Contacts of the strand formed by residues 156 - 163 (chain A) in PDB entry 1H1B


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 GLN 156 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     3.7    25.8    +      -       +      +
     19A  GLY*     3.8     7.9    +      -       -      +
     20A  ARG*     3.1    34.5    -      -       -      +
     21A  ARG*     3.4    34.6    +      -       -      +
     22A  ALA      4.6     0.9    -      -       -      -
    139A  MET*     3.1     7.6    -      -       -      +
    140A  GLY      3.1    32.3    +      -       -      +
    144A  LEU*     4.1    18.4    -      -       +      +
    152A  ALA*     3.9    15.7    -      -       +      +
    154A  VAL      3.3    18.0    -      -       -      +
    155A  LEU*     1.3    75.9    -      -       -      +
    157A  GLU*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     4.5     1.3    -      -       -      -
     19A  GLY*     3.2     4.0    -      -       -      -
     20A  ARG*     2.7    80.8    +      -       +      +
     21A  ARG      4.6     0.7    -      -       -      -
     22A  ALA*     3.5    19.6    -      -       +      +
     23A  ARG      4.5     1.7    +      -       -      -
     27A  TRP*     3.2    28.0    +      -       -      +
    137A  LEU*     4.0    21.4    -      -       +      +
    138A  ALA      3.4     9.9    -      -       -      +
    139A  MET*     4.2     4.9    -      -       +      +
    156A  GLN*     1.3    75.6    -      -       -      +
    158A  LEU*     1.3    63.4    +      -       -      +
      1C  NAG      5.8     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     3.7    13.5    -      -       +      -
     17A  VAL      4.2     2.2    -      -       -      +
     18A  GLY      3.4    26.9    -      -       -      +
     19A  GLY*     3.6     6.1    -      -       -      -
     20A  ARG*     4.6     2.9    -      -       -      +
    137A  LEU*     3.4     5.7    -      -       -      +
    138A  ALA*     2.9    40.8    +      -       +      +
    157A  GLU*     1.3    77.6    -      -       -      +
    159A  ASN*     1.3    72.2    +      -       +      +
    160A  VAL*     3.4    22.2    +      -       +      +
    185A  VAL*     4.0     5.2    -      -       +      -
    187A  ARG*     3.5    16.4    -      -       -      +
    188A  ALA*     4.2     4.5    -      -       +      -
    189A  GLY*     3.7    37.0    -      -       -      +
    190A  VAL*     5.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ARG*     2.9    35.0    +      -       -      +
    135A  GLN*     5.4     5.2    -      -       -      +
    136A  CYS      3.6     7.5    +      -       -      -
    137A  LEU*     3.6     3.4    -      -       -      +
    158A  LEU*     1.3    78.3    -      -       +      +
    160A  VAL*     1.3    64.4    +      -       -      +
    185A  VAL*     3.7     9.9    -      -       -      +
    187A  ARG*     5.4     1.0    +      -       -      -
      1C  NAG      1.4    75.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  GLN*     3.8     7.1    +      -       -      -
    136A  CYS*     2.9    42.4    +      -       +      +
    138A  ALA*     4.0    13.2    -      -       +      +
    158A  LEU*     3.5    29.6    -      -       +      +
    159A  ASN*     1.3    79.3    -      -       -      +
    162A  THR*     1.4    66.0    +      -       -      +
    183A  THR*     3.8    22.4    -      -       +      +
    184A  LEU*     4.5     5.2    -      -       -      +
    185A  VAL*     3.9    10.1    -      -       +      +
    189A  GLY*     5.6     1.3    -      -       -      -
    190A  VAL*     6.5     0.2    -      -       +      -
    199A  LEU*     3.7    29.2    -      -       +      -
    226A  ASP*     5.8     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  GLY*     3.7    24.9    -      -       -      +
    134A  VAL      3.6     5.8    -      -       -      +
    135A  GLN*     3.7    17.3    +      -       -      +
    160A  VAL*     1.4    79.2    +      -       -      +
    163A  VAL*     1.3    67.5    +      -       -      +
    164A  VAL*     3.4     3.5    -      -       -      +
    183A  THR*     3.2     4.2    -      -       -      -
    184A  LEU      2.9    37.9    +      -       -      -
    186A  ARG*     3.6    36.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  LEU*     4.3    22.0    -      -       +      +
    131A  GLY      3.8    24.5    -      -       -      +
    132A  ASN*     2.8     4.0    +      -       -      +
    133A  GLY      2.8    27.0    +      -       -      -
    134A  VAL*     3.0    17.4    +      -       +      +
    136A  CYS*     3.5    29.6    -      -       -      -
    162A  THR*     1.3    73.4    -      -       -      +
    164A  VAL*     1.3    68.6    +      -       -      +
    165A  THR*     5.4     2.2    -      -       +      -
    181A  VAL*     4.3    20.2    -      -       +      -
    182A  CYS      3.3    13.9    -      -       -      +
    183A  THR*     4.3     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  ASN*     3.1    15.0    -      -       -      +
    162A  THR*     3.4    11.2    -      -       -      +
    163A  VAL*     1.3    83.8    -      -       -      +
    165A  THR*     1.3    67.6    +      -       -      +
    166A  SER*     4.0    16.6    -      -       -      +
    168A  CYS*     3.9     4.0    -      -       -      +
    182A  CYS*     2.8    29.6    +      -       +      +
    183A  THR      4.3     1.1    -      -       -      -
    184A  LEU*     4.0    17.5    -      -       +      -
    186A  ARG*     4.1    22.7    -      -       -      +
    225A  PRO*     3.7    30.7    -      -       +      -
----------------------------------------------------------
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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