Contacts of the strand formed by residues 264 - 269 (chain B) in PDB entry 4R95


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 ILE 264 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  VAL*     5.0     1.3    -      -       +      -
    263B  ILE*     1.4    71.7    -      -       -      +
    265B  VAL*     1.3    61.5    +      -       -      +
    266B  ARG      3.7    16.8    -      -       -      +
    267B  VAL*     3.8    17.9    -      -       +      -
    278B  CYS      4.0     4.9    -      -       -      +
    281B  TYR*     4.0    13.2    -      -       +      +
    282B  ASN*     2.8    33.1    +      -       -      +
    286B  SER*     3.8    14.4    -      -       -      +
    297B  LEU*     6.1     0.7    -      -       +      -
    346B  LEU*     4.5    21.5    -      -       +      -
    347B  TYR      3.3    15.0    -      -       -      +
    348B  LEU*     3.7    18.8    -      -       +      -
    392B  THR*     3.7    31.2    -      -       +      +
    394B  MET*     4.7     5.4    -      -       -      -
    443B  CYS*     3.8     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263B  ILE*     4.0     9.2    -      -       +      -
    264B  ILE*     1.3    76.6    -      -       -      +
    266B  ARG*     1.3    64.1    +      -       +      +
    278B  CYS*     3.6    17.8    -      -       -      +
    281B  TYR*     4.4     1.6    -      -       -      -
    347B  TYR*     2.9    28.1    +      -       +      +
    348B  LEU      4.4     0.2    -      -       -      -
    349B  MET*     3.9    17.0    -      -       +      +
    356B  SER*     3.8    14.6    -      -       -      +
    437B  THR*     3.8    28.6    -      -       +      +
    440B  MET*     3.7    31.2    -      -       +      -
    443B  CYS*     4.0    12.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 266 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264B  ILE*     3.7     2.6    -      -       -      +
    265B  VAL*     1.3    82.9    -      -       +      +
    267B  VAL*     1.3    73.6    +      -       -      +
    268B  GLU*     2.8    34.9    +      -       -      +
    271B  GLY      4.2     5.7    +      -       -      -
    273B  ASP*     3.3    47.5    +      -       -      +
    281B  TYR*     4.0     7.2    -      -       -      -
    347B  TYR*     2.9    58.7    +      -       +      -
    437B  THR*     5.9     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 267 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264B  ILE*     3.8    19.3    -      -       +      -
    266B  ARG*     1.3    80.9    -      -       -      +
    268B  GLU*     1.4    72.7    +      -       -      +
    269B  ILE*     4.5     9.2    -      -       +      -
    273B  ASP*     3.6     7.5    +      -       -      +
    274B  LEU*     2.9    44.1    +      -       +      +
    281B  TYR*     3.8    35.1    +      -       +      +
    297B  LEU*     6.4     1.6    -      -       +      -
    301B  VAL*     5.4     3.8    -      -       +      -
    305B  ALA*     6.0     0.7    -      -       +      -
    344B  ILE*     4.7     2.9    -      -       +      -
    345B  SER      3.4     7.6    -      -       -      +
    346B  LEU*     3.8    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 268 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  ARG*     2.8    41.0    +      -       -      +
    267B  VAL*     1.4    75.3    -      -       -      +
    269B  ILE*     1.4    66.3    +      -       -      +
    270B  ASN      4.0     0.4    -      -       -      -
    271B  GLY*     3.4    31.3    +      -       -      +
    272B  GLN      3.2     8.7    -      -       -      +
    273B  ASP*     4.2     0.7    -      -       -      -
    343B  VAL      4.0     0.2    -      -       -      +
    344B  ILE*     3.4     5.4    -      -       -      +
    345B  SER*     2.9    46.8    +      -       -      +
    347B  TYR*     2.6    34.3    +      -       +      -
    358B  ARG*     4.4     6.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 269 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267B  VAL*     4.5     8.1    -      -       +      -
    268B  GLU*     1.4    77.8    -      -       -      +
    270B  ASN*     1.4    68.5    +      -       -      +
    272B  GLN*     2.9    25.9    +      -       -      +
    274B  LEU*     3.9    13.5    -      -       +      -
    305B  ALA*     4.6    10.8    -      -       +      -
    308B  SER*     3.2    39.4    +      -       -      +
    309B  ILE*     4.1    18.6    -      -       +      -
    312B  ALA*     4.8     2.2    -      -       +      -
    342B  PRO*     3.5    31.9    -      -       +      -
    343B  VAL      3.5     2.2    -      -       -      +
    344B  ILE*     3.8    26.5    -      -       +      -
----------------------------------------------------------
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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