Contacts of the strand formed by residues 116 - 118 (chain P) in PDB entry 1MVW


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 TYR 116 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16P  TYR      5.5     2.0    +      -       -      -
     17P  LEU*     5.2     6.6    -      -       +      +
    109P  ARG*     2.8    13.3    +      -       -      -
    114P  MET*     3.4     1.9    -      -       -      +
    115P  ILE*     1.3   103.5    -      -       +      +
    117P  THR*     1.3    63.0    +      -       -      +
    123P  CYS*     4.4     9.6    -      -       -      -
    124P  VAL      3.6     5.2    -      -       -      +
    125P  THR*     2.8    33.9    -      -       +      -
    134P  VAL*     3.9     9.0    -      -       +      -
    135P  TYR*     2.7    34.7    +      -       -      -
    153P  PRO*     2.8    42.0    -      -       +      +
    154P  HIS*     2.9    41.3    +      +       -      +
    155P  ILE*     4.2    16.6    -      -       +      +
    188P  ASN*     4.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 117 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89P  GLU      3.9     5.1    +      -       -      -
     91P  MET*     3.5    18.2    -      -       -      +
    105P  ASN*     4.0     4.9    +      -       -      -
    106P  LEU*     3.4    28.3    -      -       +      +
    109P  ARG*     3.4    33.0    -      -       +      +
    114P  MET      4.7     3.8    -      -       -      +
    115P  ILE      4.2    10.8    -      -       -      +
    116P  TYR*     1.3    78.8    -      -       -      +
    118P  TYR*     1.3    61.3    +      -       -      +
    123P  CYS*     5.0     0.7    -      -       -      -
    124P  VAL*     2.9    36.9    +      -       +      +
    126P  VAL*     4.8     4.5    -      -       +      -
    153P  PRO*     3.9     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 118 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89P  GLU*     2.6    36.3    +      -       +      +
     90P  ASP*     4.0     6.5    -      -       +      -
     91P  MET*     3.0    22.8    +      -       -      +
    117P  THR*     1.3    74.1    -      -       -      +
    119P  SER*     1.4    60.4    +      -       -      +
    120P  GLY      3.7     1.3    -      -       -      +
    122P  PHE      3.3    17.3    -      -       -      +
    123P  CYS*     4.1    12.8    -      -       +      -
    148P  ARG*     3.3    64.5    +      -       -      +
    152P  PRO      4.1     1.6    +      -       -      -
    153P  PRO*     3.6    36.5    -      -       +      +
    154P  HIS      3.9     0.8    +      -       -      -
    157P  SER*     3.2    28.8    +      -       -      -
    158P  ILE*     3.8    22.4    -      -       +      -
    719P  ASP*     5.6     1.8    -      -       -      -
----------------------------------------------------------
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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