Contacts of the strand formed by residues 119 - 122 (chain D) in PDB entry 3V5I


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 GLU 119 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  VAL*     6.1     0.3    -      -       -      +
     72C  THR*     3.9    12.3    -      -       -      +
     75C  PHE*     5.9     0.6    -      -       -      -
    142C  HIS*     3.0    33.2    +      -       -      -
    146C  THR*     3.8    14.3    +      -       -      +
    149C  LYS*     3.4    29.1    +      -       -      +
     92D  CYS*     4.0     2.1    -      -       -      -
     94D  GLY      3.0    10.8    +      -       -      +
     95D  MET*     3.1    29.4    -      -       +      +
     96D  ALA      2.9    25.6    +      -       -      -
    117D  ASN      4.6     0.4    -      -       -      +
    118D  ALA*     1.3    74.1    -      -       -      +
    120D  VAL*     1.3    65.4    +      -       -      +
    174D  PHE*     4.6     2.4    -      -       +      -
    175D  LEU      3.7    11.9    -      -       -      +
    176D  THR*     5.3     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 120 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92D  CYS*     4.6     6.5    -      -       +      -
     95D  MET*     4.6     0.9    -      -       -      -
     96D  ALA      3.3     3.8    -      -       -      +
    101D  SER*     3.6    23.3    -      -       -      -
    104D  LEU*     3.8    25.8    -      -       +      -
    114D  ALA*     5.5     5.2    -      -       +      -
    118D  ALA      5.5     1.3    -      -       -      +
    119D  GLU*     1.3    80.9    -      -       -      +
    121D  MET*     1.3    65.9    +      -       -      +
    122D  ILE*     4.6     0.9    -      -       +      -
    174D  PHE*     3.7     2.4    -      -       -      +
    175D  LEU*     2.7    44.7    +      -       +      +
    176D  THR      5.2     1.1    -      -       -      +
    177D  ALA*     5.7     0.9    -      -       -      -
    180D  ALA*     4.0    21.1    -      -       +      -
    185D  LEU*     3.9    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 121 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67D  PRO      5.8     0.4    -      -       -      +
     95D  MET*     4.5     3.1    -      -       +      -
     96D  ALA      3.0     7.1    +      -       -      -
     97D  ALA*     3.3    24.7    -      -       +      -
     98D  ALA      2.9    24.9    +      -       -      -
    101D  SER*     3.2     8.1    +      -       -      -
    120D  VAL*     1.3    77.1    -      -       -      +
    122D  ILE*     1.3    79.2    +      -       -      +
    123D  HIS*     3.8    24.7    -      -       +      +
    172D  ASP*     4.1    21.3    -      -       -      +
    173D  ASN      3.4    17.0    -      -       -      +
    174D  PHE*     3.6    36.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 122 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98D  ALA*     4.7     2.2    -      -       -      +
    101D  SER*     3.4    24.7    -      -       -      +
    120D  VAL*     4.6     1.6    -      -       +      -
    121D  MET*     1.3    77.7    -      -       -      +
    123D  HIS*     1.3    60.9    +      -       -      +
    154D  LEU*     5.1    11.9    -      -       +      -
    165D  ILE*     6.0     0.4    -      -       +      -
    168D  ASP      4.4     0.8    -      -       -      +
    169D  THR*     3.6    23.6    -      -       +      -
    171D  ARG      3.7     0.7    -      -       -      +
    173D  ASN*     3.0    56.6    +      -       +      +
    175D  LEU*     4.7     9.0    -      -       +      -
    183D  TYR*     4.2    28.3    -      -       +      +
    185D  LEU*     4.3    23.1    -      -       +      -
----------------------------------------------------------
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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