Contacts of the strand formed by residues 113 - 116 (chain A) in PDB entry 3A9L


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 THR 113 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  ASN*     1.3    83.5    +      -       -      +
    114A  LEU*     1.3    61.5    +      -       -      +
    115A  VAL*     3.8    19.7    +      -       +      -
    130A  LEU*     4.2     6.3    -      -       +      -
    136A  ALA      3.3    13.7    +      -       -      -
    137A  ALA*     3.2     5.6    -      -       -      +
    138A  GLU      2.8    31.2    +      -       -      +
    164A  LEU*     4.2    14.6    -      -       +      -
    165A  GLU      3.6     9.0    -      -       -      +
    166A  ILE*     3.8     6.4    -      -       +      +
    170A  GLN*     4.5     1.4    -      -       -      +
    195A  TYR*     2.6    39.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  TYR*     3.8    22.0    -      -       +      +
    112A  ASN*     3.6    19.3    -      -       -      +
    113A  THR*     1.3    71.0    -      -       -      +
    115A  VAL*     1.3    62.2    +      -       -      +
    116A  GLY      4.0     0.7    +      -       -      -
    138A  GLU*     3.4    31.9    -      -       +      -
    140A  ALA*     4.2    20.5    -      -       +      +
    143A  ARG*     3.6    40.8    -      -       +      +
    144A  PHE*     3.9    12.9    -      -       +      +
    163A  GLN      3.7     2.8    -      -       -      +
    165A  GLU*     3.0    37.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  THR*     3.8    22.4    -      -       +      +
    114A  LEU*     1.3    75.8    -      -       -      +
    116A  GLY*     1.3    60.2    +      -       -      +
    123A  ARG*     3.7    27.3    -      -       +      +
    126A  ILE*     4.6    10.3    -      -       +      -
    127A  VAL*     3.5    28.0    -      -       +      -
    130A  LEU*     4.8     2.5    -      -       +      -
    137A  ALA*     4.9     0.4    -      -       +      -
    138A  GLU      2.9    10.0    +      -       -      +
    139A  VAL*     3.5     6.6    -      -       -      +
    140A  ALA*     2.9    20.9    +      -       -      +
    162A  VAL*     3.7    23.1    -      -       +      -
    163A  GLN      3.2    10.1    -      -       -      +
    164A  LEU*     4.5     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  LEU      4.0     1.4    +      -       -      -
    115A  VAL*     1.3    74.8    -      -       -      +
    117A  GLY*     1.3    62.1    +      -       -      -
    123A  ARG*     4.0    13.7    -      -       -      +
    139A  VAL*     5.8     0.2    -      -       -      -
    140A  ALA*     4.4     2.5    -      -       -      -
    144A  PHE      4.1    10.2    +      -       -      -
    145A  THR*     3.6    11.0    -      -       -      -
    162A  VAL*     3.3    11.4    -      -       -      +
    163A  GLN*     2.8    30.0    +      -       -      +
----------------------------------------------------------
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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