Contacts of the strand formed by residues 258 - 264 (chain B) 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 PRO 258 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    607A  SER*     3.9    29.8    -      -       -      +
    132B  GLY*     6.1     2.7    -      -       -      -
    156B  GLY*     4.4     9.0    -      -       -      +
    157B  ALA      4.7     1.0    -      -       -      +
    158B  VAL*     3.6    31.1    -      -       +      +
    256B  GLU      3.6     5.6    -      -       -      +
    257B  ASP*     1.3    92.6    -      -       +      +
    259B  LEU*     1.3    59.5    +      -       -      +
    275B  LEU*     4.2    22.7    -      -       +      -
    276B  HIS      3.9     5.6    -      -       -      +
    277B  THR*     4.2     5.4    -      -       +      -
    278B  THR*     4.2     2.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77B  LEU*     3.7    27.1    -      -       +      -
    153B  ALA*     3.7    33.6    -      -       +      +
    157B  ALA      3.8     4.7    -      -       -      +
    158B  VAL*     3.6     7.2    -      -       -      -
    159B  HIS*     3.5    18.6    +      -       -      +
    257B  ASP      3.4     0.8    +      -       -      -
    258B  PRO*     1.3    73.3    -      -       -      +
    260B  PHE*     1.3    80.2    +      -       +      +
    276B  HIS      2.9     7.5    +      -       -      +
    277B  THR      3.5    17.9    -      -       -      +
    278B  THR*     3.7    18.2    -      -       +      +
    281B  TYR*     3.6    33.0    -      -       +      -
    318B  TYR*     4.6     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  VAL*     3.8     4.3    -      -       -      -
    159B  HIS*     3.2    34.1    -      +       +      +
    258B  PRO      3.9     0.4    -      -       -      -
    259B  LEU*     1.3    97.4    -      -       +      +
    261B  ILE*     1.3    74.4    +      -       -      +
    262B  LEU*     4.0    16.2    -      -       +      -
    275B  LEU*     3.6     4.1    -      -       -      +
    276B  HIS*     3.0    64.6    +      +       +      +
    281B  TYR*     3.5    38.4    -      +       -      -
    310B  VAL*     5.0     4.9    -      -       +      -
    313B  HIS*     3.7    31.4    -      +       +      -
    318B  TYR*     4.5     2.2    -      +       -      -
    416B  THR*     5.6     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  VAL*     4.1    17.0    -      -       +      -
    158B  VAL*     3.9    19.3    -      -       +      -
    159B  HIS      3.0     7.5    +      -       -      +
    160B  SER*     3.4    26.6    +      -       -      +
    161B  VAL      4.1     1.7    +      -       -      -
    178B  SER*     4.9     3.4    -      -       -      -
    260B  PHE*     1.3    80.9    -      -       -      +
    262B  LEU*     1.3    66.8    +      -       -      +
    263B  TYR*     3.9    18.4    -      -       +      -
    273B  GLY*     3.2    31.0    -      -       -      -
    274B  VAL      3.2     4.0    -      -       -      -
    275B  LEU*     4.1    12.8    -      -       +      -
    313B  HIS*     5.0     0.2    +      -       -      -
    478B  PHE*     3.4    44.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160B  SER*     5.0     0.4    -      -       -      -
    161B  VAL      3.4    24.2    -      -       -      +
    260B  PHE*     4.0    12.1    -      -       +      -
    261B  ILE*     1.3    75.3    -      -       -      +
    263B  TYR*     1.3    71.2    +      -       -      +
    264B  THR*     2.9    17.4    +      -       -      +
    273B  GLY*     4.2     0.2    -      -       -      -
    274B  VAL*     2.9    27.0    +      -       -      +
    308B  GLY      3.6    16.6    -      -       -      +
    309B  TRP*     4.6     1.8    -      -       +      -
    310B  VAL*     3.5    43.5    -      -       +      +
    313B  HIS*     3.6    30.7    -      -       +      +
    416B  THR*     4.1    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160B  SER*     3.6    24.0    +      -       -      -
    161B  VAL      5.3     1.3    +      -       -      -
    162B  ILE*     5.7     0.4    -      -       +      -
    166B  PHE*     5.8     1.4    -      -       -      -
    174B  ARG*     3.4    64.2    +      -       +      +
    177B  ASP*     2.6    47.9    +      -       +      +
    178B  SER*     3.3    18.7    +      -       -      -
    261B  ILE*     3.9     9.3    -      -       +      +
    262B  LEU*     1.3    83.6    -      -       -      +
    264B  THR*     1.3    59.1    +      -       -      +
    271B  PRO*     3.6    18.6    -      -       +      -
    272B  LYS      3.4     6.1    -      -       -      -
    273B  GLY*     3.3    23.6    -      -       -      -
    309B  TRP*     5.2     9.7    -      -       -      -
    478B  PHE*     4.4     3.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  LEU      2.9    14.9    +      -       -      -
    263B  TYR*     1.3    75.0    +      -       -      +
    265B  SER*     1.3    62.3    +      -       -      +
    266B  GLY      3.8     0.7    +      -       -      -
    271B  PRO*     3.3     5.4    -      -       -      +
    272B  LYS*     3.1    25.5    +      -       -      +
    274B  VAL*     3.4    19.7    -      -       +      +
    416B  THR*     3.4    23.8    +      -       -      +
    417B  GLU*     4.1     5.8    -      -       -      +
    488B  TYR*     5.4     0.9    -      -       -      +
    526B  ARG*     3.2    44.4    -      -       -      +
----------------------------------------------------------
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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