -      +
    582A  GLU*     2.8    41.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 551 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533A  GLU*     3.5     1.5    -      -       -      +
    534A  VAL*     2.9    53.4    +      -       +      +
    535A  GLY*     5.1     1.6    -      -       -      -
    550A  ALA*     1.3    76.7    -      -       -      +
    552A  TYR*     1.3    68.7    +      -       -      +
    580A  GLY      3.0    15.9    -      -       -      +
    581A  VAL*     4.4    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 552 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  ARG*     3.0    61.3    +      -       +      +
    531A  GLN*     3.9    11.2    -      -       -      +
    532A  TYR      3.1    12.3    -      -       -      +
    533A  GLU*     3.9     7.0    -      -       +      +
    550A  ALA      5.2     0.9    -      -       -      -
    551A  VAL*     1.3    85.8    -      -       -      +
    553A  ASN*     1.3    59.9    +      -       -      +
    554A  LEU*     3.9    11.0    -      -       +      -
    578A  ALA*     3.3    25.2    -      -       +      +
    579A  ARG*     3.2     6.2    -      -       -      +
    580A  GLY*     3.0    50.2    +      -       -      -
    581A  VAL      4.1     0.7    -      -       -      -
    582A  GLU*     3.7    15.7    +      -       +      -
    600A  THR*     5.7     1.6    -      -       +      +
    601A  TYR      4.6     0.6    +      -       -      -
    602A  THR*     3.5    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 553 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    530A  LYS      3.6     1.7    -      -       -      +
    531A  GLN*     3.1     4.2    -      -       -      -
    532A  TYR*     2.7    57.0    +      -       +      +
    552A  TYR*     1.3    74.1    -      -       -      +
    554A  LEU*     1.3    60.1    +      -       -      +
    555A  THR*     4.1    13.3    +      -       -      -
    577A  ARG*     3.7    29.9    +      -       -      +
    578A  ALA      3.7     0.7    -      -       -      -
    579A  ARG*     3.8    17.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 554 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  ARG*     4.1    18.4    -      -       +      +
     95A  PHE*     3.6    29.3    -      -       +      -
    134A  GLY*     4.8     0.4    -      -       -      -
    135A  PRO*     3.8    17.7    -      -       +      -
    145A  PRO*     4.3    11.0    -      -       +      -
    146A  GLY*     3.8    20.4    -      -       -      +
    530A  LYS      3.3     5.6    -      -       -      +
    531A  GLN*     3.5    30.3    -      -       +      +
    552A  TYR*     3.9    10.1    -      -       +      -
    553A  ASN*     1.3    74.6    -      -       -      +
    555A  THR*     1.3    68.4    +      -       -      +
    576A  ILE      4.0     0.5    -      -       -      +
    577A  ARG*     3.5     1.7    -      -       -      +
    578A  ALA*     2.7    44.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 555 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  PRO*     5.7     0.2    -      -       -      -
    528A  LYS      3.4     3.5    -      -       -      +
    529A  GLY*     3.4     1.3    -      -       -      -
    530A  LYS*     2.5    52.5    +      -       +      +
    553A  ASN*     4.1    11.3    +      -       -      -
    554A  LEU*     1.3    80.7    +      -       -      +
    556A  LYS*     1.3    62.9    -      -       -      +
    557A  THR*     3.5    25.3    +      -       +      -
    575A  GLU*     4.1    14.9    +      -       +      +
    576A  ILE      3.6     3.8    -      -       -      +
    577A  ARG*     4.0    15.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 556 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  PHE*     3.7    37.0    -      -       +      -
     96A  ALA      5.2     6.5    +      -       -      -
     98A  GLU*     6.3     1.4    -      -       -      +
    145A  PRO*     4.2    16.4    -      -       +      -
    512A  GLU*     4.9     8.9    +      -       -      -
    527A  SER*     3.6    27.6    -      -       -      +
    528A  LYS      3.0    10.5    -      -       -      +
    529A  GLY*     4.8     0.9    -      -       -      -
    554A  LEU      4.3     0.2    +      -       -      -
    555A  THR*     1.3    73.7    -      -       -      +
    557A  THR*     1.3    65.3    +      -       -      +
    559A  ASN*     2.9    33.2    +      -       -      +
