Contacts of the strand formed by residues 84 - 98 (chain J) in PDB entry 1H2I


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 TRP 84 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26J  PHE*     3.9     5.8    -      -       -      -
     72J  ILE*     4.2    12.3    -      -       +      -
     75J  ALA*     3.5    33.7    -      -       +      -
     76J  ASN*     2.8    26.1    +      -       -      +
     79J  PHE*     3.9    11.9    -      +       +      -
     80J  GLY      3.5    15.9    -      -       -      -
     81J  TYR      4.2     6.1    +      -       -      +
     82J  ASN      3.6     0.2    -      -       -      -
     83J  GLY*     1.3    79.4    +      -       -      +
     85J  ALA*     1.3    81.0    +      -       -      +
     86J  HIS*     3.8    16.4    -      +       -      -
    113J  VAL*     4.1    11.0    -      -       +      -
    114J  GLN      3.1    10.5    -      -       -      +
    115J  LEU*     3.9    13.5    -      -       +      -
    151J  LEU*     3.9    27.4    -      -       +      -
    155J  LEU*     4.2     7.4    -      -       +      -
    119K  SER*     4.5     4.0    -      -       -      -
    121K  HIS*     3.3    40.0    +      +       -      -
    157K  SER*     3.8    19.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 85 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26J  PHE*     3.7    11.7    -      -       +      -
     84J  TRP*     1.3    82.1    -      -       -      +
     86J  HIS*     1.3    60.1    +      -       -      +
    113J  VAL*     3.0     8.0    -      -       -      +
    114J  GLN      2.7    29.0    +      -       -      +
    120K  TYR*     2.8    57.4    -      -       +      +
    121K  HIS*     3.8     4.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 86 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84J  TRP*     3.8     4.7    -      +       +      -
     85J  ALA*     1.3    79.1    -      -       -      +
     87J  SER*     1.3    62.2    +      -       -      +
     88J  ILE*     5.5     0.4    -      -       +      -
    111J  VAL*     4.0    15.3    -      -       +      -
    112J  ARG      3.1    11.9    -      -       -      +
    113J  VAL*     4.0     3.6    -      -       +      -
    147J  VAL*     5.1     5.8    -      -       +      +
    151J  LEU*     3.7    43.9    -      -       +      +
    120K  TYR*     3.1    13.8    +      -       -      -
    121K  HIS*     2.9    45.7    -      +       +      -
    122K  GLU      3.1    46.4    +      -       -      -
    123K  ASP*     4.9     5.6    +      -       -      -
    157K  SER*     3.5    18.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 87 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86J  HIS*     1.3    76.7    -      -       -      +
     88J  ILE*     1.3    64.5    +      -       -      +
     89J  THR*     3.6     6.6    +      -       -      +
    111J  VAL*     3.4     7.2    -      -       -      +
    112J  ARG*     2.9    42.8    +      -       -      +
    112K  ARG*     5.1     6.7    -      -       -      -
    120K  TYR*     3.9    18.3    +      -       -      -
    122K  GLU*     3.5    17.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 88 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86J  HIS*     5.5     0.7    -      -       +      -
     87J  SER*     1.3    73.0    -      -       -      +
     89J  THR*     1.3    63.7    +      -       -      +
     90J  GLN*     3.6    28.9    -      -       -      +
     91J  GLN*     4.2     4.5    -      -       +      +
    109J  ALA*     5.1     3.1    -      -       +      -
    110J  PHE      3.5     7.2    -      -       -      +
    111J  VAL*     4.7     6.5    -      -       +      -
    147J  VAL*     3.9    25.1    -      -       +      -
    110K  PHE*     3.8    31.6    -      -       +      -
    122K  GLU*     2.9    32.5    +      -       +      +
    123K  ASP*     3.7    33.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 89 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87J  SER*     3.6     6.6    +      -       -      +
     88J  ILE*     1.3    73.9    -      -       -      +
     90J  GLN*     1.3    64.9    +      -       -      +
    110J  PHE*     2.8    22.7    +      -       -      +
    112J  ARG*     3.9    28.0    -      -       +      -
    122J  GLU*     2.7    30.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 90 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88J  ILE*     3.1    10.3    -      -       -      +
     89J  THR*     1.3    86.5    +      -       -      +
     91J  GLN*     1.3    66.4    +      -       -      +
     92J  ASN*     3.7    33.1    -      -       -      +
    109J  ALA*     3.4     1.4    -      -       -      -
    110J  PHE*     2.8    49.5    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 91 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88J  ILE*     4.2     4.0    -      -       +      +
