Contacts of the strand formed by residues 130 - 136 (chain A) in PDB entry 4SBV


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 ALA 130 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  GLY*     1.3    77.8    -      -       -      +
    131A  ILE*     1.3    61.1    -      -       -      +
    132A  HIS*     3.6    20.1    -      -       +      +
    158A  THR*     4.4     3.6    -      -       -      +
    159A  GLY      3.0    18.2    -      -       -      +
    160A  PRO*     4.3     0.9    -      -       +      -
    161A  VAL*     3.2     8.0    -      -       -      +
    227A  ALA      3.8     0.5    -      -       -      +
    228A  MET*     3.9     2.6    -      -       -      +
    229A  GLU*     2.8    38.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  LEU*     4.1    19.1    -      -       +      -
    119A  TYR*     3.4    56.8    -      -       +      -
    130A  ALA*     1.3    71.2    -      -       -      +
    132A  HIS*     1.3    76.4    +      -       -      +
    133A  MET*     4.1    18.4    -      -       +      -
    158A  THR*     3.1    28.7    +      -       -      -
    159A  GLY      2.9    12.3    +      -       -      +
    161A  VAL*     4.2     2.6    -      -       +      +
    183A  ILE*     4.1    16.6    -      -       +      -
    226A  THR*     5.1     1.6    -      -       -      -
    227A  ALA      3.6     4.5    -      -       -      +
    228A  MET*     3.7    20.6    -      -       +      -
    242A  LEU*     4.5     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  ALA*     3.6    17.5    -      -       +      +
    131A  ILE*     1.3    85.1    -      -       -      +
    133A  MET*     1.3    69.5    +      -       -      +
    147A  VAL*     2.9    32.7    -      -       +      +
    150A  LEU*     4.3    14.1    -      -       +      +
    156A  TYR*     2.6    33.3    +      -       +      -
    157A  VAL      3.4     7.9    -      -       -      -
    158A  THR*     3.6    13.7    +      -       +      -
    226A  THR*     3.4     6.1    -      -       -      -
    227A  ALA*     3.2    31.5    +      -       +      +
    229A  GLU*     3.0    21.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with MET 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  TYR*     4.1    13.7    -      -       +      +
    119A  TYR*     4.7     0.9    -      -       +      -
    131A  ILE*     4.1    16.4    -      -       +      -
    132A  HIS*     1.3    79.1    -      -       -      +
    134A  GLY*     1.3    60.4    -      -       -      +
    150A  LEU*     4.2     7.4    -      -       -      +
    155A  GLY      3.6     2.8    -      -       -      +
    156A  TYR*     3.2    26.7    -      -       -      -
    157A  VAL*     3.3    26.8    +      -       +      -
    183A  ILE*     4.0    24.5    -      -       +      +
    185A  ILE*     4.0    16.8    -      -       +      -
    224A  LEU*     3.7    18.8    -      -       +      -
    225A  VAL      3.0    15.5    -      -       -      +
    226A  THR*     4.5     6.1    -      -       -      -
    242A  LEU*     3.2    34.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  MET*     1.3    77.6    -      -       -      +
    135A  PHE*     1.3    61.2    +      -       -      -
    150A  LEU*     4.0     2.8    -      -       -      +
    153A  LEU*     3.7    25.1    -      -       -      -
    155A  GLY      4.1     4.5    -      -       -      -
    156A  TYR      4.4     0.9    -      -       -      -
    185A  ILE*     3.7    12.3    -      -       -      +
    224A  LEU*     3.5     1.5    -      -       -      +
    225A  VAL*     2.7    34.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  VAL*     4.5     7.4    -      -       +      -
    115A  ILE      5.2     0.2    -      -       -      -
    117A  TYR*     4.2    22.7    -      +       -      -
    134A  GLY*     1.3    73.6    -      -       -      -
    136A  GLN*     1.3    64.3    -      -       -      +
    137A  TYR*     3.5    30.8    -      -       +      +
    153A  LEU*     3.1    18.7    -      -       -      +
    154A  LYS*     3.9    10.2    +      -       +      +
    155A  GLY      4.0    11.3    -      -       -      +
    185A  ILE*     3.2    52.7    -      -       +      -
    186A  ALA      3.3    16.6    -      -       -      -
    187A  LEU*     3.6    40.8    -      -       +      -
    222A  ALA*     4.5     7.2    -      -       +      -
    223A  ARG      3.4    14.8    -      -       -      -
    224A  LEU*     4.5     7.2    -      -       +      -
    108B  SER*     5.7     0.2    +      -       -      -
    253B  PRO      5.2     0.7    -      -       -      +
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Residues in contact with GLN 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  PHE*     1.3    78.2    -      -       -      +
    137A  TYR*     1.3    73.2    +      -       -      +
    138A  ASP      5.0     1.6    -      -       -      +
    139A  MET*     5.3     0.2    -      -       -      +
    141A  ASP*     4.1     7.3    +      -       +      +
    142A  THR      3.3    25.4    +      -       -      +
    143A  LEU*     3.8     9.1    -      -       -      +
    144A  PRO*     3.8     5.9    -      -       -      +
    153A  LEU*     3.7    20.3    -      -       +      +
    222A  ALA*     3.5     2.1    -      -       -      +
    223A  ARG*     2.7    77.0    +      -       +      +
    225A  VAL*     4.1    10.2    -      -       +      +
    108B  SER*     5.4     2.0    -      -       -      -
    254B  ILE*     3.9    24.0    -      -       +      +
    258B  LEU*     4.1     1.7    -      -       -      +
----------------------------------------------------------
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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