Contacts of the strand formed by residues 319 - 324 (chain B) in PDB entry 3NMV


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 319 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  VAL      3.6     1.7    -      -       -      +
    247B  ALA*     3.4     1.0    -      -       -      -
    248B  ASN*     2.9    34.9    +      -       +      +
    267B  VAL*     4.7    15.1    -      -       -      +
    269B  HIS*     2.7    28.8    +      -       +      +
    273B  ARG*     2.9    30.4    +      -       -      -
    303B  ARG*     4.2    12.9    +      -       -      +
    317B  ASP      3.9     0.4    +      -       -      -
    318B  PRO*     1.3    76.1    -      -       -      +
    320B  VAL*     1.3    59.6    +      -       -      +
    321B  THR*     4.2     6.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  LYS*     3.9    57.2    +      -       +      +
    209B  LEU*     4.1    17.7    -      -       +      -
    210B  PHE*     4.2     9.9    -      -       +      +
    245B  PHE*     5.2     0.4    -      -       +      -
    246B  VAL      3.2     8.7    -      -       -      +
    247B  ALA*     3.9    15.3    -      -       +      -
    318B  PRO*     4.0    18.1    +      -       +      +
    319B  GLU*     1.3    79.4    -      -       -      +
    321B  THR*     1.3    69.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 321 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  LYS*     4.4     5.8    -      -       -      +
    245B  PHE*     3.2     6.2    -      -       -      +
    246B  VAL*     2.7    38.1    +      -       -      +
    265B  LEU*     2.8    36.6    +      -       -      +
    266B  SER*     5.5     1.8    -      -       -      -
    267B  VAL*     6.5     1.8    -      -       +      -
    319B  GLU*     5.3     5.4    -      -       +      +
    320B  VAL*     1.3    82.1    -      -       -      +
    322B  SER*     1.3    64.5    +      -       -      +
    323B  VAL*     5.9     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202B  GLN*     3.5    26.9    +      -       -      -
    206B  LYS*     3.5    13.4    +      -       -      +
    243B  HIS*     4.8     3.6    -      -       -      -
    244B  ILE      3.1     8.3    -      -       -      -
    245B  PHE*     3.6    29.8    -      -       -      -
    321B  THR*     1.3    77.6    -      -       -      +
    323B  VAL*     1.3    68.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243B  HIS*     3.4     5.6    -      -       -      -
    244B  ILE*     2.9    47.3    +      -       +      +
    256B  LEU*     4.1    16.4    -      -       +      -
    258B  ARG*     4.7     7.0    -      -       -      +
    263B  LEU*     4.6    12.1    -      -       +      -
    265B  LEU*     3.7    33.9    -      -       +      -
    321B  THR*     5.7     1.3    -      -       -      +
    322B  SER*     1.3    78.3    -      -       -      +
    324B  ARG*     1.3    67.2    +      -       -      +
    325B  ARG      3.9     0.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199B  ASP*     4.9     9.9    +      -       -      -
    202B  GLN*     5.1     5.4    -      -       -      +
    242B  THR*     3.6    18.6    -      -       +      -
    243B  HIS*     3.8    35.5    +      -       +      +
    258B  ARG*     3.0    20.7    +      -       -      -
    323B  VAL*     1.3    72.3    -      -       -      +
    325B  ARG*     1.3    66.1    +      -       -      +
    326B  VAL*     3.9     6.3    -      -       +      +
----------------------------------------------------------
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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