Contacts of the strand formed by residues 432 - 443 (chain B) in PDB entry 2O5C


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 GLY 432 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  TRP*     4.7     8.5    -      -       -      -
    428B  ASP*     3.7     5.5    -      -       -      +
    429B  ILE      3.0    33.0    +      -       -      +
    430B  ALA      3.1     3.6    +      -       -      -
    431B  LYS*     1.3    80.4    -      -       -      +
    433B  LYS*     1.3    65.3    +      -       -      +
    434B  PHE*     3.6    10.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 433 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  TRP*     3.2    12.7    -      -       -      +
    241B  GLN*     2.8    53.3    +      -       +      +
    277B  THR*     5.7     3.6    -      -       -      -
    427B  LEU      4.1     6.1    -      -       -      +
    428B  ASP*     2.8    32.1    +      -       -      -
    431B  LYS      4.7     7.4    +      -       -      +
    432B  GLY*     1.3    72.4    -      -       -      -
    434B  PHE*     1.3    57.0    +      -       -      +
    435B  VAL*     5.8     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 434 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224B  VAL*     4.0     5.4    -      -       +      -
    226B  ALA*     3.7    26.7    -      -       +      -
    238B  ALA*     4.2    10.1    -      -       +      -
    239B  ILE      3.3     6.1    -      -       -      -
    240B  TRP*     3.4    48.7    -      +       +      -
    265B  VAL*     4.1     7.0    -      -       +      -
    269B  ILE*     3.7    41.1    -      -       +      -
    426B  GLU*     3.5     1.2    -      -       -      +
    427B  LEU*     2.9    37.3    +      -       +      +
    429B  ILE*     3.7    33.7    -      -       +      -
    432B  GLY*     3.6    13.2    -      -       -      -
    433B  LYS*     1.3    76.8    -      -       -      +
    435B  VAL*     1.3    68.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 435 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  ALA*     3.4     2.6    -      -       -      -
    239B  ILE*     2.7    43.5    +      -       -      +
    241B  GLN*     3.6    30.5    -      -       +      +
    424B  VAL*     3.8    17.7    -      -       +      -
    425B  ILE      3.5     3.4    -      -       -      +
    426B  GLU*     4.1    19.7    -      -       +      +
    433B  LYS*     5.4     2.0    -      -       +      -
    434B  PHE*     1.3    82.0    -      -       -      +
    436B  ALA*     1.3    60.5    +      -       -      +
    437B  LYS*     3.7    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 436 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  PHE*     3.8    25.4    -      -       +      -
    237B  THR      3.4    24.7    -      -       -      +
    238B  ALA*     4.0     3.3    -      -       +      +
    424B  VAL*     3.4     5.5    -      -       -      +
    425B  ILE*     3.0    37.5    +      -       +      +
    435B  VAL*     1.3    73.6    -      -       -      +
    437B  LYS*     1.3    62.4    +      -       -      +
    464B  LEU*     3.7    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 437 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422B  LYS*     3.5    28.5    -      -       +      +
    423B  CYS      3.4     4.7    -      -       -      +
    424B  VAL*     4.0    22.9    -      -       +      -
    435B  VAL*     3.7    23.3    +      -       +      +
    436B  ALA*     1.3    79.0    -      -       -      +
    438B  ALA*     1.3    61.9    +      -       -      +
    460B  ASP*     4.3    11.5    -      -       -      +
    461B  GLY*     4.2    13.5    -      -       -      -
    462B  THR      4.6     2.1    +      -       -      +
    464B  LEU*     3.8     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 438 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421B  ARG      3.7     1.0    -      -       -      +
    422B  LYS*     3.4     4.6    -      -       -      +
    423B  CYS*     2.8    38.2    +      -       +      +
    437B  LYS*     1.3    75.2    -      -       -      +
    439B  ARG*     1.3    62.2    +      -       -      +
    440B  PHE*     4.2     8.3    -      -       +      -
    460B  ASP*     3.3    11.7    -      -       -      +
    462B  THR      3.5    26.7    -      -       -      +
    463B  PRO*     4.4     4.0    -      -       +      -
    464B  LEU*     4.0    13.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 439 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284B  GLU*     2.6    37.1    +      -       -      +
    285B  SER      5.5     1.2    +      -       -      -
    286B  GLU*     5.3     4.9    +      -       -      +
    420B  PHE*     3.6    52.3    -      -       +      +
    421B  ARG      3.3     6.1    -      -       -      +
    422B  LYS*     4.1    20.0    -      -       +      +
    438B  ALA*     1.3    75.3    -      -       -      +
    440B  PHE*     1.3    60.9    +      -       -      +
    458B  GLU*     4.0    21.4    +      -       -      +
    459B  ASN*     3.2     7.4    -      -       -      +
    460B  ASP*     2.9    45.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 440 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420B  PHE*     3.8     3.6    -      -       -      -
    421B  ARG*     2.8    35.0    +      -       +      +
    438B  ALA*     4.3     5.6    -      -       +      -
    439B  ARG*     1.3    83.5    -      -       -      +
    441B  LEU*     1.3    67.9    +      -       -      +
    442B  ALA*     4.2     1.9    -      -       -      +
    459B  ASN*     3.6    31.6    -      -       +      -
    460B  ASP      3.7    10.5    -      -       -      -
    461B  GLY      3.4    26.2    -      -       -      -
    462B  THR      4.0     1.6    -      -       -      -
    463B  PRO*     3.6    42.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 441 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418B  ALA*     3.7    22.2    -      -       +      -
    419B  VAL      3.7     4.9    -      -       -      +
    420B  PHE*     3.4    18.9    -      -       +      -
    440B  PHE*     1.3    77.2    -      -       -      +
    442B  ALA*     1.3    59.6    +      -       -      +
    443B  GLU      3.5    22.0    -      -       -      +
    444B  ALA*     3.9    19.3    -      -       +      +
    447B  ARG*     3.9    10.3    -      -       -      -
    455B  ARG*     3.6    43.5    -      -       +      +
    456B  ASP*     4.5     4.5    -      -       -      +
    459B  ASN*     3.0    23.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 442 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    419B  VAL*     2.7    17.1    +      -       +      +
    421B  ARG*     3.6    45.2    +      -       +      +
    440B  PHE      3.3     3.3    +      -       -      +
    441B  LEU*     1.3    75.0    -      -       -      +
    443B  GLU*     1.3    67.0    +      -       +      +
    444B  ALA      4.1     1.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 443 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283B  ARG*     3.2    28.9    +      -       -      +
    417B  ASP      5.0     2.6    -      -       -      +
    418B  ALA*     3.3     0.9    -      -       -      -
    419B  VAL*     2.8    55.5    +      -       +      +
    421B  ARG*     6.2     1.1    -      -       -      +
    441B  LEU*     3.5     4.7    -      -       -      +
    442B  ALA*     1.3    82.6    -      -       +      +
    444B  ALA*     1.3    64.6    +      -       -      +
    445B  GLY      3.3     4.5    +      -       -      +
----------------------------------------------------------
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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