Contacts of the strand formed by residues 397 - 405 (chain A) in PDB entry 3V4V


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 PHE 397 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  PRO*     3.3     6.8    -      -       -      +
    364A  GLN      3.1    17.6    +      -       -      +
    365A  GLY*     3.1     6.5    -      -       -      +
    366A  ALA*     3.0    33.2    +      -       -      -
    367A  ILE*     3.7    22.7    -      -       +      -
    385A  ILE*     3.8    23.8    -      -       +      -
    386A  GLU      4.5     0.7    -      -       -      -
    387A  GLY*     3.8    21.1    -      -       -      -
    390A  ILE*     4.5     8.3    -      -       +      -
    394A  LEU*     4.1    16.8    -      -       +      -
    395A  SER      3.2     2.0    -      -       -      -
    396A  MET*     1.3    74.7    -      -       -      +
    398A  GLY*     1.3    59.0    +      -       -      +
    417A  VAL*     3.5    30.7    -      -       +      -
    418A  GLY      5.2     0.4    -      -       -      -
    419A  ALA*     3.6    17.9    -      -       +      -
    426A  VAL*     4.2    20.9    -      -       +      -
    428A  LEU*     4.7     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 398 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  SER*     3.0    18.2    +      -       -      -
    356A  GLY*     3.4    10.0    -      -       -      -
    358A  PRO*     4.2     6.5    -      -       -      +
    366A  ALA      4.4     2.5    -      -       -      -
    367A  ILE*     3.5    25.6    -      -       -      -
    397A  PHE*     1.3    76.4    -      -       -      +
    399A  GLN*     1.3    65.5    +      -       -      +
    400A  SER*     3.2     3.7    +      -       -      -
    401A  ILE*     4.3     1.4    -      -       -      +
    417A  VAL*     3.7     7.7    -      -       -      +
    418A  GLY      3.0     9.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 399 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLY      4.8     2.0    -      -       -      +
     21A  TYR*     3.8    43.7    +      -       +      +
    337A  GLU*     3.8    29.1    +      -       -      +
    338A  SER*     3.6    14.3    -      -       -      -
    358A  PRO*     3.9    13.8    -      -       +      +
    359A  GLN*     5.9     0.7    +      -       -      -
    396A  MET*     3.4     9.5    +      -       -      +
    397A  PHE      3.6     0.2    -      -       -      -
    398A  GLY*     1.3    78.2    -      -       -      +
    400A  SER*     1.3    58.9    +      -       -      +
    418A  GLY      3.5     3.9    +      -       -      +
    420A  PHE*     3.4    45.0    -      -       +      -
    280B  LYS*     5.7     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 400 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLY      2.9    20.4    +      -       -      -
     21A  TYR      3.4    17.0    -      -       -      -
     22A  SER*     3.4    18.2    -      -       -      -
     23A  VAL*     3.5    12.6    -      -       -      +
    338A  SER*     4.5     2.7    -      -       -      -
    398A  GLY      4.2     0.2    -      -       -      -
    399A  GLN*     1.3    81.5    -      -       -      +
    401A  ILE*     1.3    68.3    +      -       -      +
    417A  VAL*     3.4     3.5    -      -       -      +
    418A  GLY*     2.9    27.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 401 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  VAL*     4.4     5.2    -      -       -      +
    338A  SER*     4.1    13.2    +      -       -      +
    340A  VAL*     3.3    35.4    -      -       +      +
    354A  ALA*     3.8    24.5    -      -       +      +
    355A  ILE      4.0     0.4    -      -       -      -
    356A  GLY*     3.9    20.4    -      -       -      +
    367A  ILE*     3.6    31.4    -      -       +      -
    398A  GLY      4.3     3.6    -      -       -      +
    400A  SER*     1.3    81.4    -      -       -      +
    402A  SER*     1.3    66.1    +      -       -      +
    415A  VAL*     3.7    22.7    -      -       +      -
    416A  ALA      3.2    12.8    -      -       -      +
    417A  VAL*     4.2     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 402 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  VAL*     3.3    25.5    -      -       -      +
     24A  VAL*     3.6    16.6    -      -       -      +
     25A  LEU*     3.4    20.3    +      -       -      +
    340A  VAL*     3.7     9.4    -      -       -      +
    342A  LEU*     4.8     1.3    -      -       -      -
    401A  ILE*     1.3    77.4    -      -       -      +
    403A  GLY*     1.3    65.6    +      -       -      +
    415A  VAL*     3.6     3.2    -      -       -      +
    416A  ALA      2.8    33.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 403 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LEU*     3.7     5.6    -      -       -      +
    340A  VAL*     4.0     9.5    -      -       -      +
    342A  LEU*     4.3    11.9    -      -       -      +
    402A  SER*     1.3    83.1    +      -       -      +
    404A  GLN*     1.3    66.0    +      -       -      +
    405A  ILE*     3.0    21.9    +      -       -      +
    414A  ASP      3.2    17.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 404 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  PRO*     5.4    12.7    -      -       -      +
    172A  PHE*     6.0     2.9    -      -       -      -
    340A  VAL*     5.4     2.4    -      -       +      +
    341A  ASN*     3.5    30.5    -      -       -      +
    342A  LEU*     3.4    20.9    +      -       -      +
    343A  GLY*     4.1     5.2    -      -       -      +
    403A  GLY*     1.3    72.8    -      -       -      +
    405A  ILE*     1.3    67.9    +      -       +      +
    413A  VAL*     3.1    32.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 405 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LEU*     3.4    45.1    -      -       +      +
     26A  HIS      4.5     3.1    -      -       -      +
     27A  SER*     3.6    40.2    -      -       -      +
     32A  ARG*     4.6     5.2    -      -       -      -
    100A  ARG*     3.7    22.9    -      -       -      +
    403A  GLY      3.0     5.6    +      -       -      +
    404A  GLN*     1.3    90.8    -      -       +      +
    406A  ASP*     1.3    72.0    -      -       -      +
    407A  ALA*     3.5     7.0    +      -       +      +
    413A  VAL*     3.8     3.3    -      -       -      +
    414A  ASP*     3.0    25.0    +      -       -      +
----------------------------------------------------------
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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