Contacts of the strand formed by residues 264 - 271 (chain A) in PDB entry 1W9O


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 VAL 264 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  THR*     3.3    32.3    -      -       +      -
    201A  MET      3.5     4.7    -      -       -      +
    202A  HIS*     4.2    21.1    -      -       +      +
    242A  ASN*     3.6    17.3    +      -       -      +
    261A  SER*     3.7     4.2    +      -       -      -
    262A  GLY      3.5     1.9    +      -       -      +
    263A  THR*     1.3    78.6    -      -       +      +
    265A  VAL*     1.3    58.9    +      -       -      +
    266A  THR*     4.0     7.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  ILE      3.7     2.3    -      -       -      +
    200A  THR*     3.5     1.3    -      -       -      -
    201A  MET*     2.8    43.4    +      -       +      +
    203A  LYS*     4.1     7.6    -      -       -      -
    209A  VAL*     3.9    26.9    -      -       +      -
    241A  ILE*     4.2     8.3    -      -       +      -
    242A  ASN*     3.8     2.5    -      -       -      -
    258A  LEU*     3.9    22.4    -      -       +      -
    261A  SER*     3.4    23.8    -      -       -      +
    262A  GLY      3.9     4.0    -      -       -      +
    263A  THR      3.8     9.2    -      -       -      +
    264A  VAL*     1.3    73.4    -      -       -      +
    266A  THR*     1.3    59.7    +      -       -      +
    267A  ILE*     3.9    22.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  THR*     3.8    23.3    -      -       +      -
    199A  ILE      3.5     3.4    -      -       -      -
    200A  THR*     3.5    29.3    +      -       -      +
    240A  GLU      4.0     1.0    -      -       -      +
    241A  ILE*     3.6     0.9    -      -       -      -
    242A  ASN*     2.9    43.5    +      -       -      -
    264A  VAL*     4.0     6.9    -      -       -      +
    265A  VAL*     1.3    73.1    -      -       -      +
    267A  ILE*     1.3    59.7    +      -       -      +
    268A  THR*     5.5     2.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  ARG      4.0     0.2    -      -       -      +
    198A  THR*     3.4     3.0    -      -       -      +
    199A  ILE*     2.8    47.8    +      -       +      +
    201A  MET*     3.6    20.9    -      -       +      -
    211A  PHE*     4.5     9.4    -      -       +      -
    218A  ILE*     4.3     8.3    -      -       +      -
    232A  LEU*     3.8    15.5    -      -       +      -
    238A  ILE*     4.6     7.9    -      -       +      -
    240A  GLU      3.2     8.1    -      -       -      +
    241A  ILE*     3.8    25.4    -      -       +      -
    258A  LEU*     4.9     2.9    -      -       +      -
    265A  VAL*     3.9    19.7    -      -       +      -
    266A  THR*     1.3    75.5    -      -       -      +
    268A  THR*     1.3    63.5    +      -       -      +
    269A  ILE*     3.7    24.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  GLU*     4.4    18.2    +      -       -      +
    197A  ARG      3.1    10.1    -      -       -      -
    198A  THR*     3.3    22.7    -      -       +      +
    238A  ILE*     3.8     1.7    -      -       -      +
    239A  CYS*     2.9    37.7    +      -       -      +
    240A  GLU*     3.1    48.2    +      -       +      +
    266A  THR*     5.5     2.9    -      -       +      +
    267A  ILE*     1.3    75.7    -      -       -      +
    269A  ILE*     1.3    59.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 269 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  GLU*     3.4     1.9    -      -       -      +
    197A  ARG*     2.9    67.4    +      -       +      +
    199A  ILE*     4.2    15.5    -      -       +      -
    218A  ILE*     4.0    14.1    -      -       +      -
    232A  LEU*     4.1    17.9    -      -       +      -
    233A  LEU      5.1     2.2    -      -       -      +
    236A  HIS*     3.9    18.2    -      -       +      -
    237A  ASN      3.0    14.1    -      -       -      +
    238A  ILE*     4.6     2.7    -      -       -      -
    239A  CYS*     4.4     1.6    -      -       -      +
    267A  ILE*     3.7    28.9    -      -       +      +
    268A  THR*     1.3    77.5    -      -       -      +
    270A  MET*     1.3    71.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 270 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  PHE*     3.1    52.3    -      -       +      +
    155A  GLY*     3.8    22.2    -      -       -      +
    193A  ARG*     4.0    17.3    -      -       -      -
    195A  PHE*     4.0    11.2    -      -       +      -
    196A  GLU*     3.9    15.7    -      -       +      +
    236A  HIS*     3.2     5.9    -      -       -      -
    237A  ASN*     2.7    34.4    +      -       +      +
    239A  CYS*     3.7    16.4    -      -       -      -
    269A  ILE*     1.3    80.0    -      -       -      +
    271A  PRO*     1.3    76.7    -      -       +      +
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Residues in contact with PRO 271 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  PHE*     3.5    30.7    -      -       +      +
    197A  ARG*     4.2     4.3    -      -       -      +
    235A  GLU      3.8     5.2    -      -       -      +
    236A  HIS*     3.4    28.5    -      -       +      +
    237A  ASN*     4.7     1.2    +      -       -      -
    270A  MET*     1.3    90.1    -      -       +      +
    272A  ALA*     1.3    66.8    +      -       -      +
    273A  PHE*     3.4    36.5    +      -       +      +
    133B  ASP*     5.3     2.5    -      -       -      +
    195B  PHE*     4.6    14.1    -      -       +      -
----------------------------------------------------------
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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