Contacts of the strand formed by residues 124 - 127 (chain B) in PDB entry 3ECS


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 124 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  GLY      4.4     3.8    +      -       -      -
    123B  ALA*     1.3    72.5    -      -       -      +
    125B  ILE*     1.3    64.4    +      -       -      +
    149B  SER*     3.2    23.9    +      -       -      +
    151B  TYR*     3.5    31.2    -      -       +      -
    189B  LYS      3.3    26.9    +      -       -      +
    190B  ALA*     3.6     5.4    -      -       +      -
    191B  ASP*     2.6    41.4    +      -       -      +
    192B  LEU*     3.7     3.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  ILE*     3.6    48.0    -      -       +      -
    123B  ALA*     4.9     0.2    -      -       +      -
    124B  THR*     1.3    81.2    -      -       -      +
    126B  LEU*     1.3    67.8    +      -       -      +
    127B  THR*     4.8     4.9    -      -       -      +
    134B  VAL*     6.1     0.2    -      -       +      -
    138B  LEU*     3.6    19.3    -      -       +      -
    148B  PHE*     4.0    10.3    -      -       +      -
    149B  SER      2.9    10.3    +      -       -      +
    150B  VAL*     3.2    16.0    -      -       +      +
    151B  TYR      2.8    31.2    +      -       -      -
    192B  LEU*     3.6    16.8    -      -       +      +
    194B  ILE*     3.9    27.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  THR      4.0     0.8    +      -       -      -
    125B  ILE*     1.3    73.2    -      -       -      +
    127B  THR*     1.3    81.8    +      -       -      +
    151B  TYR*     3.3    21.5    -      -       +      +
    152B  VAL*     4.6     1.6    -      -       -      -
    153B  THR*     4.9     3.6    -      -       +      -
    178B  VAL*     6.3     2.0    -      -       +      -
    183B  VAL*     4.3    10.3    -      -       +      -
    186B  ILE*     4.0    23.1    -      -       +      -
    187B  MSE      4.1    24.2    -      -       +      -
    190B  ALA*     4.0    15.0    -      -       +      +
    192B  LEU      3.1     6.7    +      -       -      -
    193B  VAL*     3.0    14.7    -      -       +      +
    194B  ILE      3.0    24.1    +      -       -      +
    215B  MSE      3.6    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  ILE*     5.0     4.3    -      -       -      -
    126B  LEU*     1.3    83.2    -      -       -      +
    128B  HIS*     1.3    68.5    +      -       -      +
    129B  ALA      4.8     1.1    +      -       -      +
    131B  SER*     5.6     0.3    -      -       -      -
    134B  VAL*     4.0    20.4    -      -       +      +
    138B  LEU*     5.9     0.7    -      -       +      -
    150B  VAL*     4.0    12.6    -      -       +      -
    151B  TYR      2.8     9.8    +      -       -      +
    152B  VAL*     3.2    48.1    -      -       +      -
    153B  THR      3.2     4.2    +      -       -      -
    164B  MSE      4.7    16.9    -      -       +      +
    194B  ILE      2.7    21.9    +      -       -      -
    195B  VAL*     4.3     1.0    -      -       -      -
    215B  MSE      3.8     5.3    -      -       -      +
----------------------------------------------------------
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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