Contacts of the strand formed by residues 76 - 82 (chain A) in PDB entry 1A9Q


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 ARG 76 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  GLN*     3.4    28.9    -      -       -      +
     27A  VAL*     3.9    20.4    -      -       +      -
     72A  ILE*     3.1     5.1    -      -       -      -
     73A  LEU*     2.7    40.8    +      -       -      +
     74A  ASN      3.3     1.1    +      -       -      +
     75A  GLY*     1.3    82.2    +      -       -      +
     77A  ALA*     1.3    68.1    +      -       -      +
     78A  CYS*     3.6     1.3    +      -       -      -
    279A  MET*     2.7    43.1    +      -       +      +
    280A  ALA*     4.0    10.7    +      -       -      +
    282A  ILE*     3.1    40.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  GLN*     4.9     5.8    -      -       +      +
     24A  ARG      3.9    23.8    -      -       -      +
     25A  PRO*     3.9     4.7    -      -       +      -
     26A  GLN*     3.2    20.5    +      -       +      +
     27A  VAL      3.7     3.6    +      -       -      -
     71A  GLY      3.6     4.9    -      -       -      +
     72A  ILE*     3.7    19.9    -      -       +      +
     75A  GLY      4.3     0.6    +      -       -      -
     76A  ARG*     1.3    81.6    -      -       -      +
     78A  CYS*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  GLN*     5.9     0.2    -      -       -      +
     25A  PRO*     3.6     8.2    -      -       -      +
     27A  VAL*     3.2    28.3    -      -       +      +
     29A  VAL*     4.8     5.8    -      -       +      -
     42A  LEU*     4.1    20.0    -      -       -      -
     69A  VAL      4.0     0.4    -      -       -      +
     70A  PHE*     3.5     2.9    -      -       -      +
     71A  GLY      2.8    38.3    +      -       -      -
     73A  LEU*     4.1    17.5    -      -       -      -
     76A  ARG      4.6     1.6    -      -       -      +
     77A  ALA*     1.3    76.7    -      -       -      +
     79A  VAL*     1.3    62.9    +      -       -      +
     80A  MET*     4.1    17.3    -      -       -      -
    279A  MET*     4.9     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  PRO*     3.9    15.7    -      -       +      -
     27A  VAL      3.1     8.6    +      -       -      +
     28A  ALA*     3.2    15.5    -      -       +      +
     29A  VAL      2.8    23.4    +      -       -      -
     68A  LEU*     3.7    31.9    -      -       +      -
     69A  VAL      3.2    10.5    -      -       -      +
     70A  PHE*     3.8    28.9    -      -       +      -
     78A  CYS*     1.3    75.8    -      -       -      +
     80A  MET*     1.3    66.2    +      -       -      +
    103A  PHE*     4.0    18.0    -      -       +      -
    106A  LEU*     5.2     0.7    -      -       +      -
    108A  VAL*     4.5     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL*     3.1    19.7    -      -       +      +
     31A  CYS*     3.5    23.6    -      -       -      -
     38A  LEU*     3.9    24.9    -      -       +      -
     39A  VAL*     3.4    42.2    -      -       +      +
     42A  LEU*     4.1    23.1    -      -       +      -
     68A  LEU*     3.4     8.4    -      -       -      +
     69A  VAL*     2.7    45.7    +      -       +      +
     73A  LEU*     4.9     1.3    -      -       -      -
     78A  CYS*     4.1    13.9    -      -       -      -
     79A  VAL*     1.3    79.9    -      -       -      +
     81A  MET*     1.3    63.4    +      -       -      +
     82A  GLN      3.7     1.5    +      -       -      -
    103A  PHE*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL      2.8    12.6    +      -       -      +
     30A  ILE*     4.0    26.7    -      -       +      -
     31A  CYS*     3.1    25.8    +      -       -      +
     50A  TYR*     3.3    20.6    -      -       +      +
     56A  PHE*     4.9     0.7    -      -       +      -
     67A  ARG      3.9     0.7    -      -       -      -
     68A  LEU*     3.8     8.7    -      -       +      -
     80A  MET*     1.3    72.5    -      -       -      +
     82A  GLN*     1.3    60.4    +      -       -      +
     83A  GLY      3.3    16.3    +      -       -      +
     84A  ARG*     4.1    11.9    -      -       +      -
     85A  PHE*     4.0    16.2    -      -       +      -
     96A  VAL      5.7     0.7    -      -       -      +
     99A  PRO*     3.6    38.6    -      -       +      -
    103A  PHE*     3.7    23.1    -      -       +      -
    224A  GLU*     5.6     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  CYS*     4.9     5.4    -      -       +      -
     36A  GLY*     4.3    22.7    -      -       -      +
     39A  VAL*     4.0    29.1    -      -       +      +
     50A  TYR*     3.4     0.2    +      -       -      -
     64A  HIS*     3.7    25.4    -      -       +      +
     65A  ALA      2.7    26.0    -      -       -      +
     66A  GLY*     3.2    11.8    -      -       -      -
     67A  ARG*     2.8    63.5    +      -       +      +
     69A  VAL*     4.4     3.7    -      -       +      +
     80A  MET      3.7     1.2    +      -       -      -
     81A  MET*     1.3    71.0    -      -       -      +
     83A  GLY*     1.3    58.1    +      -       -      +
----------------------------------------------------------
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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