     90J  GLN*     1.3    80.7    +      -       -      +
     92J  ASN*     1.3    65.6    +      -       -      +
     93J  VAL      4.3     0.2    +      -       -      -
    107J  VAL*     3.7    18.8    -      -       +      +
    108J  CYS      3.3    11.7    -      -       -      +
    109J  ALA*     3.9     2.1    -      -       -      +
    143J  ARG*     2.9    69.4    +      -       -      +
    146J  ALA*     3.8     5.9    -      -       -      +
    147J  VAL*     3.5    16.0    -      -       -      +
    110K  PHE*     3.3    35.7    -      -       +      -
    124K  VAL*     3.8     1.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 92 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143I  ARG*     4.8     4.1    +      -       -      +
     90J  GLN*     3.7    23.1    -      -       -      +
     91J  GLN*     1.3    76.0    +      -       -      +
     93J  VAL*     1.3    76.8    +      -       -      +
     94J  ASP*     3.4    13.4    +      -       -      +
    107J  VAL*     3.6     2.4    -      -       -      -
    108J  CYS*     2.9    50.4    +      -       -      -
    110J  PHE*     5.6     0.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 93 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92J  ASN*     1.3    80.4    +      -       -      +
     94J  ASP*     1.3    62.6    +      -       -      +
     95J  PHE*     3.8    13.5    -      -       -      +
     96J  VAL*     3.9    25.1    -      -       +      -
    106J  GLY      3.9     2.7    -      -       -      -
    107J  VAL*     3.8    20.4    -      -       +      -
    139J  LEU*     4.5     7.0    -      -       +      -
    143J  ARG*     3.5    39.0    -      -       -      +
     94K  ASP*     5.3     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 94 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93I  VAL*     5.8     0.2    -      -       -      -
    139I  LEU*     3.5    14.6    -      -       +      +
    143I  ARG*     2.6    33.8    +      -       -      -
     92J  ASN*     3.4    19.0    +      -       -      +
     93J  VAL*     1.3    73.3    -      -       -      +
     95J  PHE*     1.3    72.3    +      -       +      +
    106J  GLY      2.7    17.6    +      -       -      +
    108J  CYS*     4.8     0.2    -      -       -      -
    126J  TYR*     2.6    32.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 95 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135I  LYS*     3.6    42.0    -      -       +      +
    136I  ALA*     3.5    37.7    -      -       +      -
    139I  LEU*     4.1     7.0    -      -       +      -
     93J  VAL*     3.4     3.5    -      -       -      +
     94J  ASP*     1.3    90.2    -      -       +      +
     96J  VAL*     1.3    70.0    +      -       -      +
     97J  ASP*     3.7    17.5    -      -       -      +
    104J  TYR*     3.1    36.3    -      -       +      -
    105J  VAL*     3.4     4.6    -      -       -      +
    106J  GLY*     3.3    36.0    +      -       -      +
    126J  TYR*     4.0     5.4    -      -       -      -
    130J  GLU*     5.8     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 96 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93J  VAL*     3.9    17.7    -      -       +      -
     95J  PHE*     1.3    80.4    -      -       -      +
     97J  ASP*     1.3    64.9    +      -       -      +
     98J  LEU      4.2     0.5    +      -       -      -
    103J  PHE*     4.2    21.1    -      -       +      -
    104J  TYR      3.6     3.6    -      -       -      -
    105J  VAL*     4.2    11.0    -      -       +      -
    135J  LYS*     4.4    24.7    -      -       +      -
    139J  LEU*     4.0    22.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 97 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135I  LYS*     3.0    33.1    +      -       -      +
     95J  PHE*     3.7    13.5    -      -       -      +
     96J  VAL*     1.3    82.0    +      -       -      +
     98J  LEU*     1.3    59.9    +      -       -      +
     99J  ASN*     3.9    19.5    -      -       -      +
    103J  PHE*     3.2     7.1    -      -       -      -
    104J  TYR*     2.7    51.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 98 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96J  VAL      4.2     0.8    +      -       -      -
     97J  ASP*     1.3    71.6    -      -       -      +
     99J  ASN*     1.3    67.5    +      -       -      +
    100J  ASN      3.8    22.0    -      -       -      +
    101J  GLY*     4.0    12.1    -      -       -      -
    102J  LYS      3.4    11.4    -      -       -      +
    103J  PHE*     3.8    34.5    -      -       +      -
----------------------------------------------------------
 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