Contacts of the strand formed by residues 223 - 229 (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 ARG 223 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  SER*     4.1    19.6    +      -       -      -
     89A  GLU      3.3    11.7    -      -       -      +
     90A  LEU*     4.5     2.3    -      -       +      +
     91A  VAL*     4.3     1.8    -      -       -      -
    135A  PHE*     3.4     3.1    -      -       -      -
    136A  GLN*     2.7    77.4    +      -       +      +
    138A  ASP      4.2     4.0    +      -       -      -
    139A  MET*     3.0    60.7    +      -       +      +
    141A  ASP      3.4    15.2    +      -       -      -
    143A  LEU*     4.2    12.7    -      -       -      +
    205A  TYR*     5.6     0.6    +      -       -      -
    222A  ALA*     1.3    76.0    -      -       -      +
    224A  LEU*     1.3    70.0    -      -       -      +
    225A  VAL*     4.5     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  SER*     3.0     8.1    -      -       -      -
     89A  GLU*     2.6    47.5    +      -       +      +
     91A  VAL*     4.1     3.4    -      -       +      +
    117A  TYR*     3.6    46.0    -      -       +      -
    133A  MET*     3.7    21.8    -      -       +      -
    134A  GLY      3.5    14.8    -      -       -      +
    135A  PHE*     4.5     9.2    -      -       +      -
    185A  ILE*     4.1    15.0    -      -       +      -
    223A  ARG*     1.3    71.9    -      -       -      +
    225A  VAL*     1.3    68.6    -      -       -      +
    226A  THR*     3.8    15.2    -      -       +      +
    242A  LEU*     3.9    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  VAL*     4.6     3.4    -      -       +      -
     87A  THR      3.3    10.8    -      -       -      +
     88A  SER*     4.5     3.8    -      -       -      -
    133A  MET*     3.0    29.3    -      -       -      +
    134A  GLY      2.7    16.1    +      -       -      +
    136A  GLN*     4.1    20.0    -      -       +      +
    143A  LEU*     4.4     9.2    -      -       +      -
    144A  PRO*     3.6    27.6    -      -       +      -
    150A  LEU*     3.6    37.2    -      -       +      -
    153A  LEU*     4.2     3.6    -      -       +      -
    223A  ARG*     4.5     5.2    -      -       +      -
    224A  LEU*     1.3    76.7    -      -       -      +
    226A  THR*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  THR*     6.0     2.2    -      -       +      -
     78A  LEU*     3.9    23.3    -      -       +      +
     85A  VAL      3.9     0.2    -      -       -      +
     86A  VAL*     3.5     1.1    -      -       -      -
     87A  THR*     2.6    57.2    +      -       -      +
     88A  SER*     5.4     0.7    -      -       -      +
     89A  GLU*     5.6     7.0    -      -       +      +
    131A  ILE*     5.1     2.5    -      -       +      -
    132A  HIS      3.4    10.1    -      -       -      -
    133A  MET*     4.5     8.7    -      -       -      -
    224A  LEU*     3.8    28.0    -      -       +      +
    225A  VAL*     1.3    80.8    -      -       -      +
    227A  ALA*     1.3    60.6    +      -       -      +
    228A  MET*     4.2     2.6    +      -       -      +
    242A  LEU*     4.9     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  ILE*     4.7     8.5    -      -       +      -
     85A  VAL      3.1    10.1    -      -       -      +
     86A  VAL*     3.7    13.9    -      -       +      -
    131A  ILE*     3.6     5.5    -      -       -      +
    132A  HIS*     3.2    41.2    +      -       +      -
    147A  VAL*     5.7     3.6    -      -       +      -
    150A  LEU*     3.5    25.9    -      -       +      +
    226A  THR*     1.3    75.0    -      -       -      +
    228A  MET*     1.3    60.9    +      -       -      +
    229A  GLU*     3.9     1.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  LEU*     3.1    44.6    -      -       +      -
     79A  ALA      3.7    25.8    -      -       -      +
     80A  VAL*     4.3    10.5    -      -       +      +
     81A  THR*     4.9     0.7    +      -       -      -
     83A  THR      3.5     4.3    -      -       -      +
     84A  ILE*     3.5     2.1    -      -       -      -
     85A  VAL*     2.9    44.6    +      -       +      +
     87A  THR*     5.8     3.1    -      -       -      +
    119A  TYR*     4.8     0.2    -      -       +      -
    130A  ALA      3.9     3.4    -      -       -      +
    131A  ILE*     3.7    35.7    -      -       +      -
    161A  VAL*     4.6     4.9    -      -       +      -
    226A  THR*     5.0     2.5    -      -       -      +
    227A  ALA*     1.3    71.2    -      -       -      +
    229A  GLU*     1.3    62.7    +      -       -      +
    239A  THR*     3.3    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 229 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  VAL*     3.6     5.5    -      -       -      +
     81A  THR      4.7     0.2    -      -       -      -
     83A  THR      4.1     7.6    -      -       -      -
     84A  ILE*     3.7    32.1    -      -       +      -
    130A  ALA*     2.8    34.8    +      -       -      +
    132A  HIS*     3.0    32.6    +      -       +      +
    147A  VAL*     3.9    10.8    -      -       +      +
    227A  ALA*     5.1     1.6    -      -       +      -
    228A  MET*     1.3    77.7    -      -       -      +
    230A  GLY*     1.3    69.0    +      -       -      +
----------------------------------------------------------
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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