Contacts of the strand formed by residues 388 - 393 (chain B) in PDB entry 3V4R


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 ASN 388 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  ILE*     3.9    25.4    +      -       +      +
     31B  GLY      5.0     1.6    -      -       -      +
     32B  LYS      2.9    27.6    -      -       -      +
     33B  LYS      4.6     2.9    -      -       -      -
     58B  LYS*     3.4    22.4    -      -       -      +
    333B  PHE      3.7     6.9    +      -       -      +
    334B  MET*     3.4    18.0    -      -       +      +
    335B  ILE*     3.0    26.3    +      -       -      +
    387B  HIS*     1.3   101.4    +      -       -      +
    389B  ILE*     1.3    60.6    +      -       -      +
    390B  VAL*     5.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 389 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  LYS      5.6     0.6    +      -       -      -
     33B  LYS      3.7    13.7    +      -       -      +
     34B  HIS*     3.5    33.3    -      -       +      +
     35B  GLN*     3.0    26.2    +      -       -      +
    335B  ILE*     3.4    33.7    -      -       +      +
    337B  VAL*     3.9    16.2    -      -       +      -
    382B  PHE*     4.6     6.3    -      -       +      -
    386B  MET*     4.2    33.9    -      -       +      -
    388B  ASN*     1.3    74.0    -      -       -      +
    390B  VAL*     1.3    67.8    +      -       -      +
    391B  TYR*     3.7    24.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 390 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  LEU*     5.8     6.3    -      -       +      -
     28B  ILE*     4.5     9.0    -      -       +      -
     35B  GLN*     3.3    31.0    -      -       +      +
     36B  THR      5.0     0.2    -      -       -      -
     37B  LEU*     4.5    13.2    -      -       +      +
     49B  VAL*     5.7     1.3    -      -       +      -
     52B  LEU*     4.3    24.9    -      -       +      -
    334B  MET*     4.6     6.1    -      -       -      -
    335B  ILE      2.9    12.6    +      -       -      +
    336B  VAL*     3.3    14.2    -      -       +      +
    337B  VAL      2.9    24.7    +      -       -      -
    389B  ILE*     1.3    79.0    -      -       -      +
    391B  TYR*     1.3    69.8    +      -       -      +
    392B  VAL*     3.8    12.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 391 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  HIS*     2.7    43.5    +      -       +      -
     35B  GLN      2.8    27.1    +      -       -      -
     36B  THR*     3.2    19.9    -      -       +      +
     37B  LEU*     2.7    32.4    +      -       -      +
    337B  VAL*     3.9    14.6    -      -       +      -
    340B  SER*     3.6    22.0    -      -       -      +
    344B  ILE*     3.9    21.3    -      -       +      -
    386B  MET*     4.1     3.3    -      -       +      +
    389B  ILE*     3.7    25.3    -      -       +      +
    390B  VAL*     1.3    71.0    -      -       -      +
    392B  VAL*     1.3    57.1    +      -       -      +
    393B  SER      4.2     0.4    -      -       -      -
    399B  TYR*     3.0    27.0    +      +       -      -
    400B  GLU*     3.5    24.5    -      -       +      -
    403B  HIS*     5.0     1.1    -      -       +      -
    404B  THR*     4.3     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 392 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  LEU*     3.6    39.0    -      -       +      +
     39B  GLY*     5.3     3.1    -      -       -      +
     45B  LYS*     4.3    18.2    -      -       +      -
     49B  VAL*     4.1     8.1    -      -       +      -
    336B  VAL*     3.7    28.9    -      -       +      -
    337B  VAL      2.8    11.6    +      -       -      +
    338B  ASP*     4.6     6.1    -      -       +      -
    339B  GLU      2.9    26.8    +      -       -      +
    340B  SER*     3.1     7.4    +      -       -      -
    390B  VAL*     4.1     5.6    -      -       +      +
    391B  TYR*     1.3    76.8    -      -       -      +
    393B  SER*     1.3    64.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 393 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  THR*     5.4     1.2    -      -       -      +
     37B  LEU      3.2    17.3    +      -       -      +
     38B  LEU*     3.4     5.5    -      -       -      -
     39B  GLY      3.3    11.7    +      -       -      -
    339B  GLU*     4.5     4.3    -      -       -      +
    340B  SER*     3.4    17.9    -      -       -      -
    341B  HIS*     2.7    30.0    +      -       -      -
    391B  TYR      4.2     0.6    +      -       -      -
    392B  VAL*     1.3    79.4    -      -       -      +
    394B  ALA*     1.3    65.2    +      -       -      +
    395B  THR      3.1    11.8    +      -       -      -
    396B  PRO*     3.8    17.6    -      -       -      +
----------------------------------------------------------
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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