Contacts of the strand formed by residues 175 - 178 (chain H) 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 VAL 175 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  LEU*     3.1    21.2    +      -       +      +
    267B  LYS*     3.1    24.7    +      -       -      +
    150H  VAL*     2.9    23.1    -      -       +      +
    152H  VAL*     4.1    16.2    -      -       +      -
    165H  ALA*     3.6    42.8    -      -       +      +
    168H  LEU*     4.3    12.8    -      -       +      -
    169H  CYS      4.3     2.5    -      -       -      +
    173H  VAL      3.4    14.1    -      -       -      +
    174H  PRO*     1.3    75.2    -      -       -      +
    176H  THR*     1.3    66.6    +      -       -      +
    177H  VAL*     5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 176 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267B  LYS*     3.5    21.9    -      -       +      +
    268B  GLU*     3.8     5.6    -      -       -      +
    269B  GLU*     3.4    44.0    -      -       +      +
    150H  VAL      2.8     9.7    +      -       -      -
    151H  TYR*     3.5    29.5    -      -       +      -
    152H  VAL      3.0    23.4    +      -       -      -
    175H  VAL*     1.3    74.4    -      -       -      +
    177H  VAL*     1.3    64.9    +      -       -      +
    178H  VAL*     3.7     1.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 177 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  LEU      5.7     1.8    -      -       -      +
    267B  LYS      3.1    14.5    +      -       -      +
    268B  GLU*     3.5    15.4    -      -       +      +
    269B  GLU      3.2    23.2    +      -       -      +
    270B  HIS*     5.3     3.4    +      -       +      -
    152H  VAL*     3.3    15.7    -      -       +      +
    153H  THR      4.7     0.2    -      -       -      -
    154H  GLU*     4.1    22.2    -      -       +      +
    161H  GLY      4.5     2.2    -      -       -      +
    162H  LYS*     4.3    20.4    -      -       +      -
    165H  ALA*     3.4    33.7    -      -       +      -
    175H  VAL*     5.1     0.4    -      -       +      +
    176H  THR*     1.3    72.3    -      -       -      +
    178H  VAL*     1.3    71.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 178 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269B  GLU*     4.2    16.2    -      -       +      +
    126H  LEU*     5.5     2.0    -      -       +      -
    151H  TYR*     4.0    21.3    -      -       +      -
    152H  VAL      2.8    12.4    +      -       -      +
    153H  THR*     3.3    18.1    -      -       +      -
    154H  GLU*     2.9    27.0    +      -       -      +
    176H  THR*     3.9    16.4    -      -       +      +
    177H  VAL*     1.3    82.3    -      -       -      +
    179H  LEU*     1.3    77.5    +      -       -      +
    182H  ALA*     4.0    19.5    -      -       +      +
    186H  ILE*     4.7    16.4    -      -       +      -
----------------------------------------------------------
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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