Contacts of the strand formed by residues 139 - 148 (chain A) in PDB entry 2A1H


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 SER 139 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  LYS*     3.2    34.0    +      -       -      +
     80A  ALA      3.4    14.1    -      -       -      -
     81A  PHE*     3.9    20.9    -      -       -      +
    132A  VAL*     5.2     0.4    -      -       -      -
    133A  PRO*     3.6    19.6    -      -       -      +
    137A  GLY      5.0     0.9    +      -       -      -
    138A  THR*     1.3    79.4    -      -       -      +
    140A  LEU*     1.3    61.2    +      -       -      +
    169A  PRO*     3.6     0.7    -      -       -      +
    170A  VAL*     2.9    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  THR*     3.9    20.0    -      -       +      -
     79A  LYS*     3.4     3.3    -      -       -      -
     80A  ALA*     2.9    44.9    +      -       +      +
    125A  ILE*     3.9    20.2    -      -       +      -
    128A  ASP      5.2     1.6    -      -       -      +
    131A  TRP*     4.2    12.8    -      -       +      +
    132A  VAL*     3.8    28.2    -      -       +      +
    133A  PRO*     4.5     0.2    -      -       -      +
    139A  SER*     1.3    77.2    -      -       -      +
    141A  TYR*     1.3    66.2    +      -       -      +
    142A  VAL*     3.7     2.2    +      -       +      +
    167A  LEU*     3.9    24.0    -      -       +      -
    168A  CYS      3.7    22.2    -      -       -      +
    169A  PRO*     3.9    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE*     3.7    30.3    -      +       -      -
     75A  PHE*     5.1     0.7    -      -       -      -
     77A  GLY*     3.4    28.5    -      -       -      -
     78A  MET      3.6     8.7    -      -       -      -
     79A  LYS*     4.3    13.9    -      -       +      -
    139A  SER      4.1     1.6    +      -       -      -
    140A  LEU*     1.3    71.9    -      -       -      +
    142A  VAL*     1.3    61.7    +      -       -      +
    143A  ARG*     2.9    47.6    +      -       +      -
    166A  ILE      4.0     0.5    -      -       -      +
    167A  LEU*     3.4     6.9    -      -       -      +
    168A  CYS*     2.8    49.9    +      -       -      +
    170A  VAL*     4.2    13.6    -      -       +      +
    202A  LYS*     5.7     0.3    -      -       -      -
    313A  THR*     4.1    14.4    -      -       +      -
    314A  ALA      5.4     0.2    -      -       -      -
    502A  GBN      3.5    18.0    -      -       -      +
    153B  LEU*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  GLY*     3.5     4.9    -      -       -      -
     78A  MET*     2.8    51.2    +      -       +      +
     80A  ALA*     4.6     1.6    -      -       +      -
     90A  LEU*     4.0    12.8    -      -       +      -
    121A  ILE*     3.9    19.5    -      -       +      -
    125A  ILE*     3.9    24.0    -      -       +      -
    140A  LEU*     4.1     9.6    -      -       +      +
    141A  TYR*     1.3    77.9    -      -       -      +
    143A  ARG*     1.3    62.2    +      -       -      +
    144A  PRO*     3.4    10.5    -      -       +      +
    165A  VAL*     3.8    21.8    -      -       +      -
    166A  ILE      3.9     2.0    -      -       -      -
    167A  LEU*     3.9    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PHE*     3.5    19.8    -      -       -      -
     76A  GLU      3.0    19.6    +      -       -      -
    141A  TYR*     2.9    35.3    +      -       +      -
    142A  VAL*     1.3    75.2    -      -       -      +
    144A  PRO*     1.4    68.8    -      -       -      +
    145A  VAL*     3.8     3.8    +      -       +      +
    164A  PHE      3.8     0.5    -      -       -      +
    165A  VAL*     3.5     3.0    -      -       -      -
    166A  ILE*     2.9    41.0    +      -       +      +
    168A  CYS*     6.1     0.2    -      -       -      -
