Contacts of the strand formed by residues 397 - 404 (chain A) in PDB entry 2VWJ


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 TRP 397 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393A  GLU*     3.6    28.8    +      -       +      +
    394A  ARG      3.1    23.0    +      -       -      -
    395A  GLY      3.3    14.6    +      -       -      -
    396A  LEU*     1.3    74.6    -      -       -      +
    398A  GLU*     1.3    64.7    +      -       -      +
    400A  ILE*     4.2     4.0    -      -       +      -
    535A  LYS*     4.2    19.5    -      -       +      -
    537A  LEU*     3.4    47.6    -      -       +      +
    547A  THR*     4.1    13.5    -      -       +      -
    549A  PRO*     4.7    22.7    -      -       +      -
    585A  ARG*     3.0    28.1    -      -       -      +
    586A  GLY      3.1    15.2    +      -       -      +
    588A  PHE*     4.5     8.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 398 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396A  LEU*     5.0     5.6    -      -       +      +
    397A  TRP*     1.3    80.5    -      -       -      +
    399A  ASN*     1.3    72.1    +      -       -      +
    400A  ILE*     3.5     2.7    -      -       -      -
    547A  THR*     2.7    32.4    +      -       -      +
    548A  ILE      5.3     0.2    -      -       -      +
    551A  ALA      5.5     1.0    -      -       -      +
    584A  LYS      3.4     7.3    -      -       -      +
    585A  ARG*     2.9    39.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 399 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398A  GLU*     1.3    79.1    -      -       -      +
    400A  ILE*     1.3    56.9    +      -       -      +
    547A  THR*     2.7    22.7    +      -       -      +
    551A  ALA      3.1    24.0    +      -       -      +
    552A  ASP*     3.6     2.4    -      -       -      +
    553A  ALA*     3.4    36.8    -      -       -      +
    556A  VAL*     3.5    21.3    -      -       +      +
    582A  PHE*     3.5    20.5    -      -       +      -
    583A  TYR      3.5     5.4    -      -       -      -
    584A  LYS*     2.8    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 400 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397A  TRP*     4.0     5.8    -      -       +      +
    398A  GLU      3.9    12.6    -      -       -      +
    399A  ASN*     1.3    76.7    -      -       -      +
    401A  VAL*     1.3    64.1    +      -       -      +
    537A  LEU*     3.8    15.7    -      -       +      -
    545A  PHE*     3.7    33.2    -      -       +      -
    546A  ALA      3.4    17.0    -      -       -      +
    547A  THR*     4.3     0.2    -      -       -      -
    582A  PHE*     3.3     3.4    -      -       -      -
    583A  TYR*     2.7    50.5    +      -       +      +
    585A  ARG*     3.8     3.1    -      -       -      +
    586A  GLY*     3.5    36.3    -      -       -      +
    588A  PHE*     4.0    17.0    -      -       +      -
    596A  VAL*     4.9     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 401 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399A  ASN      4.1     0.4    +      -       -      -
    400A  ILE*     1.3    77.3    -      -       -      +
    402A  TYR*     1.3    60.3    +      -       -      +
    403A  LEU*     4.5    15.9    -      -       +      +
    528A  ILE*     5.7     1.6    -      -       +      -
    534A  PHE*     4.2    16.6    -      -       +      -
    544A  PHE*     3.9     0.7    -      -       -      +
    545A  PHE*     3.2     6.2    -      -       -      -
    546A  ALA*     2.9    45.6    +      -       +      +
    556A  VAL*     3.8    21.8    -      -       +      +
    557A  LYS*     4.9     1.8    -      -       -      -
    560A  ALA*     3.9    14.4    -      -       +      -
    579A  TYR*     3.8    34.1    -      -       +      +
    581A  GLY      3.5     3.4    -      -       -      -
    582A  PHE*     3.9     6.3    -      -       +      -
    583A  TYR*     5.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 402 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401A  VAL*     1.3    75.8    -      -       -      +
    403A  LEU*     1.3    76.3    +      -       -      +
    404A  ASP*     4.3     7.2    -      -       +      -
    406A  ARG*     6.1     1.1    -      -       -      -
    538A  TYR*     5.8     0.2    -      +       -      -
    540A  ASP*     4.3     3.0    +      -       -      -
    542A  ASP*     3.4    13.7    +      -       -      +
    543A  GLY*     3.2    27.9    +      -       -      -
    544A  PHE      3.3    21.5    -      -       -      -
    545A  PHE*     3.5    39.3    -      +       +      -
    579A  TYR*     3.9     0.9    -      -       -      -
    580A  GLU*     3.1    47.6    +      -       +      +
    581A  GLY      2.8    19.9    +      -       -      +
    583A  TYR*     3.9    21.3    -      +       +      -
    594A  TYR*     5.7     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 403 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401A  VAL*     4.5    12.8    -      -       +      -
    402A  TYR*     1.3    88.2    -      -       -      +
    404A  ASP*     1.3    59.9    +      -       -      +
    405A  PHE*     4.5     0.6    -      -       -      -
    528A  ILE*     4.4     4.0    -      -       +      -
    543A  GLY*     3.0    24.8    -      -       -      -
    544A  PHE*     2.9    53.5    +      -       +      -
    560A  ALA*     5.3     5.6    -      -       +      +
    563A  PHE*     4.2    17.7    -      -       +      -
    564A  LEU*     4.9    10.8    -      -       +      -
    577A  LEU*     3.8    18.8    -      -       +      -
    578A  GLU      3.4     5.6    -      -       -      +
    579A  TYR*     3.6    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 404 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402A  TYR*     4.3     5.4    -      -       +      -
    403A  LEU*     1.3    71.6    -      -       -      +
    405A  PHE*     1.3    61.8    +      -       -      +
    406A  ARG*     2.6    70.1    +      -       -      -
    407A  SER*     4.8     3.4    +      -       -      -
    487A  LYS*     3.2    18.6    +      -       -      -
    542A  ASP      3.0    10.2    -      -       -      +
    543A  GLY*     4.3     0.2    -      -       -      -
    576A  GLU      4.7     1.0    -      -       -      +
    577A  LEU*     3.8     9.9    -      -       -      +
    578A  GLU*     2.8    34.1    +      -       +      +
    580A  GLU*     3.3    22.2    -      -       +      +
----------------------------------------------------------
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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