Contacts of the strand formed by residues 256 - 263 (chain D) in PDB entry 3VZC


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 ASP 256 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205D  THR*     4.7     9.9    +      -       -      +
    206D  TYR      3.5     3.6    -      -       -      +
    207D  ARG*     3.0    31.6    +      -       -      +
    254D  ASP*     3.7     4.1    -      -       +      +
    255D  GLU*     1.3    78.5    -      -       -      +
    257D  PHE*     1.3    64.0    +      -       -      +
    291D  ARG*     3.7     7.1    -      -       -      +
    292D  ALA*     2.8    39.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 257 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171D  TRP*     3.7    29.6    -      +       +      -
    205D  THR*     3.4     8.4    -      -       -      -
    206D  TYR*     2.9    38.8    +      -       -      +
    208D  GLY      3.2    28.7    -      -       -      -
    209D  ARG      5.1     0.2    -      -       -      -
    210D  LEU*     4.0    24.9    -      -       +      -
    252D  VAL*     4.1     4.3    -      -       +      -
    254D  ASP*     3.3    31.4    -      -       -      -
    255D  GLU*     3.9     2.9    -      -       -      -
    256D  ASP*     1.3    77.0    -      -       -      +
    258D  VAL*     1.3    63.3    +      -       -      +
    259D  LEU      4.0     9.9    -      -       -      +
    260D  VAL*     4.3     3.1    -      -       +      -
    289D  TYR*     3.6    41.7    -      +       +      -
    290D  VAL      3.3    11.9    -      -       -      +
    291D  ARG*     4.5     1.3    -      -       -      -
    292D  ALA      4.1     1.3    -      -       -      +
    329D  LEU*     5.3     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 258 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172D  GLY*     3.6     0.2    -      -       -      -
    173D  PHE*     2.7    43.1    +      -       +      +
    203D  LEU*     5.4     6.1    -      -       +      -
    204D  ARG      4.8     7.4    -      -       -      +
    205D  THR*     4.9     6.1    -      -       +      -
    206D  TYR*     3.2    14.6    -      -       -      -
    257D  PHE*     1.3    75.7    -      -       -      +
    259D  LEU*     1.3    74.3    +      -       +      +
    290D  VAL*     2.8    29.8    +      -       +      +
    291D  ARG      4.2     4.3    -      -       -      +
    292D  ALA*     4.4     6.7    -      -       -      -
    293D  GLY      5.3     0.2    -      -       -      +
    294D  VAL*     3.7    16.8    -      -       +      -
    299D  LEU*     3.7    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 259 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171D  TRP*     3.4    11.2    -      -       -      +
    172D  GLY*     4.5     0.4    -      -       -      -
    173D  PHE*     4.1    12.3    -      -       +      +
    174D  ILE*     3.6    37.5    -      -       +      +
    257D  PHE*     3.6     3.8    -      -       -      +
    258D  VAL*     1.3    96.8    -      -       +      +
    260D  VAL*     1.3    68.6    +      -       -      +
    261D  LEU*     4.7     5.2    -      -       +      +
    288D  PHE*     4.7     5.8    -      -       +      +
    289D  TYR*     3.1    13.2    -      -       -      +
    290D  VAL*     2.9    50.1    +      -       +      +
    299D  LEU*     5.2     0.4    -      -       +      -
   1001D  UUL      4.0    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 260 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169D  LEU*     3.9     3.6    -      -       +      +
    170D  ALA*     3.4     3.3    -      -       -      +
    171D  TRP*     2.8    62.7    +      -       +      +
    174D  ILE*     5.2     0.3    -      -       -      +
    210D  LEU*     4.3    15.5    -      -       +      -
    257D  PHE*     4.3    10.3    -      -       +      -
    259D  LEU*     1.3    79.1    -      -       -      +
    261D  LEU*     1.3    66.2    +      -       -      +
    262D  ALA*     5.0     1.1    -      -       +      +
    287D  LEU*     4.1    17.9    -      -       +      -
    288D  PHE      3.5     7.6    -      -       -      +
    289D  TYR*     4.1     9.6    -      -       +      -
    327D  PHE*     5.7     3.6    -      -       +      -
    329D  LEU*     3.9    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 261 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168D  SER*     4.1     8.5    -      -       -      -
    169D  LEU      3.5     6.7    -      -       -      +
    170D  ALA*     4.2    11.9    -      -       +      -
    174D  ILE*     4.2    13.0    -      -       +      -
    259D  LEU*     4.3     1.5    -      -       +      -
    260D  VAL*     1.3    76.5    -      -       -      +
    262D  ALA*     1.3    72.7    +      -       -      +
    263D  LEU*     4.0    14.4    -      -       +      -
    268D  LEU*     3.6    46.2    -      -       +      -
    274D  ALA*     5.0     0.4    -      -       +      -
    286D  HIS      3.7     0.9    -      -       -      +
    287D  LEU*     3.3     6.1    -      -       -      -
    288D  PHE*     2.7    68.2    +      -       +      +
   1001D  UUL      4.2    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 262 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153D  LEU*     4.7     0.7    -      -       +      -
    168D  SER*     3.2     7.3    -      -       -      -
    169D  LEU*     2.8    44.0    +      -       +      +
    260D  VAL*     4.3     1.6    -      -       +      +
    261D  LEU*     1.3    73.5    -      -       -      +
    263D  LEU*     1.3    58.5    +      -       -      +
    285D  MET*     3.1    24.0    -      -       +      -
    286D  HIS      3.4     5.6    -      -       -      -
    287D  LEU*     4.1    13.0    -      -       +      +
    327D  PHE*     4.2    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 263 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167D  LEU*     3.6    17.7    -      -       +      +
    168D  SER*     4.3     7.2    -      -       -      -
    261D  LEU*     4.0    17.9    -      -       +      -
    262D  ALA*     1.3    74.8    -      -       -      +
    264D  LEU*     1.3    67.1    +      -       -      +
    265D  HIS      3.1    27.6    -      -       -      +
    266D  SER      4.4     2.0    -      -       -      +
    267D  HIS      3.9    16.8    -      -       -      +
    268D  LEU*     4.5     7.6    -      -       +      -
    274D  ALA*     3.7    30.1    -      -       +      -
    275D  ALA*     4.3     4.5    -      -       +      -
    285D  MET*     3.3     1.5    -      -       -      +
    286D  HIS*     2.6    50.8    +      -       +      +
    288D  PHE*     4.1    14.8    -      -       +      -
----------------------------------------------------------
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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