Contacts of the strand formed by residues 264 - 268 (chain B) in PDB entry 1IR1


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
----------------------------------------------------------
    199B  PHE*     4.7     7.4    -      -       +      -
    237B  GLY*     4.3     8.3    -      -       -      -
    238B  HIS      3.4    33.7    -      -       -      +
    239B  TYR*     3.6    40.4    -      -       +      -
    240B  LEU*     3.6     3.7    +      -       -      +
    262B  VAL*     3.6     8.9    -      -       -      +
    263B  PRO*     1.3    82.7    -      -       +      +
    265B  VAL*     1.3    78.0    +      -       -      +
    289B  LEU*     4.7     1.6    -      -       -      -
    290B  LEU*     3.4    33.0    -      -       +      +
    291B  LEU      4.7     0.7    -      -       -      +
    292B  HIS*     4.0    10.8    -      -       +      +
    325B  HIS*     3.9    19.3    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
    218B  PHE*     5.7     1.6    -      -       +      -
    239B  TYR*     4.6     0.4    -      -       -      -
    240B  LEU*     3.3    20.6    -      -       +      +
    242B  ALA*     5.0     6.1    -      -       +      -
    254B  ALA*     5.0     6.7    -      -       +      -
    257B  ALA*     3.6    30.7    -      -       +      -
    264B  ILE*     1.3    85.3    -      -       -      +
    266B  MET*     1.3    61.9    +      -       -      +
    280B  LEU*     5.1     8.3    -      -       +      -
    284B  CYS*     3.9    22.2    -      -       -      -
    289B  LEU*     4.4    16.4    -      -       +      -
    290B  LEU      3.1    11.2    +      -       -      +
    291B  LEU*     3.5     7.2    -      -       +      -
    292B  HIS      2.9    23.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 266 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201B  KCX      3.9    18.2    -      -       -      +
    202B  ASP      3.5    25.4    -      -       -      +
    204B  GLU*     4.1     5.2    -      -       -      -
    239B  TYR*     3.7    29.8    -      -       +      +
    240B  LEU      2.9     8.4    +      -       -      +
    241B  ASN*     3.4    39.9    -      -       -      +
    242B  ALA*     3.0    29.3    +      -       -      +
    265B  VAL*     1.3    76.7    -      -       -      +
    267B  HIS*     1.3    63.9    +      -       -      +
    268B  ASP*     3.8    15.7    -      -       -      +
    280B  LEU*     4.7     0.3    -      -       -      +
    291B  LEU*     4.3     2.9    -      -       -      -
    292B  HIS*     3.1    18.6    -      -       +      +
    294B  HIS*     4.0    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 267 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243B  THR*     3.6    32.7    -      -       -      +
    244B  ALA      5.3     1.0    +      -       -      -
    250B  MET*     3.8    14.2    -      -       -      -
    266B  MET*     1.3    76.9    -      -       -      +
    268B  ASP*     1.3    77.8    +      -       -      +
    269B  TYR*     3.2     8.5    +      -       -      -
    272B  GLY*     4.2    12.3    -      -       -      -
    273B  GLY      4.2     4.3    -      -       -      -
    276B  ALA*     4.3     4.1    -      -       +      +
    277B  ASN*     3.0    53.0    +      -       +      +
    280B  LEU*     3.6    24.6    -      -       +      +
    291B  LEU*     4.2     5.8    -      -       +      -
    292B  HIS      2.9     6.5    +      -       -      -
    293B  ILE*     3.5     7.2    -      -       +      +
    294B  HIS*     3.0    21.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 268 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  GLU*     2.7    35.7    -      -       -      +
    207B  ASN*     5.2     0.2    -      -       -      +
    241B  ASN*     4.0     0.2    +      -       -      -
    243B  THR*     2.9    30.4    +      -       +      +
    266B  MET*     3.8    10.6    -      -       -      +
    267B  HIS*     1.3    75.6    +      -       -      +
    269B  TYR*     1.3    57.3    +      -       -      +
    270B  LEU      3.4     2.2    -      -       -      -
    271B  THR*     3.2    19.5    +      -       -      +
    272B  GLY*     3.0    26.5    +      -       -      -
    294B  HIS*     3.5    27.0    -      -       -      +
    296B  ALA*     4.5    10.2    -      -       +      +
----------------------------------------------------------
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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