Contacts of the strand formed by residues 154 - 160 (chain A) in PDB entry 1GN6


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 154 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  GLY*     3.3     0.5    -      -       -      -
    130A  TRP*     2.9    39.6    +      -       +      +
    132A  THR*     4.6     7.2    -      -       +      -
    152A  ALA      4.1     8.5    -      -       -      +
    153A  ILE*     1.3    77.0    -      -       -      +
    155A  PRO*     1.3    76.0    -      -       +      +
    156A  LEU*     3.6     6.5    -      -       +      +
    193A  ARG*     4.9     4.0    -      -       +      +
    196A  ALA*     6.5     0.2    -      -       +      -
    197A  ALA*     3.9    32.8    -      -       +      +
    152C  ALA*     4.8     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  VAL*     5.3     0.2    -      -       +      -
     78A  ILE*     3.4    30.4    -      -       +      +
    127A  ALA*     5.8     0.2    -      -       +      -
    128A  LEU      3.8     5.6    -      -       -      +
    129A  GLY*     4.3     2.2    -      -       -      -
    153A  ILE*     3.7     3.8    -      -       -      +
    154A  VAL*     1.3    90.2    -      -       +      +
    156A  LEU*     1.3    65.0    +      -       -      +
    158A  LEU*     4.5    13.2    -      -       +      -
    193A  ARG*     3.9    15.2    +      -       -      +
    151C  LEU*     4.2    33.9    -      -       +      -
    152C  ALA*     3.7    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  ILE*     5.0     2.2    -      -       -      -
     82A  ASN*     3.3    10.7    +      -       -      -
     95A  LEU*     5.0     3.6    -      -       +      -
    128A  LEU*     2.7    30.6    +      -       +      +
    129A  GLY*     4.4     2.5    -      -       -      -
    130A  TRP*     4.6     3.1    -      -       +      -
    137A  LEU*     3.3    34.1    -      -       +      -
    154A  VAL*     3.6    18.6    -      -       +      +
    155A  PRO*     1.3    82.9    -      -       -      +
    157A  LEU*     1.3    58.6    +      -       -      +
    190A  VAL*     3.8    14.8    -      -       +      +
    193A  ARG*     3.2    50.8    -      -       +      +
    194A  TYR*     4.0    22.7    -      -       +      +
    197A  ALA*     4.4     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ASN*     3.2    26.9    -      -       +      +
    109A  PHE*     4.3    13.0    -      -       +      -
    113A  PHE*     4.1    14.3    -      -       +      -
    127A  ALA*     3.6     0.7    -      -       -      -
    128A  LEU*     3.0    41.4    +      -       +      -
    156A  LEU*     1.3    78.0    -      -       -      +
    158A  LEU*     1.3    67.8    +      -       -      +
    181A  PHE*     3.9    19.7    -      -       +      -
    182A  TRP*     4.2    16.4    -      -       +      -
    185A  VAL*     4.0     9.0    -      -       +      -
    187A  TRP*     4.0    30.3    -      -       +      -
    190A  VAL*     3.8    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  ASN*     3.7    44.4    -      -       +      +
     78A  ILE*     4.2    20.6    -      -       +      -
     79A  TRP*     3.3    20.4    -      -       +      +
     82A  ASN*     2.8    15.1    +      -       -      +
    113A  PHE*     4.5     2.7    -      -       -      -
    125A  TRP*     3.8    21.8    -      -       +      -
    126A  ALA      3.4     3.6    -      -       -      +
    127A  ALA*     3.1    33.0    -      -       +      -
    128A  LEU      4.8     0.2    -      -       -      +
    142A  VAL*     5.6     0.4    -      -       +      -
    155A  PRO*     4.5     9.2    -      -       +      -
    157A  LEU*     1.3    79.4    -      -       -      +
    159A  LEU*     1.3    61.5    +      -       -      +
    160A  ASP      4.1     0.4    -      -       -      -
    181A  PHE*     3.9     8.2    -      -       -      -
    151C  LEU*     4.3    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  TRP*     3.9     5.6    -      -       +      -
    113A  PHE*     3.7    26.7    -      -       +      -
    114A  HIS*     6.2     0.7    -      -       -      -
    117A  ALA*     3.5    27.6    -      -       +      -
    125A  TRP*     3.1    10.9    -      -       -      -
    126A  ALA      3.0    30.0    +      -       -      +
    158A  LEU*     1.3    74.0    -      -       -      +
    160A  ASP*     1.3    61.1    +      -       -      +
    161A  MET*     3.4    11.4    +      -       -      +
    177A  PHE*     3.8    26.5    -      -       +      -
    178A  ALA*     4.2    14.4    -      -       +      +
    181A  PHE*     3.8    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  HIS*     2.8    14.9    +      -       -      -
     76A  HIS*     3.3     2.3    +      -       -      -
     79A  TRP*     3.7    18.3    -      -       +      -
    125A  TRP*     3.3    30.9    -      -       +      -
    159A  LEU*     1.3    70.2    -      -       -      +
    161A  MET*     1.3    59.6    +      -       -      +
    162A  TRP*     3.1    25.8    +      -       -      +
    164A  HIS*     3.5     0.5    +      -       -      -
    165A  ALA*     3.5    16.3    -      -       +      +
    177A  PHE*     3.4    24.8    -      -       -      -
    999A   FE      2.0    33.2    -      -       -      -
----------------------------------------------------------
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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