Contacts of the strand formed by residues 84 - 98 (chain R) 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 R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26R  PHE*     3.9     6.1    -      -       -      -
     72R  ILE*     4.2    12.3    -      -       +      -
     75R  ALA*     3.5    31.6    -      -       +      -
     76R  ASN*     2.8    32.3    +      -       -      +
     79R  PHE*     3.9    10.8    -      +       +      -
     80R  GLY      3.6    15.3    -      -       -      -
     81R  TYR      4.2     6.7    +      -       -      +
     82R  ASN      3.5     1.3    -      -       -      -
     83R  GLY*     1.3    79.8    +      -       -      +
     85R  ALA*     1.3    75.6    +      -       -      +
     86R  HIS*     3.8    11.4    -      +       +      -
    113R  VAL*     4.0    11.0    -      -       +      -
    114R  GLN      3.1    10.5    -      -       -      +
    115R  LEU*     3.9    13.7    -      -       +      -
    151R  LEU*     4.0    26.0    -      -       +      -
    155R  LEU*     4.3     8.7    -      -       +      -
    119S  SER*     4.6     3.8    -      -       -      -
    121S  HIS*     3.3    45.1    +      +       -      -
    157S  SER*     3.9    15.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26R  PHE*     3.7    12.3    -      -       +      -
     84R  TRP*     1.3    79.3    -      -       -      +
     86R  HIS*     1.3    57.5    +      -       -      +
    113R  VAL*     3.1     9.7    -      -       -      +
    114R  GLN      2.7    30.8    +      -       -      +
    120S  TYR*     2.9    55.6    -      -       +      +
    121S  HIS*     3.8     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 86 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84R  TRP*     3.8     4.0    -      -       +      -
     85R  ALA*     1.3    80.0    -      -       -      +
     87R  SER*     1.3    62.4    +      -       -      +
     88R  ILE*     5.5     0.2    -      -       +      -
    111R  VAL*     3.9    20.6    -      -       +      -
    112R  ARG      3.1    11.2    -      -       -      +
    113R  VAL*     4.0     4.9    -      -       +      -
    147R  VAL*     5.1     5.3    -      -       +      +
    151R  LEU*     3.9    38.7    -      -       +      +
    120S  TYR*     3.2    12.1    +      -       -      -
    121S  HIS*     2.7    48.1    -      +       +      -
    122S  GLU      3.0    46.6    +      -       -      -
    123S  ASP*     5.0     5.4    +      -       -      -
    157S  SER*     3.5    18.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 87 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86R  HIS*     1.3    76.7    -      -       -      +
     88R  ILE*     1.3    64.8    +      -       -      +
     89R  THR*     3.6     6.6    +      -       -      +
    111R  VAL*     3.4     6.9    -      -       -      +
    112R  ARG*     2.9    44.6    +      -       -      +
    112S  ARG*     5.2     7.0    -      -       -      -
    120S  TYR*     3.9    17.9    +      -       -      -
    122S  GLU*     3.4    18.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 88 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86R  HIS*     5.5     0.4    -      -       +      -
     87R  SER*     1.3    75.8    -      -       -      +
     89R  THR*     1.3    62.2    +      -       -      +
     90R  GLN*     3.7    28.7    -      -       -      +
     91R  GLN*     4.1     5.2    -      -       +      +
    109R  ALA*     5.1     3.1    -      -       +      -
    110R  PHE      3.4     7.0    -      -       -      +
    111R  VAL*     4.6     7.2    -      -       +      -
    147R  VAL*     4.0    26.0    -      -       +      -
    110S  PHE*     3.9    30.1    -      -       +      -
    122S  GLU*     2.8    35.5    +      -       +      +
    123S  ASP*     3.7    31.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 89 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87R  SER*     3.6     5.8    +      -       -      +
     88R  ILE*     1.3    74.9    -      -       -      +
     90R  GLN*     1.3    63.4    +      -       -      +
    110R  PHE*     2.8    21.6    +      -       -      +
    112R  ARG*     4.0    28.5    -      -       +      -
    122R  GLU*     2.6    30.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 90 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88R  ILE*     3.1     9.1    -      -       -      +
     89R  THR*     1.3    85.7    +      -       -      +
     91R  GLN*     1.3    66.1    +      -       -      +
     92R  ASN*     3.7    33.3    -      -       -      +
    109R  ALA*     3.4     1.7    -      -       -      -
    110R  PHE*     2.8    51.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 91 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88R  ILE*     4.1     5.0    -      -       +      +
