Contacts of the strand formed by residues 556 - 565 (chain A) in PDB entry 1PG3


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 GLY 556 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  ARG*     3.6    15.9    -      -       -      +
    521A  ASN*     4.1     9.4    -      -       -      -
    551A  PRO*     3.5     5.4    -      -       -      +
    552A  HIS      3.0    32.8    +      -       -      +
    554A  ILE      3.3     4.2    +      -       -      -
    555A  LYS*     1.3    73.1    -      -       -      +
    557A  GLN*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 557 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    519A  VAL      4.6     1.4    -      -       -      +
    520A  LEU*     3.6    16.6    -      -       +      +
    521A  ASN*     2.9    46.1    +      -       +      +
    522A  VAL*     3.7    17.6    -      -       +      +
    549A  GLY*     3.7    24.0    +      -       -      +
    550A  ILE*     3.0    11.6    -      -       -      +
    551A  PRO*     5.1     0.9    -      -       +      +
    552A  HIS*     4.1     0.7    -      -       -      -
    555A  LYS*     3.0    26.3    +      -       -      +
    556A  GLY*     1.3    79.0    -      -       -      +
    558A  ALA*     1.3    63.6    +      -       -      +
    616A  ARG*     6.0     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 558 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520A  LEU*     5.5     0.2    -      -       -      +
    522A  VAL*     5.1     0.8    -      -       -      +
    549A  GLY*     3.2     8.5    -      -       -      -
    550A  ILE*     2.7    49.7    +      -       +      +
    551A  PRO      5.0     0.2    -      -       -      +
    552A  HIS*     4.1    21.0    -      -       +      +
    555A  LYS*     4.2     3.6    -      -       +      -
    557A  GLN*     1.3    74.7    -      -       -      +
    559A  ILE*     1.3    63.7    +      -       -      +
    560A  TYR      3.9     0.2    -      -       -      -
    594A  ASP*     3.2    22.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 559 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520A  LEU*     4.4     7.2    -      -       +      -
    522A  VAL*     3.8    27.1    -      -       +      -
    527A  LEU*     4.6     0.9    -      -       +      -
    532A  ILE*     4.2    13.2    -      -       +      -
    547A  VAL*     3.8    24.0    -      -       +      -
    548A  VAL      3.9     2.2    -      -       -      -
    549A  GLY*     4.9     0.4    -      -       -      -
    550A  ILE*     5.6     0.2    -      -       -      -
    558A  ALA*     1.3    73.0    -      -       -      +
    560A  TYR*     1.3    60.4    +      -       -      +
    561A  ALA*     5.0     0.2    -      -       +      -
    590A  LEU      3.8     8.5    -      -       -      +
    591A  ALA*     3.3    38.8    -      -       -      +
    592A  THR      3.8     5.8    -      -       -      +
    593A  PRO*     3.6    27.3    -      -       +      +
    594A  ASP*     3.0    33.1    +      -       -      +
    595A  VAL*     3.4     7.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 560 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    546A  ALA      3.9     1.0    -      -       -      +
    547A  VAL*     3.6     1.2    -      -       -      -
    548A  VAL*     2.9    47.9    +      -       +      +
    550A  ILE*     4.1    24.0    -      -       +      -
    558A  ALA      3.7     0.8    +      -       -      -
    559A  ILE*     1.3    73.7    -      -       -      +
    561A  ALA*     1.3    62.4    +      -       -      +
    562A  TYR*     3.4    37.7    -      +       -      -
    595A  VAL*     3.6    32.3    -      -       +      +
    597A  HIS*     2.8    41.9    +      -       +      +
    619A  ALA*     3.7    25.6    -      -       +      -
    645A  LYS*     3.5    24.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 561 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536A  LEU*     4.0    26.2    -      -       +      -
    546A  ALA      3.7     2.5    -      -       -      -
    547A  VAL*     4.0     9.9    -      -       +      +
    559A  ILE*     4.0     0.6    +      -       +      -
    560A  TYR*     1.3    76.5    -      -       -      +
    562A  TYR*     1.3    59.1    +      -       -      +
    563A  VAL*     3.6     3.5    +      -       +      +
    593A  PRO*     4.3    10.3    -      -       +      -
    595A  VAL      3.0    16.8    +      -       -      +
    596A  LEU*     3.5    15.3    -      -       +      -
    597A  HIS      2.7    31.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 562 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    545A  ALA*     3.2     8.3    -      -       -      +
    546A  ALA      2.9    45.9    +      -       -      +
    548A  VAL*     4.0     9.0    -      -       +      -
    560A  TYR*     3.4    30.2    -      +       -      -
    561A  ALA*     1.3    71.1    -      -       -      +
    563A  VAL*     1.3    60.8    +      -       -      +
    597A  HIS*     3.3    37.7    -      +       -      +
    599A  THR*     4.3     7.6    -      -       +      -
    602A  LEU*     3.7    20.2    -      -       +      +
    615A  LEU*     2.7    63.4    +      -       +      -
    618A  ILE*     3.9     9.1    -      -       +      +
    619A  ALA*     3.3    17.7    +      -       -      +
    641A  LEU*     4.5     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 563 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536A  LEU*     4.6    13.2    -      -       +      -
    542A  ILE*     3.9    33.7    -      -       +      -
    544A  GLU      3.8     2.2    -      -       -      -
    545A  ALA*     4.8     1.3    -      -       +      -
    561A  ALA*     3.9    15.7    -      -       +      +
    562A  TYR*     1.3    77.6    -      -       -      +
    564A  THR*     1.3    64.5    +      -       -      +
    565A  LEU*     4.1     5.9    +      -       +      +
    579A  VAL*     5.0     0.7    -      -       +      -
    596A  LEU*     3.9    23.3    -      -       +      -
    597A  HIS      2.8    11.0    +      -       -      +
    598A  TRP*     3.4    35.8    -      -       +      +
    599A  THR*     2.9    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 564 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    542A  ILE*     3.8     3.3    -      -       -      +
    543A  ALA*     2.9    27.1    +      -       +      -
    544A  GLU*     2.9    29.9    +      -       +      +
    563A  VAL*     1.3    73.8    -      -       -      +
    565A  LEU*     1.3    69.5    +      -       -      +
    599A  THR      3.0    20.1    +      -       -      +
    600A  ASP*     3.9    16.6    -      -       +      +
    602A  LEU*     3.7    25.3    -      -       -      +
     64B  ASN*     4.1    15.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 565 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541A  LYS*     3.4    16.2    -      -       +      +
    542A  ILE*     4.2     8.5    -      -       +      -
    543A  ALA*     4.4     1.3    -      -       -      -
    563A  VAL*     4.0    10.2    +      -       +      +
    564A  THR*     1.3    84.0    -      -       -      +
    566A  ASN*     1.3    71.6    +      -       -      +
    567A  HIS*     4.8     2.4    -      -       -      -
    569A  GLU*     3.9     7.9    -      -       +      +
    570A  GLU*     4.0     7.9    -      -       -      +
    571A  PRO*     3.9    26.2    -      -       +      -
    575A  LEU*     3.7    30.1    -      -       +      -
    579A  VAL*     5.3     0.7    -      -       +      -
    598A  TRP*     3.5    38.8    -      -       +      -
    600A  ASP*     4.2    10.1    +      -       -      +
     64B  ASN*     4.0     4.2    +      -       -      +
----------------------------------------------------------
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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