    575A  GLU*     3.4     5.4    -      -       -      +
    576A  ILE*     2.9    35.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 557 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    527A  SER*     3.2     3.8    -      -       -      -
    528A  LYS*     2.9    44.7    +      -       -      +
    530A  LYS*     5.2     8.1    -      -       +      +
    555A  THR*     3.5    24.0    -      -       +      +
    556A  LYS*     1.3    79.2    -      -       -      +
    558A  ASN*     1.3    76.6    +      -       -      +
    559A  ASN      3.3     1.3    -      -       -      -
    574A  GLY      3.8     2.9    -      -       -      -
    575A  GLU*     3.6    20.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 558 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525A  ALA*     3.4    21.4    +      -       -      +
    526A  PRO      2.6    27.3    +      -       -      +
    527A  SER*     3.5    11.5    -      -       -      -
    528A  LYS*     4.8     2.0    -      -       +      +
    557A  THR*     1.3    82.9    -      -       -      +
    559A  ASN*     1.3    67.0    +      -       -      +
    560A  LEU*     3.4     7.0    +      -       -      +
    572A  GLU*     3.1    28.5    +      -       -      +
    573A  GLY*     2.9    29.3    +      -       -      +
    574A  GLY      2.8     9.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 559 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    527A  SER*     4.9     0.2    -      -       -      -
    556A  LYS*     2.9    36.6    +      -       +      +
    557A  THR      3.3     1.0    -      -       -      -
    558A  ASN*     1.3    78.5    -      -       -      +
    560A  LEU*     1.3    78.3    +      -       -      +
    561A  MET      3.3     0.9    +      -       -      -
    572A  GLU      3.9     2.8    -      -       -      -
    574A  GLY*     2.7    40.5    +      -       -      +
    575A  GLU*     4.1     5.8    -      -       -      +
    576A  ILE*     3.1    31.2    -      -       +      +
    606A  TYR*     4.2    10.9    -      -       -      -
    608A  THR      5.9     0.2    +      -       -      -
    609A  ASP*     4.7     5.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 560 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    514A  SER*     3.7     9.9    -      -       -      +
    516A  GLN*     3.5    20.6    -      -       +      -
    524A  PHE*     3.2    62.6    -      -       +      -
    525A  ALA      5.6     1.3    -      -       -      +
    558A  ASN*     3.4     5.6    +      -       -      +
    559A  ASN*     1.3    88.6    +      -       -      +
    561A  MET*     1.3    58.3    +      -       -      +
    570A  SER*     4.2    12.6    -      -       -      +
    571A  VAL      3.5     5.2    -      -       -      +
    572A  GLU*     3.7    17.3    -      -       +      -
    609A  ASP*     4.8     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 561 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    559A  ASN      3.3     2.2    +      -       -      +
    560A  LEU*     1.3    74.1    -      -       -      +
    562A  ALA*     1.3    60.9    +      -       -      +
    564A  PRO*     5.3     4.0    -      -       +      -
    570A  SER*     3.1    11.9    +      -       -      -
    571A  VAL*     2.7    45.7    +      -       +      +
    572A  GLU      3.2    21.1    -      -       -      +
    573A  GLY*     4.2     4.7    -      -       -      +
    574A  GLY*     3.7    17.0    -      -       -      +
    608A  THR*     4.1     8.5    -      -       +      +
    609A  ASP*     3.3    32.3    -      -       -      +
    610A  THR*     3.1    37.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 562 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    561A  MET*     1.3    82.2    -      -       -      +
    563A  ASP*     1.3    66.3    +      -       -      +
    564A  PRO*     3.0     4.0    -      -       -      +
    569A  PHE      4.8     1.8    -      -       -      -
    570A  SER*     4.8     0.7    -      -       -      +
    571A  VAL*     4.5     0.7    -      -       -      -
    609A  ASP*     5.0     1.2    +      -       -      -
    610A  THR*     2.3    36.4    +      -       +      -
    611A  THR*     3.4    25.8    -      -       -      +
    612A  TYR*     6.4     0.7    -      -       +      -
----------------------------------------------------------
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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