Contacts of the strand formed by residues 285 - 291 (chain B) 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 MET 285 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  LEU*     3.7    26.2    -      -       +      -
    262B  ALA*     2.9    42.6    -      -       +      -
    263B  LEU      3.7     9.4    -      -       -      +
    264B  LEU*     4.2    15.5    -      -       +      -
    280B  CYS*     4.0     3.8    -      -       -      -
    284B  VAL*     1.3    77.0    -      -       -      +
    286B  HIS*     1.3    64.9    +      -       -      +
    287B  LEU*     3.6     0.4    +      -       +      -
    323B  PRO*     3.6     3.6    -      -       -      +
    324B  VAL*     2.9    50.8    +      -       +      +
    325B  VAL      5.2     1.6    -      -       -      +
    326B  ALA*     5.8     0.2    -      -       -      -
    327B  PHE*     3.8    21.1    -      -       +      -
    354B  VAL*     3.2    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 286 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261B  LEU      3.6     1.6    -      -       -      +
    262B  ALA*     3.6     2.6    -      -       -      +
    263B  LEU*     2.7    44.5    +      -       +      +
    265B  HIS      3.7    10.4    +      -       -      -
    275B  ALA*     3.3    27.0    -      -       +      +
    277B  MET*     3.6    12.5    -      -       +      +
    278B  GLY      3.3    24.2    +      -       -      -
    279B  ARG      4.8     0.2    -      -       -      -
    280B  CYS*     3.3    31.3    -      -       +      -
    284B  VAL*     5.4     3.8    -      -       +      -
    285B  MET*     1.3    73.1    -      -       -      +
    287B  LEU*     1.3    60.6    +      -       -      +
    288B  PHE*     3.8    12.5    -      -       +      -
    321B  TYR*     2.9    41.0    +      +       +      -
    322B  VAL      4.1     0.2    -      -       -      -
    357D  ASN*     5.6     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 287 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  LEU*     4.3    15.3    -      -       +      -
    212B  TYR*     3.7    42.4    -      -       +      -
    260B  VAL*     4.0    15.7    -      -       +      -
    261B  LEU      3.3    20.6    -      -       -      +
    262B  ALA*     4.2     9.9    -      -       +      +
    285B  MET      3.6     0.8    +      -       -      -
    286B  HIS*     1.3    73.6    -      -       -      +
    288B  PHE*     1.3    71.6    +      -       -      +
    289B  TYR*     4.8     6.0    -      -       +      -
    320B  VAL      3.9     0.2    -      -       -      +
    321B  TYR*     3.4     7.1    -      -       -      -
    322B  VAL*     2.8    47.6    +      -       +      +
    324B  VAL*     3.9    17.7    -      -       +      -
    327B  PHE*     5.0     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 288 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259B  LEU*     4.9     2.5    -      -       +      -
    260B  VAL*     3.7     0.7    -      -       -      -
    261B  LEU*     2.8    54.4    +      -       +      +
    263B  LEU*     4.6     7.2    -      -       +      -
    274B  ALA      3.4    22.2    -      -       -      -
    275B  ALA*     4.2    13.2    -      -       +      -
    277B  MET*     4.5     0.7    -      -       -      -
    286B  HIS*     3.8    22.9    -      -       +      -
    287B  LEU*     1.3    79.5    -      -       -      +
    289B  TYR*     1.3    67.7    +      -       -      +
    312B  MET*     3.8    27.1    -      -       +      -
    319B  LEU*     4.2    10.5    -      -       +      -
    320B  VAL      3.3    13.2    -      -       -      -
    321B  TYR*     3.6    25.6    -      +       +      -
   1001B  UUL      3.2    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 289 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  LEU*     3.6    21.8    -      -       +      -
    212B  TYR*     4.5    15.6    +      +       -      -
    252B  VAL*     3.8    27.4    -      -       +      +
    253B  PRO*     5.8     0.2    -      -       -      +
    254B  ASP*     5.4     0.2    +      -       -      -
    257B  PHE*     3.6    27.8    -      +       +      -
    259B  LEU*     3.3    15.7    -      -       -      +
    260B  VAL*     4.1     7.2    -      -       +      -
    287B  LEU*     4.8     7.0    -      -       +      -
    288B  PHE*     1.3    78.5    -      -       -      +
    290B  VAL*     1.3    61.9    +      -       -      +
    291B  ARG*     3.8    28.7    -      -       +      -
    318B  TYR      3.2     2.1    -      -       -      +
    319B  LEU*     3.6     2.4    -      -       -      +
    320B  VAL*     2.8    73.1    +      -       +      +
    322B  VAL*     4.9     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 290 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257B  PHE*     3.5     6.6    -      -       -      +
    258B  VAL*     3.0    38.5    +      -       +      -
    259B  LEU*     3.1    40.0    +      -       +      +
    289B  TYR*     1.3    75.4    -      -       -      +
    291B  ARG*     1.3    60.4    +      -       -      +
    294B  VAL*     3.4    31.9    -      -       +      -
    299B  LEU*     5.1     9.9    -      -       +      -
    302B  LEU*     5.3     5.2    -      -       +      -
    316B  CYS*     5.9     0.2    -      -       -      -
    318B  TYR*     3.3     7.9    -      -       +      +
    319B  LEU*     3.9    24.2    -      -       +      +
   1001B  UUL      4.7     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 291 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254B  ASP*     2.8    44.9    +      -       -      +
    256B  ASP      4.0     4.7    -      -       -      +
    257B  PHE*     4.5     3.8    -      -       -      +
    258B  VAL*     3.5    10.3    -      -       -      +
    289B  TYR*     3.8    25.1    -      -       +      -
    290B  VAL*     1.3    81.2    -      -       -      +
    292B  ALA*     1.3    66.7    +      -       -      +
    293B  GLY      3.5     2.1    +      -       -      -
    294B  VAL*     3.7     6.9    -      -       -      +
    317B  PRO*     2.8    43.1    +      -       -      +
    318B  TYR*     2.9    41.1    +      -       +      +
    320B  VAL*     4.5     4.9    -      -       +      +
----------------------------------------------------------
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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