Contacts of the strand formed by residues 15 - 23 (chain A) in PDB entry 1G13


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 ALA 15 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ASN*     4.6     1.2    -      -       -      +
     13A  ASP*     4.1     2.1    -      -       -      +
     14A  PRO*     1.3    77.2    -      -       +      +
     16A  VAL*     1.3    66.7    +      -       -      +
     40A  SER      3.4     6.1    -      -       -      +
     41A  THR*     4.0    16.8    -      -       -      +
     45A  LEU*     4.4    13.9    -      -       +      -
    143A  LEU*     4.5    10.1    -      -       +      -
    150A  LEU*     3.0    18.8    +      -       +      +
    151A  GLY*     3.5    19.7    -      -       -      -
    152A  CYS      4.6     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ASN*     3.5    21.1    -      -       +      +
      9A  ASP      5.7     0.2    -      -       -      -
     10A  GLU*     4.0    21.5    -      -       +      +
     13A  ASP*     3.4    22.0    -      -       +      +
     14A  PRO      4.7     2.2    -      -       -      +
     15A  ALA*     1.3    82.2    -      -       -      +
     17A  ILE*     1.3    68.5    +      -       -      +
     18A  ARG*     4.5    11.0    -      -       +      +
     39A  GLY*     3.1     2.8    -      -       -      -
     40A  SER*     2.8    54.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  TRP*     3.4    30.0    -      -       +      -
      7A  ASN*     2.9    31.1    +      -       -      +
     16A  VAL*     1.3    79.9    -      -       -      +
     18A  ARG*     1.3    63.2    +      -       -      +
     19A  SER      3.5    22.0    -      -       -      +
     20A  LEU*     4.1    10.1    -      -       +      -
     37A  VAL*     4.2    18.6    -      -       +      -
     38A  MSE      3.8     2.0    -      -       -      +
     39A  GLY*     4.5     6.7    -      -       -      -
    153A  ILE*     3.9    26.2    -      -       +      -
    900A  EPE      5.7     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  TRP*     3.8    10.8    -      -       -      -
     16A  VAL*     4.5     9.3    -      -       +      +
     17A  ILE*     1.3    77.5    -      -       -      +
     19A  SER*     1.3    59.2    +      -       -      +
     38A  MSE      2.7    46.7    +      -       +      +
     39A  GLY*     4.6     1.8    -      -       -      -
     40A  SER*     3.2    30.8    +      -       -      +
    113A  THR*     3.3    26.3    +      -       -      +
    900A  EPE      5.1     5.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  TRP*     3.8     6.1    -      -       -      -
     17A  ILE*     3.5     5.3    -      -       -      +
     18A  ARG*     1.3    80.3    -      -       -      +
     20A  LEU*     1.3    63.5    +      -       -      +
     21A  THR*     6.0     2.5    -      -       -      -
     36A  SER*     5.4     1.7    +      -       -      -
     37A  VAL*     3.3     3.5    -      -       -      -
     38A  MSE      2.9    50.8    +      -       -      +
     86B  MSE      4.7     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     3.7    17.1    -      -       +      -
      5A  TRP*     3.4    49.5    +      -       +      +
     17A  ILE*     4.1     5.6    -      -       +      -
     19A  SER*     1.3    76.9    -      -       -      +
     21A  THR*     1.3    68.7    +      -       -      +
     22A  LEU*     5.7     1.1    -      -       +      -
     35A  LEU*     3.3    34.3    -      -       +      -
     36A  SER      3.4     9.0    -      -       -      +
     37A  VAL*     3.8    13.2    -      -       +      -
    153A  ILE*     3.9    12.1    -      -       +      -
    155A  ILE*     3.8    28.7    -      -       +      -
    900A  EPE      5.1     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     4.2     5.2    -      -       -      -
     19A  SER*     6.0     1.8    -      -       -      -
     20A  LEU*     1.3    82.9    -      -       -      +
     22A  LEU*     1.3    61.6    +      -       -      +
     23A  GLU*     4.5     9.0    +      -       -      -
     34A  THR      4.1     1.1    -      -       -      -
     35A  LEU*     3.3    14.3    -      -       -      +
     36A  SER*     2.8    51.4    +      -       -      +
    118A  LYS*     4.0    20.7    -      -       -      +
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Residues in contact with LEU 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     3.7    46.2    -      -       +      +
     20A  LEU*     5.7     0.9    -      -       +      -
     21A  THR*     1.3    74.1    -      -       -      +
     23A  GLU*     1.3    64.9    +      -       -      +
     24A  PRO      4.0     7.1    -      -       -      +
     25A  ASP*     4.6     6.4    -      -       -      +
     27A  ILE*     3.8    22.6    -      -       +      +
     33A  VAL*     3.2    30.3    -      -       +      -
     34A  THR      3.4     0.9    -      -       -      -
     35A  LEU*     3.9    28.5    -      -       +      -
    155A  ILE*     5.0     6.7    -      -       +      -
    157A  ALA*     4.3    10.3    -      -       +      -
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Residues in contact with GLU 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  THR*     4.5     7.4    +      -       -      -
     22A  LEU*     1.3    81.5    -      -       -      +
     24A  PRO*     1.3    70.8    -      -       +      +
     25A  ASP*     5.5     1.1    -      -       +      +
     33A  VAL*     3.2     9.1    -      -       -      +
     34A  THR*     2.6    51.8    +      -       -      +
    118A  LYS*     3.0    40.5    +      -       -      +
----------------------------------------------------------
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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