Contacts of the strand formed by residues 84 - 98 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  PHE*     3.8     4.5    -      -       -      -
     72C  ILE*     4.1    11.9    -      -       +      -
     75C  ALA*     3.5    30.5    -      -       +      -
     76C  ASN*     2.8    25.9    +      -       -      +
     79C  PHE*     3.9    11.7    -      +       +      -
     80C  GLY      3.5    16.2    -      -       -      -
     81C  TYR      4.3     5.7    -      -       -      +
     82C  ASN      3.6     0.6    -      -       -      -
     83C  GLY*     1.3    80.2    +      -       -      +
     85C  ALA*     1.3    75.9    +      -       -      +
     86C  HIS*     3.6    17.3    -      +       -      -
    113C  VAL*     4.2    11.0    -      -       +      -
    114C  GLN      3.1    10.5    -      -       -      +
    115C  LEU*     3.9    13.5    -      -       +      -
    151C  LEU*     3.9    26.5    -      -       +      -
    155C  LEU*     4.2     9.4    -      -       +      -
    119D  SER*     4.7     3.6    -      -       -      -
    121D  HIS*     3.3    42.2    +      +       -      -
    157D  SER*     3.7    22.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  PHE*     3.5    19.5    -      -       +      -
     84C  TRP*     1.3    81.5    -      -       -      +
     86C  HIS*     1.3    58.4    +      -       -      +
    113C  VAL*     3.1    10.0    -      -       -      +
    114C  GLN      2.7    28.4    +      -       -      +
    120D  TYR*     2.9    49.8    -      -       +      +
    121D  HIS*     3.9     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 86 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  TRP*     3.6     5.3    -      +       +      -
     85C  ALA*     1.3    78.6    -      -       -      +
     87C  SER*     1.3    63.5    +      -       -      +
     88C  ILE*     5.4     0.4    -      -       +      -
    111C  VAL*     4.1    17.9    -      -       +      -
    112C  ARG      3.1    11.7    -      -       -      +
    113C  VAL*     4.1     3.4    -      -       +      -
    147C  VAL*     5.2     6.2    -      -       +      +
    151C  LEU*     3.9    38.3    -      -       +      +
    120D  TYR*     3.1    14.0    +      -       -      -
    121D  HIS*     2.8    46.8    -      +       +      -
    122D  GLU*     2.9    47.2    +      -       -      +
    123D  ASP*     5.0     4.8    +      -       -      -
    157D  SER*     3.4    19.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 87 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86C  HIS*     1.3    76.1    -      -       -      +
     88C  ILE*     1.3    64.2    +      -       -      +
     89C  THR*     3.7     6.1    +      -       -      +
    111C  VAL*     3.3     7.5    -      -       -      +
    112C  ARG*     2.9    43.9    +      -       -      +
    112D  ARG*     5.1     6.3    -      -       -      -
    120D  TYR*     3.9    18.7    +      -       -      -
    122D  GLU*     3.5    17.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 88 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86C  HIS*     5.4     0.9    -      -       +      -
     87C  SER*     1.3    75.6    -      -       -      +
     89C  THR*     1.3    62.2    +      -       -      +
     90C  GLN*     3.7    27.8    -      -       -      +
     91C  GLN*     4.2     4.5    -      -       +      +
    109C  ALA*     5.0     3.8    -      -       +      -
    110C  PHE      3.5     7.4    -      -       -      +
    111C  VAL*     4.6     6.5    -      -       +      -
    147C  VAL*     3.8    31.9    -      -       +      -
    110D  PHE*     3.8    28.3    -      -       +      -
    122D  GLU*     3.0    32.9    +      -       +      +
    123D  ASP*     3.8    27.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 89 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  SER*     3.7     6.9    +      -       -      +
     88C  ILE*     1.3    73.6    -      -       -      +
     90C  GLN*     1.3    64.7    +      -       -      +
    110C  PHE*     2.8    21.9    +      -       -      +
    112C  ARG*     4.1    27.4    -      -       +      -
    122C  GLU*     2.7    30.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 90 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  ILE*     3.1     8.8    -      -       -      +
     89C  THR*     1.3    86.2    +      -       -      +
     91C  GLN*     1.3    65.9    +      -       -      +
     92C  ASN*     3.7    33.1    -      -       -      +
    109C  ALA*     3.4     1.6    -      -       -      -
