Contacts of the strand formed by residues 202 - 209 (chain B) in PDB entry 2I65


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 ASP 202 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  ASN*     3.7    25.0    +      -       +      +
    201B  CYS*     1.3    77.1    -      -       -      +
    203B  VAL*     1.3    81.5    +      -       -      +
    234B  LYS      2.8    16.0    +      -       -      -
    235B  VAL*     3.6     2.3    -      -       -      +
    236B  GLN*     2.7    43.3    +      -       -      +
    237B  THR      3.1     8.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  CYS      5.0     0.2    -      -       -      +
    120B  ASN      3.7    17.9    -      -       -      +
    122B  ILE      4.7     1.6    +      -       -      +
    201B  CYS      3.6     7.6    -      -       -      +
    202B  ASP*     1.3   100.5    +      -       -      +
    204B  VAL*     1.3    65.1    +      -       -      +
    205B  HIS*     3.5    36.0    +      -       +      +
    236B  GLN*     5.4     1.3    -      -       +      -
    237B  THR*     3.4    28.9    -      -       +      +
    239B  GLU*     4.3     9.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  CYS      5.0     1.3    -      -       -      +
    122B  ILE*     4.1    11.0    -      -       +      +
    124B  LEU*     3.8    34.5    -      -       +      -
    200B  ALA*     3.3    32.1    -      -       +      -
    201B  CYS      4.0     5.6    -      -       -      +
    203B  VAL*     1.3    76.0    -      -       -      +
    205B  HIS*     1.3    64.3    +      -       -      +
    230B  LEU*     4.3     6.5    -      -       +      -
    235B  VAL*     3.8    24.9    -      -       +      -
    237B  THR      2.9     9.3    +      -       -      +
    238B  LEU*     3.3    16.7    -      -       +      +
    239B  GLU      2.8    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120B  ASN      5.3     3.3    +      -       -      -
    122B  ILE      3.3     7.9    +      -       -      +
    123B  LEU*     3.5    19.3    -      -       +      -
    124B  LEU*     2.8    31.7    +      -       -      +
    142B  MET*     4.0    20.2    -      -       +      +
    203B  VAL*     3.5    34.0    +      -       +      +
    204B  VAL*     1.3    77.3    -      -       -      +
    206B  VAL*     1.3    55.9    +      -       -      +
    239B  GLU*     3.2    30.5    +      -       +      +
    241B  TRP*     3.3    37.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  LEU*     4.3     1.3    -      -       -      -
    124B  LEU*     3.1    19.1    -      -       +      +
    125B  TRP*     3.8     4.0    -      -       -      +
    205B  HIS*     1.3    75.6    -      -       -      +
    207B  MET*     1.3    59.2    +      -       -      +
    208B  LEU*     3.8    21.2    +      -       +      -
    222B  PHE*     3.6    45.1    -      -       +      -
    238B  LEU*     3.9    14.1    -      -       +      -
    239B  GLU      2.9     8.7    +      -       -      +
    240B  ALA*     3.3    23.5    -      -       +      +
    241B  TRP*     2.7    33.9    +      -       -      +
    262B  LEU*     4.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  LEU*     4.0     8.7    -      -       +      +
    124B  LEU      2.9    11.8    +      -       -      +
    125B  TRP*     3.2     9.2    -      -       +      +
    126B  SER      2.9    27.4    +      -       -      +
    128B  ILE*     4.5     6.8    -      -       +      +
    131B  LEU*     4.0    23.8    -      -       +      +
    132B  ALA*     3.5    26.9    -      -       +      -
    135B  PHE*     3.8    26.0    -      -       +      -
    206B  VAL*     1.3    71.7    -      -       -      +
    208B  LEU*     1.3    62.0    +      -       -      +
    241B  TRP*     3.4    24.0    -      -       +      -
    243B  ILE*     4.2    13.5    -      -       +      -
    284B  PHE*     3.8    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  SER*     3.7    25.1    -      -       -      -
    128B  ILE*     4.6     2.2    -      -       -      -
    206B  VAL*     3.8    20.0    -      -       +      +
    207B  MET*     1.3    83.0    -      -       -      +
    209B  ASP*     1.3    60.4    +      -       -      +
    210B  GLY      3.4     0.2    +      -       -      -
    215B  ILE*     3.8    25.6    -      -       +      +
    216B  PHE*     4.7     3.8    -      -       +      -
    222B  PHE*     4.1    10.8    -      -       +      -
    240B  ALA*     4.1    13.2    -      -       +      -
    241B  TRP      2.8     9.1    +      -       -      +
    242B  VAL*     4.5     3.4    -      -       +      -
    243B  ILE*     2.8    33.7    +      -       -      +
    259B  ILE*     3.7    29.2    -      -       +      -
    262B  LEU*     4.0    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 209 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  SER      3.6     5.7    +      -       -      -
    127B  ARG*     3.5    15.3    -      -       +      +
    128B  ILE*     3.2    38.2    -      -       +      +
    208B  LEU*     1.3    72.1    -      -       -      +
    210B  GLY*     1.3    57.6    +      -       -      +
    211B  SER*     2.6    30.6    +      -       -      -
    212B  ARG*     3.1    46.7    +      -       +      +
    215B  ILE*     3.7    16.0    +      -       -      +
    243B  ILE*     4.3     4.3    -      -       -      +
    245B  GLY*     5.1     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