Contacts of the strand formed by residues 57 - 63 (chain A) in PDB entry 1A3S


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 LEU 57 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  GLY      4.7    11.4    -      -       -      +
     25A  VAL*     5.4     5.6    -      -       +      -
     44A  ALA*     3.2    33.9    -      -       +      -
     45A  ILE      3.9    12.8    -      -       -      +
     46A  PRO*     4.3     6.1    -      -       +      -
     55A  GLY      3.9     0.2    +      -       -      -
     56A  GLY*     1.3    73.7    -      -       -      +
     58A  PHE*     1.3    60.7    +      -       -      +
     59A  LYS*     3.9     2.3    +      -       -      +
    155A  PHE*     3.2    28.5    +      -       -      +
    157A  PRO*     4.2    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  ALA*     3.0     5.0    -      -       -      -
     45A  ILE*     2.7    50.0    +      -       +      +
     47A  GLY*     4.0     8.1    -      -       -      -
     53A  TRP*     3.9    39.5    -      +       -      -
     56A  GLY*     3.7    26.7    -      -       -      -
     57A  LEU*     1.3    71.0    -      -       -      +
     59A  LYS*     1.3    61.1    +      -       -      +
     60A  LEU*     3.8     1.7    +      -       -      +
     77A  PHE*     3.9    20.7    -      -       +      -
     81A  LEU*     3.8    30.3    -      -       +      -
    120A  LEU*     4.2    14.6    -      -       +      -
    151A  GLN*     4.1     8.1    -      -       +      -
    152A  ALA*     4.0     7.4    -      -       -      -
    155A  PHE*     3.9    30.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  GLU*     2.9    34.8    +      -       -      -
     43A  CYS      3.4    13.2    -      -       -      +
     44A  ALA*     4.2     4.7    -      -       +      +
     57A  LEU      3.9     2.9    +      -       -      +
     58A  PHE*     1.3    71.9    -      -       -      +
     60A  LEU*     1.3    66.3    +      -       -      +
     61A  ARG*     3.9     4.1    -      -       -      +
     77A  PHE*     3.6     6.5    -      -       -      -
     78A  GLU*     2.9    57.3    +      -       +      +
     79A  PRO      4.7     0.3    -      -       -      +
    155A  PHE*     6.1     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  GLU*     4.2     0.4    -      -       -      -
     43A  CYS*     3.0    58.7    +      -       +      +
     44A  ALA*     4.1     0.7    -      -       -      +
     45A  ILE*     3.7    31.4    -      -       +      -
     58A  PHE      4.5     1.1    -      -       -      +
     59A  LYS*     1.3    76.5    -      -       -      +
     61A  ARG*     1.3    75.3    +      -       -      +
     62A  MET*     4.6     0.9    -      -       +      +
     75A  CYS*     3.9    24.0    -      -       +      -
     76A  LYS      3.0    13.7    -      -       -      +
     77A  PHE*     3.5    22.4    -      -       +      +
     78A  GLU*     4.0     1.1    -      -       -      +
     92A  VAL*     6.0     0.2    -      -       +      -
    113A  LEU*     4.4     7.4    -      -       +      -
    116A  ILE*     4.5    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  THR*     3.5    10.3    -      -       -      +
     40A  ASN*     3.4    32.2    +      -       -      +
     41A  TRP      3.7     4.9    -      -       -      +
     42A  GLU*     3.1    46.9    +      -       -      +
     59A  LYS*     3.9     4.6    -      -       -      +
     60A  LEU*     1.3    77.5    -      -       -      +
     62A  MET*     1.3    59.2    +      -       -      +
     63A  LEU*     4.1    16.4    -      -       +      -
     74A  LYS      3.7     0.5    -      -       -      +
     75A  CYS*     3.3     3.5    -      -       -      -
     76A  LYS*     2.4    47.4    +      -       +      +
     78A  GLU*     2.7    54.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  ASN*     3.5     4.2    +      -       -      -
     41A  TRP*     3.0    39.8    +      -       +      +
     43A  CYS*     3.9    20.6    -      -       -      -
     60A  LEU*     4.8     1.1    -      -       +      -
     61A  ARG*     1.3    73.6    -      -       -      +
     63A  LEU*     1.3    61.0    +      -       -      +
     64A  PHE*     3.7    24.1    -      -       +      -
     73A  PRO*     4.0    10.5    -      -       +      -
     74A  LYS      3.5     2.2    -      -       -      -
     75A  CYS*     3.8    18.6    -      -       -      -
    109A  ILE*     3.9    29.2    -      -       +      +
    112A  ILE*     3.4    48.2    -      -       +      -
    113A  LEU*     4.7     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  MET      3.7     6.5    -      -       -      +
     40A  ASN*     3.5    34.8    -      -       +      +
     61A  ARG*     4.5    14.4    -      -       +      -
     62A  MET*     1.3    74.3    -      -       -      +
     64A  PHE*     1.3    64.9    +      -       -      +
     73A  PRO*     3.2     4.2    -      -       -      +
     74A  LYS*     2.8    57.4    +      -       +      +
     76A  LYS*     4.6    27.6    -      -       +      +
----------------------------------------------------------
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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