Contacts of the strand formed by residues 262 - 268 (chain B) in PDB entry 3H8E


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 PHE 262 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    260B  LYS      4.5     4.5    -      -       -      -
    261B  PRO*     1.3    74.4    -      -       -      +
    263B  VAL*     1.3    63.4    +      -       -      +
    264B  LEU*     5.8     2.2    -      -       +      -
    311B  VAL*     4.0    29.2    -      -       +      -
    312B  ASN      2.9    17.5    +      -       -      +
    313B  LEU*     3.4    10.6    -      -       +      +
    314B  VAL      2.9    23.4    +      -       -      -
    369B  GLN*     2.2    39.7    -      -       +      -
    370B  ALA*     3.6    12.8    -      -       +      +
    372B  ILE*     6.4     0.4    -      -       +      -
    490B  TYR*     3.3    33.9    -      +       +      -
    491B  LEU*     3.9    20.2    -      -       +      -
    494B  ARG*     3.6    30.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261B  PRO*     4.7     2.5    -      -       +      -
    262B  PHE*     1.3    76.6    -      -       -      +
    264B  LEU*     1.3    68.3    +      -       -      +
    265B  VAL*     4.0    13.0    -      -       +      -
    314B  VAL*     3.1    23.3    -      -       +      +
    316B  LEU*     3.8    30.1    -      -       +      -
    363B  ALA*     4.1     8.1    -      -       +      +
    366B  PHE*     4.3    15.0    -      -       +      -
    368B  PRO*     3.7    24.7    -      -       +      -
    370B  ALA      2.9    11.9    +      -       -      +
    371B  VAL*     3.4     8.8    -      -       +      -
    372B  ILE*     2.9    26.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  PHE*     4.1     1.8    +      -       +      -
    263B  VAL*     1.3    80.6    -      -       -      +
    265B  VAL*     1.3    56.1    +      -       -      +
    266B  GLY      4.1     0.2    -      -       -      -
    297B  VAL*     3.9    31.2    -      -       +      +
    300B  THR*     3.9    32.3    -      -       +      -
    313B  LEU*     3.9    26.9    -      -       +      -
    314B  VAL      2.8     8.2    +      -       -      +
    315B  CYS*     3.3     3.4    -      -       -      -
    316B  LEU      2.8    31.2    +      -       -      +
    372B  ILE*     3.4    33.2    -      -       +      +
    374B  ILE*     4.3     2.0    -      -       +      -
    487B  LEU*     4.2    17.3    -      -       +      -
    490B  TYR*     5.8     2.7    -      -       +      -
    491B  LEU*     4.5     5.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263B  VAL*     4.0    19.1    -      -       +      -
    264B  LEU*     1.3    73.8    -      -       -      +
    266B  GLY*     1.3    63.4    +      -       -      +
    267B  LYS      4.2     0.2    +      -       -      -
    297B  VAL*     4.3     1.8    -      -       -      -
    316B  LEU*     3.3    15.9    -      -       +      +
    318B  ALA*     5.3     0.4    -      -       +      -
    356B  LEU*     3.6    25.1    -      -       +      +
    359B  THR*     3.7    26.7    -      -       +      -
    360B  LEU*     4.3    10.5    -      -       +      -
    363B  ALA*     4.9     1.8    -      -       +      -
    371B  VAL*     4.0    17.7    -      -       +      -
    372B  ILE      2.8     7.9    +      -       -      +
    373B  ASP*     3.1    12.4    -      -       +      +
    374B  ILE*     2.8    27.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 266 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265B  VAL*     1.3    75.0    -      -       -      +
    267B  LYS*     1.3    65.2    +      -       -      -
    268B  GLY      3.3     0.2    +      -       -      -
    293B  GLY      3.8     5.4    -      -       -      -
    294B  ALA*     3.7    18.5    -      -       -      +
    297B  VAL*     4.0     7.6    -      -       -      +
    316B  LEU      2.9    10.5    +      -       -      -
    317B  LEU*     3.7     3.0    -      -       -      +
    318B  ALA*     3.0    27.5    +      -       -      +
    356B  LEU*     4.3     3.8    -      -       -      -
    374B  ILE      3.5     5.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 267 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  GLY*     1.3    69.2    -      -       -      -
    268B  GLY*     1.3    59.3    +      -       -      +
    269B  ILE*     3.5    36.8    -      -       +      +
    291B  MET*     3.5    12.0    -      -       -      +
    293B  GLY      3.6     3.1    +      -       -      -
    294B  ALA      3.0    16.2    +      -       -      +
    318B  ALA*     4.2     2.7    -      -       -      -
    351B  GLU*     4.2     9.9    +      -       -      -
    352B  GLY*     3.5    28.9    -      -       -      +
    355B  VAL*     4.8     3.6    -      -       +      -
    356B  LEU*     4.0    14.3    -      -       +      +
    374B  ILE      3.0     9.0    +      -       -      +
    375B  ALA*     3.6    32.8    -      -       +      -
    376B  THR*     3.2    35.8    +      -       -      +
    377B  LEU*     4.3    10.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 268 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199B  PRO*     5.0     2.3    -      -       -      +
    202B  LEU*     4.8     2.1    -      -       -      +
    266B  GLY      3.3     1.6    +      -       -      -
    267B  LYS*     1.3    75.0    -      -       -      +
    269B  ILE*     1.4    61.4    +      -       -      +
    291B  MET*     3.8    10.2    -      -       -      +
    294B  ALA*     3.6    17.5    -      -       -      -
    318B  ALA      2.8    23.4    +      -       -      -
    319B  CYS*     3.1    27.2    -      -       -      +
    320B  ALA      3.1     4.9    +      -       -      +
----------------------------------------------------------
 Back to top of page


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