    110C  PHE*     2.8    48.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 91 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  ILE*     4.2     4.8    -      -       +      +
     90C  GLN*     1.3    80.7    +      -       -      +
     92C  ASN*     1.3    66.7    +      -       -      +
    107C  VAL*     3.6    18.8    -      -       +      +
    108C  CYS      3.3    10.5    -      -       -      +
    109C  ALA*     3.9     2.3    -      -       +      +
    143C  ARG*     2.9    70.5    +      -       -      +
    146C  ALA*     3.7     6.3    -      -       -      +
    147C  VAL*     3.6    13.9    -      -       -      +
    110D  PHE*     3.3    36.9    -      -       +      -
    124D  VAL*     3.8     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 92 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  ARG*     4.9     3.7    +      -       -      +
     90C  GLN*     3.7    22.4    -      -       -      +
     91C  GLN*     1.3    76.4    +      -       -      +
     93C  VAL*     1.3    76.2    +      -       -      +
     94C  ASP*     3.4    13.9    +      -       -      +
    107C  VAL*     3.5     2.5    -      -       -      +
    108C  CYS*     2.8    52.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91C  GLN      4.3     0.4    +      -       -      -
     92C  ASN*     1.3    79.5    +      -       -      +
     94C  ASP*     1.3    64.8    +      -       -      +
     95C  PHE*     3.9     9.9    -      -       -      +
     96C  VAL*     3.8    28.9    -      -       +      -
    106C  GLY      3.9     6.1    -      -       -      +
    107C  VAL*     3.8    18.6    -      -       +      -
    139C  LEU*     4.4     7.4    -      -       +      -
    143C  ARG*     3.6    38.7    -      -       -      +
     94D  ASP*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  VAL*     5.4     1.0    -      -       -      +
    139B  LEU*     3.4    15.4    -      -       +      +
    143B  ARG*     2.6    34.8    +      -       -      -
     92C  ASN*     3.4    17.7    +      -       -      +
     93C  VAL*     1.3    73.6    -      -       -      +
     95C  PHE*     1.3    72.2    +      -       +      +
    106C  GLY      2.7    15.7    +      -       -      +
    126C  TYR*     2.5    33.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  LYS*     3.6    38.8    -      -       +      +
    136B  ALA*     3.4    40.6    -      -       +      -
    139B  LEU*     3.9    13.2    -      -       +      -
     93C  VAL*     3.5     3.7    -      -       -      +
     94C  ASP*     1.3    90.7    -      -       +      +
     96C  VAL*     1.3    69.2    +      -       -      +
     97C  ASP*     3.5    19.1    -      -       -      +
    104C  TYR*     3.2    35.0    -      -       +      -
    105C  VAL*     3.4     5.2    -      -       -      +
    106C  GLY*     3.3    37.2    +      -       -      +
    126C  TYR*     4.1     0.4    -      -       -      -
    130C  GLU*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93C  VAL*     3.8    18.8    -      -       +      -
     95C  PHE*     1.3    80.6    -      -       -      +
     97C  ASP*     1.3    62.7    +      -       -      +
     98C  LEU      4.3     0.7    +      -       -      -
    103C  PHE*     4.2    22.2    -      -       +      -
    104C  TYR      3.6     3.4    -      -       -      -
    105C  VAL*     4.2    11.2    -      -       +      -
    135C  LYS*     4.4    23.1    -      -       +      -
    139C  LEU*     4.1    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  PHE*     5.9     0.2    -      -       -      -
    135B  LYS*     2.8    40.7    +      -       -      +
     95C  PHE*     3.5     9.1    -      -       -      +
     96C  VAL*     1.3    81.8    +      -       -      +
     98C  LEU*     1.3    60.4    +      -       -      +
     99C  ASN*     3.9    17.4    -      -       -      +
    103C  PHE*     3.2     8.2    -      -       -      -
    104C  TYR*     2.6    52.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  VAL      4.3     0.8    +      -       -      -
     97C  ASP*     1.3    72.6    -      -       -      +
     99C  ASN*     1.3    67.1    +      -       -      +
    100C  ASN      3.8    18.8    -      -       -      +
    101C  GLY*     4.0    12.8    -      -       -      +
    102C  LYS      3.4    12.8    -      -       -      +
    103C  PHE*     3.9    32.5    -      -       +      -
----------------------------------------------------------
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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