     90R  GLN*     1.3    81.7    +      -       -      +
     92R  ASN*     1.3    65.0    +      -       -      +
     93R  VAL      4.2     0.3    +      -       -      -
    107R  VAL*     3.6    18.8    -      -       +      +
    108R  CYS      3.3    11.0    -      -       -      +
    109R  ALA*     3.9     2.1    -      -       +      +
    143R  ARG*     2.9    68.2    +      -       -      +
    146R  ALA*     3.7     6.5    -      -       -      +
    147R  VAL*     3.6    14.8    -      -       -      +
    110S  PHE*     3.3    37.2    -      -       +      -
    124S  VAL*     3.7     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 92 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143Q  ARG*     4.9     3.9    +      -       -      +
     90R  GLN*     3.7    22.4    -      -       -      +
     91R  GLN*     1.3    75.6    +      -       -      +
     93R  VAL*     1.3    73.7    +      -       -      +
     94R  ASP*     3.4    15.0    +      -       -      +
    107R  VAL*     4.1     2.2    -      -       -      -
    108R  CYS*     2.8    50.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91R  GLN      4.2     0.6    +      -       -      -
     92R  ASN*     1.3    78.7    +      -       -      +
     94R  ASP*     1.3    63.4    +      -       -      +
     95R  PHE*     3.8    13.9    -      -       -      +
     96R  VAL*     3.8    24.9    -      -       +      -
    106R  GLY      4.1     3.4    -      -       -      +
    107R  VAL*     3.8    21.5    -      -       +      -
    139R  LEU*     4.4     8.3    -      -       +      -
    143R  ARG*     3.6    37.9    -      -       -      +
     94S  ASP*     5.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 94 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93Q  VAL*     5.7     0.7    -      -       -      -
    139Q  LEU*     3.5    14.4    -      -       +      +
    143Q  ARG*     2.6    34.9    +      -       -      -
     92R  ASN*     3.4    18.1    +      -       -      +
     93R  VAL*     1.3    73.7    -      -       -      +
     95R  PHE*     1.3    71.4    +      -       +      +
    106R  GLY      2.8    16.9    +      -       -      +
    108R  CYS*     4.7     0.2    -      -       -      -
    126R  TYR*     2.6    33.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 95 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135Q  LYS*     3.7    40.8    -      -       +      +
    136Q  ALA*     3.5    37.9    -      -       +      -
    139Q  LEU*     4.0    12.1    -      -       +      -
     93R  VAL*     3.4     4.3    -      -       -      +
     94R  ASP*     1.3    89.5    -      -       +      +
     96R  VAL*     1.3    69.9    +      -       -      +
     97R  ASP*     3.5    20.0    -      -       -      +
    104R  TYR*     3.3    35.0    -      -       +      -
    105R  VAL*     3.4     3.8    -      -       -      +
    106R  GLY*     3.3    36.6    +      -       -      +
    126R  TYR*     4.0     1.3    -      -       -      -
    130R  GLU*     5.7     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93R  VAL*     3.8    18.8    -      -       +      -
     95R  PHE*     1.3    80.2    -      -       -      +
     97R  ASP*     1.3    64.0    +      -       -      +
     98R  LEU      4.2     0.7    +      -       -      -
    103R  PHE*     4.2    19.3    -      -       +      -
    104R  TYR      3.5     3.4    -      -       -      -
    105R  VAL*     4.1    13.7    -      -       +      -
    135R  LYS*     4.4    23.3    -      -       +      -
    139R  LEU*     4.0    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 97 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135Q  LYS*     2.9    34.4    +      -       -      +
     95R  PHE*     3.5    17.9    -      -       -      +
     96R  VAL*     1.3    77.4    -      -       -      +
     98R  LEU*     1.3    60.8    +      -       -      +
     99R  ASN*     3.9    19.2    -      -       -      +
    103R  PHE*     3.2     8.1    -      -       -      -
    104R  TYR*     2.7    53.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 98 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96R  VAL      4.2     0.8    +      -       -      -
     97R  ASP*     1.3    71.8    -      -       -      +
     99R  ASN*     1.3    67.8    +      -       -      +
    100R  ASN      3.8    19.3    -      -       -      +
    101R  GLY*     4.0    12.1    -      -       -      +
    102R  LYS      3.4    12.1    -      -       -      +
    103R  PHE*     3.7    35.0    -      -       +      -
----------------------------------------------------------
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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