Contacts of the strand formed by residues 422 - 428 (chain O) in PDB entry 3H1I


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 LYS 422 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241O  GLY*     4.1     9.5    -      -       -      +
    257O  VAL*     4.5     7.9    -      -       +      -
    258O  VAL      3.4     8.7    -      -       -      +
    259O  THR*     3.3    15.0    -      -       -      +
    341O  MET*     4.0    29.2    -      -       +      +
    417O  PHE*     3.9    16.6    -      -       +      +
    418O  VAL*     3.7    29.3    +      -       -      +
    419O  SER      4.9     0.7    -      -       -      -
    420O  GLY      3.9     7.0    -      -       -      +
    421O  LYS*     1.3    78.7    -      -       -      +
    423O  SER*     1.3    59.7    +      -       -      +
    436O  LEU*     2.7    50.1    -      -       +      +
    439O  LEU*     4.0    12.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 423 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163O  LEU*     4.3     5.6    -      -       -      +
    166O  ALA      3.8    15.0    -      -       -      -
    167O  ALA*     3.4    19.3    -      -       -      -
    239O  TYR*     2.6    27.4    +      -       -      -
    241O  GLY*     3.1    17.0    -      -       -      -
    242O  GLY      3.6     6.1    -      -       -      -
    257O  VAL*     3.4     4.3    -      -       -      +
    258O  VAL*     2.8    38.1    +      -       -      -
    422O  LYS*     1.3    74.1    -      -       -      +
    424O  MET*     1.3    61.0    +      -       -      +
    436O  LEU*     4.1     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 424 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163O  LEU*     3.6     3.8    -      -       -      -
    166O  ALA*     4.0     4.0    -      -       -      +
    242O  GLY      3.2    12.0    +      -       -      +
    243O  GLU*     4.2    14.3    -      -       +      +
    244O  ILE      3.3    22.0    +      -       -      -
    245O  ARG*     5.2     6.1    -      -       -      -
    255O  ALA*     5.0     2.9    -      -       +      -
    256O  ALA      3.3     5.2    -      -       -      +
    257O  VAL*     3.6    25.1    -      -       +      -
    337O  ILE*     4.4    23.6    -      -       +      -
    423O  SER*     1.3    75.0    -      -       -      +
    425O  ALA*     1.3    74.0    +      -       -      +
    426O  ALA*     5.1     4.5    -      -       +      -
    433O  THR*     4.5     5.4    -      -       +      -
    434O  PRO*     3.2    30.7    -      -       +      +
    435O  PHE      5.0     0.4    -      -       -      -
    436O  LEU*     3.7    34.4    -      -       +      +
    439O  LEU*     5.2     3.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 425 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159O  VAL*     3.3    30.7    -      -       +      +
    162O  ASN*     4.5     4.7    -      -       +      -
    163O  LEU*     3.1    29.8    -      -       +      +
    244O  ILE*     3.9     7.6    -      -       -      -
    245O  ARG*     6.0     0.2    -      -       -      -
    255O  ALA*     3.5     1.3    -      -       -      +
    256O  ALA*     2.8    29.0    +      -       +      +
    424O  MET*     1.3    78.3    -      -       -      +
    426O  ALA*     1.3    66.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 426 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159O  VAL*     4.0     9.2    -      -       -      +
    162O  ASN*     5.1     4.3    +      -       -      +
    244O  ILE      3.5    10.5    +      -       -      +
    245O  ARG*     4.8     6.7    -      -       +      +
    246O  GLU*     3.4    21.3    +      -       -      +
    254O  HIS      3.6    14.6    -      -       -      +
    255O  ALA*     4.4     4.9    -      -       +      -
    424O  MET*     5.1     6.1    -      -       +      -
    425O  ALA*     1.3    79.4    -      -       -      +
    427O  SER*     1.3    65.9    +      -       -      +
    430O  LEU*     4.0    20.2    -      -       +      -
    433O  THR*     4.9     9.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 427 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155O  PRO*     4.7    10.0    +      -       -      +
    158O  GLY*     5.7     0.4    -      -       -      -
    159O  VAL*     3.1    25.6    +      -       -      +
    162O  ASN*     5.5     0.9    -      -       -      -
    246O  GLU*     3.8    23.3    -      -       -      -
    248O  ASN*     4.4    10.4    -      -       -      +
    250O  HIS*     5.4     1.4    -      -       -      +
    252O  LEU      3.6     4.5    -      -       -      +
    254O  HIS*     3.2    31.2    +      -       -      +
    426O  ALA*     1.3    79.6    -      -       -      +
    428O  GLY*     1.3    59.1    +      -       -      +
    430O  LEU*     3.6     5.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 428 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246O  GLU      3.7     3.8    +      -       -      -
    247O  GLN*     3.4     8.2    +      -       -      +
    248O  ASN*     3.1    28.1    +      -       -      +
    250O  HIS*     3.6     8.5    -      -       -      -
    252O  LEU      4.2     4.0    -      -       -      -
    253O  VAL*     4.2     2.0    -      -       -      -
    427O  SER*     1.3    73.7    -      -       -      +
    429O  ASP*     1.3    56.6    +      -       -      -
    430O  LEU*     2.5    31.6    +      -       -      +
----------------------------------------------------------
 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