Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 2P2B


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 THR 93 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ASP      3.6     2.4    +      -       -      -
     92A  ARG*     1.3    79.4    -      -       -      +
     94A  ALA*     1.3    59.1    +      -       -      +
     95A  ILE      3.4    31.2    -      -       -      +
     96A  ILE*     3.7    17.5    -      -       +      -
    107A  HIS*     3.7    22.8    -      -       +      +
    108A  ILE      3.7    14.6    -      -       -      +
    109A  SER*     3.9     3.4    +      -       -      +
    110A  TYR*     4.1     0.2    -      -       -      -
    325A  ALA      3.9     0.9    -      -       -      +
    326A  THR*     2.6    38.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ARG      3.5     2.6    +      -       -      -
     93A  THR*     1.3    72.8    -      -       -      +
     95A  ILE*     1.3    59.3    +      -       -      +
    108A  ILE      2.7    14.3    +      -       -      +
    109A  SER      4.0     0.4    -      -       -      -
    110A  TYR*     3.5    42.0    -      -       +      +
    113A  LEU*     3.9    26.2    -      -       +      -
    321A  LEU*     3.9     3.3    -      -       +      +
    325A  ALA      3.6     3.0    -      -       -      +
    326A  THR*     3.5     2.0    -      -       -      -
    327A  THR*     2.9    32.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  THR*     3.4     4.7    -      -       -      +
     94A  ALA*     1.3    85.1    -      -       +      +
     96A  ILE*     1.3    75.8    +      -       -      +
     97A  TRP*     3.8     8.5    +      -       +      +
    106A  LYS      3.7     1.9    -      -       -      +
    108A  ILE*     2.9    45.9    +      -       +      +
    113A  LEU*     3.9    29.6    -      -       +      -
    143A  PRO*     5.0    10.1    -      -       +      +
    146A  ALA*     3.8    28.5    -      -       +      -
    317A  LEU*     4.4     9.2    -      -       +      -
    321A  LEU*     4.8     2.7    -      -       +      -
    327A  THR*     3.2    18.4    -      -       +      +
    329A  MET*     4.3    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  THR*     3.7    19.1    -      -       +      -
     94A  ALA      4.3     0.2    -      -       -      -
     95A  ILE*     1.3    75.2    -      -       -      +
     97A  TRP*     1.3    64.3    +      -       -      +
    106A  LYS      3.5     7.0    -      -       -      +
    107A  HIS*     3.8    21.3    -      -       +      +
    300A  ILE*     4.0    23.6    -      -       +      -
    326A  THR*     3.8    18.8    -      -       +      +
    327A  THR      2.9     8.4    +      -       -      +
    328A  LEU*     3.3    13.5    -      -       +      +
    329A  MET      2.7    28.4    +      -       -      +
    349A  HIS*     3.5    50.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  ILE*     3.8     6.6    +      -       +      -
     96A  ILE*     1.3    74.9    -      -       -      +
     98A  GLU*     1.3    61.4    +      -       -      +
     99A  GLY*     3.7    13.9    -      -       -      -
    104A  GLN*     4.1    24.5    -      -       +      -
    105A  SER*     3.0    17.1    -      -       -      -
    106A  LYS*     2.8    64.9    +      -       +      +
    108A  ILE*     5.0     0.7    -      -       +      -
    141A  MET      2.9    25.2    +      -       -      -
    142A  VAL*     3.6     8.6    -      -       +      +
    143A  PRO*     3.5    36.8    -      -       +      -
    222A  ARG*     4.2    12.6    -      -       -      -
    329A  MET*     3.4    22.4    -      -       -      -
    331A  GLU*     3.4    34.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ILE      3.9     1.0    +      -       -      -
     97A  TRP*     1.3    75.2    +      -       -      +
     99A  GLY*     1.3    64.4    +      -       -      +
    102A  THR*     3.3     8.0    +      -       -      -
    104A  GLN      4.0     1.8    -      -       -      -
    105A  SER*     3.6     2.4    -      -       -      -
    328A  LEU*     4.2    13.9    -      -       +      -
    329A  MET      3.0     7.1    +      -       -      +
    330A  PHE*     3.4    23.1    -      -       +      -
    331A  GLU*     2.9    29.3    +      -       -      +
    341A  ARG*     3.0    21.2    +      -       -      +
    345A  VAL*     4.1    12.6    -      -       +      +
    348A  LYS*     2.8    31.7    +      -       -      +
    349A  HIS*     2.7    35.8    +      -       -      +
----------------------------------------------------------
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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