Contacts of the strand formed by residues 930 - 936 (chain A) in PDB entry 6PAI


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 VAL 930 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    922A  LEU*     4.1    17.5    -      -       +      -
    923A  VAL      3.3     6.7    -      -       -      +
    924A  GLY*     4.5     0.4    -      -       -      -
    928A  ARG      4.6     2.2    -      -       -      +
    929A  SER*     1.3    88.8    +      -       -      +
    931A  LEU*     1.3    60.9    -      -       -      +
    947A  ARG*     3.5     2.9    +      -       -      +
    948A  ASP*     2.9    45.7    +      -       +      +
    954A  MET*     4.0    14.1    -      -       +      -
    957A  VAL*     3.7    30.3    -      -       +      -
    965A  PHE*     5.4     2.5    -      -       +      +
    966A  LEU      5.6     1.3    -      -       -      +
    967A  GLY*     5.2     2.5    -      -       -      -
    975A  PHE*     4.3     6.7    -      -       +      -
    977A  CYS*     3.8    19.3    -      -       +      -
    992A  LEU*     4.4     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 931 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    905A  HIS*     3.1    34.5    -      -       +      +
    907A  ASN      4.3     2.9    -      -       -      +
    908A  ASN*     3.7    15.7    -      -       -      +
    921A  ILE      3.6     1.0    -      -       -      +
    922A  LEU*     3.6     6.3    -      -       -      +
    923A  VAL*     2.7    47.9    +      -       +      +
    928A  ARG*     5.3     4.5    -      -       -      +
    930A  VAL*     1.3    75.9    -      -       -      +
    932A  LEU*     1.3    59.5    +      -       -      +
    933A  LEU*     4.1    11.0    -      -       +      -
    944A  GLU*     4.0    27.6    -      -       +      +
    946A  ALA      3.7     8.7    -      -       -      +
    947A  ARG*     3.7    29.6    -      -       +      +
    992A  LEU*     4.8     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 932 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    920A  PHE*     3.9    24.9    -      -       +      -
    921A  ILE      3.5    14.6    -      -       -      +
    922A  LEU*     4.6     4.9    -      -       +      +
    931A  LEU*     1.3    74.5    -      -       -      +
    933A  LEU*     1.3    62.7    -      -       -      +
    944A  GLU*     3.8     3.1    -      -       -      -
    945A  ILE*     2.9    42.4    +      -       +      -
    946A  ALA      2.7    20.2    +      -       -      +
    959A  ILE*     6.0     0.9    -      -       +      -
    965A  PHE*     3.7    34.5    -      -       +      -
    979A  LYS*     3.5    35.2    -      -       +      -
    992A  LEU*     4.3    13.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 933 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    888A  VAL*     4.7     9.4    -      -       +      -
    905A  HIS*     3.6    50.9    -      -       +      +
    920A  PHE*     3.5    10.2    -      -       -      -
    921A  ILE*     2.7    45.4    +      -       +      +
    923A  VAL*     4.1    22.7    -      -       +      -
    931A  LEU*     4.1     7.0    -      -       +      -
    932A  LEU*     1.3    76.3    -      -       -      +
    934A  ALA*     1.3    63.4    +      -       -      +
    942A  PHE*     4.3    17.5    -      -       +      -
    943A  GLU      3.4    10.3    -      -       -      +
    944A  GLU*     3.7    20.6    -      -       +      +
    945A  ILE*     4.3     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 934 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    919A  ASP*     3.4     9.6    -      -       +      +
    920A  PHE*     4.5    11.9    -      -       +      -
    921A  ILE*     5.2     0.7    -      -       -      -
    933A  LEU*     1.3    75.8    -      -       -      +
    935A  TYR*     1.3    63.8    +      -       -      +
    936A  LYS*     3.8    16.1    +      -       +      +
    942A  PHE*     3.2     9.9    -      -       -      +
    943A  GLU*     2.8    34.3    +      -       +      +
    945A  ILE*     3.7    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 935 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    876A  PHE*     3.6    28.5    -      +       +      -
    877A  ASN*     5.4     0.9    -      -       +      -
    879A  LYS*     2.7    29.9    +      -       -      -
    890A  LEU*     3.4    20.9    -      -       +      -
    902A  GLU*     2.1    34.3    +      -       -      -
    903A  CYS*     4.1     4.5    -      -       -      -
    919A  ASP*     3.0    34.9    +      -       +      +
    921A  ILE*     4.9     0.6    -      -       +      +
    934A  ALA*     1.3    72.7    -      -       -      +
    936A  LYS*     1.3    70.0    +      -       -      +
    937A  PRO*     3.3    35.1    +      -       +      +
    940A  GLY*     4.1     3.6    -      -       -      -
    941A  ASN      3.8    23.3    -      -       -      -
    942A  PHE*     4.3     8.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 936 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    920A  PHE*     6.4     0.2    -      -       -      -
    934A  ALA*     4.3     8.1    -      -       +      +
    935A  TYR*     1.3    81.5    -      -       -      +
    937A  PRO*     1.4    59.9    -      -       +      +
    938A  MET      3.3     0.4    -      -       -      -
    939A  GLU*     3.1    32.3    -      -       +      +
    940A  GLY*     2.7    35.3    +      -       -      -
    941A  ASN*     3.0    19.9    +      -       -      +
    943A  GLU*     3.0    49.6    +      -       +      +
    945A  ILE*     4.2    13.3    -      -       -      +
----------------------------------------------------------
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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