    502A  GBN      3.6    14.3    -      -       -      +
     69B  HIS*     3.0    44.1    +      -       +      -
     70B  TYR*     2.9    32.9    +      -       -      -
    153B  LEU*     3.5    28.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PHE*     3.3     4.0    -      -       -      +
     76A  GLU*     3.0    44.4    +      -       +      +
     77A  GLY      4.5     0.2    -      -       -      +
     78A  MET*     5.0     4.0    -      -       +      -
     97A  MET*     4.6     6.1    -      -       +      -
    100A  MET*     3.8    26.7    -      -       +      -
    117A  LEU*     5.2     0.9    -      -       +      -
    121A  ILE*     3.9    25.4    -      -       +      -
    142A  VAL*     3.4    16.2    -      -       +      +
    143A  ARG*     1.4    84.8    -      -       -      +
    145A  VAL*     1.3    61.2    +      -       -      +
    164A  PHE      3.5     6.1    -      -       -      +
    165A  VAL*     3.9    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LEU      3.3    15.0    -      -       -      +
     75A  PHE*     4.3     2.9    -      -       +      +
    100A  MET*     4.1     4.2    -      -       -      +
    143A  ARG*     3.9    11.4    -      -       +      +
    144A  PRO*     1.3    80.8    -      -       -      +
    146A  LEU*     1.3    64.2    +      -       -      +
    147A  ILE*     3.8    23.1    -      -       +      -
    162A  LEU      3.9     1.0    -      -       -      +
    163A  LEU*     3.3     5.7    -      -       -      +
    164A  PHE*     2.8    60.0    +      -       +      +
     68B  LEU      4.2    11.7    -      -       -      +
     69B  HIS*     3.5    33.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  TRP*     3.9    14.1    -      -       +      -
     73A  GLN*     3.5     2.1    -      -       -      -
     74A  LEU*     3.1    44.0    +      -       +      +
    100A  MET*     4.0    10.0    -      -       +      +
    104A  ALA*     3.8    28.9    -      -       +      -
    109A  LEU*     3.9    16.9    -      -       +      +
    110A  PRO*     3.9    15.3    -      -       +      +
    112A  PHE*     4.0    15.7    -      -       +      -
    145A  VAL*     1.3    74.7    -      -       -      +
    147A  ILE*     1.3    66.2    +      -       -      +
    161A  ALA*     4.4     9.2    -      -       +      -
    162A  LEU      3.5    16.8    -      -       -      +
    163A  LEU*     3.9    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  LEU*     4.2    14.4    -      -       +      -
     67A  SER*     3.7    23.1    -      -       -      +
     72A  LEU      3.3     6.1    -      -       -      +
     73A  GLN*     3.8    20.0    -      -       +      -
    109A  LEU*     4.0     5.4    -      -       -      -
    145A  VAL*     3.8    17.5    -      -       +      -
    146A  LEU*     1.3    79.6    -      -       -      +
    148A  GLY*     1.3    63.9    +      -       -      +
    149A  ASN*     4.9     2.2    -      -       -      +
    161A  ALA*     3.3     6.9    -      -       -      +
    162A  LEU*     2.9    68.3    +      -       +      +
    164A  PHE*     4.4    10.5    -      -       +      -
     68B  LEU*     4.2    20.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  SER*     3.3     1.4    +      -       -      -
     66A  SER*     3.6    16.2    -      -       -      -
     67A  SER*     3.1    27.0    +      -       -      -
     72A  LEU*     2.8    19.1    +      -       -      -
    109A  LEU*     3.7    19.5    -      -       -      +
    147A  ILE*     1.3    75.9    -      -       -      +
    149A  ASN*     1.3    60.1    +      -       -      +
    158A  PRO*     4.1     2.9    -      -       -      -
    160A  ARG      3.9     4.3    -      -       -      -
----------------------------------------------------------
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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