Contacts of the strand formed by residues 45 - 52 (chain B) in PDB entry 3VTW


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 LYS 45 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  ARG*     3.2    20.1    +      -       -      -
     42B  HIS*     3.2    42.3    +      -       +      +
     44B  THR*     1.3    87.1    -      -       -      +
     46B  ILE*     1.3    63.2    +      -       -      +
     47B  PRO*     4.1     3.1    -      -       -      +
     68B  LEU*     3.4    36.6    -      -       +      +
     69B  VAL      3.1    10.3    -      -       -      +
     70B  PRO*     4.1    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  ARG*     3.5    23.8    -      -       -      +
     45B  LYS*     1.3    73.1    -      -       -      +
     47B  PRO*     1.4    66.3    -      -       +      +
     48B  VAL*     3.4    20.9    -      -       +      +
     67B  PHE      3.4     3.6    -      -       -      +
     68B  LEU*     3.6     2.9    -      -       -      +
     69B  VAL*     2.5    35.2    +      -       +      +
     71B  ASP*     4.1    25.1    -      -       +      -
    110B  ILE*     4.1    14.6    -      -       +      -
    111B  SER*     4.2    14.6    -      -       -      +
    114B  TYR*     3.7    46.0    -      -       +      -
    124B  LEU*     4.4     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  VAL*     4.2     6.3    -      -       +      -
     38B  ILE*     4.0    23.1    -      -       +      -
     39B  ARG*     3.8    31.9    -      -       +      -
     45B  LYS      4.1     1.1    -      -       -      +
     46B  ILE*     1.4    86.6    -      -       +      +
     48B  VAL*     1.3    60.0    +      -       -      +
     67B  PHE      3.4     5.6    -      -       -      +
     68B  LEU*     4.0     3.8    -      -       +      -
    114B  TYR*     4.0     9.2    -      -       +      -
    122B  GLY      4.0    11.7    -      -       -      +
    123B  PHE*     3.6    24.8    -      -       +      -
    124B  LEU*     3.0    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  ILE*     3.4    27.1    -      -       +      +
     47B  PRO*     1.3    78.6    -      -       -      +
     49B  ILE*     1.3    67.4    +      -       -      +
     50B  ILE*     4.0    11.2    -      -       +      -
     65B  THR      3.4     1.9    -      -       -      +
     66B  LYS*     3.4     2.8    -      -       -      +
     67B  PHE*     2.6    50.3    +      -       +      +
     69B  VAL*     3.8    16.4    -      -       +      -
     78B  LEU*     5.2     0.7    -      -       +      -
    110B  ILE*     4.1     5.8    -      -       +      -
    123B  PHE*     4.0     1.6    -      -       -      -
    124B  LEU*     3.4    11.7    -      -       +      +
    126B  MET*     3.2    39.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  PHE*     3.8    19.7    -      -       +      -
     48B  VAL*     1.3    74.7    -      -       -      +
     50B  ILE*     1.3    56.5    +      -       -      +
     51B  GLU*     3.8    13.7    -      -       -      +
     65B  THR*     3.3    20.6    -      -       +      +
     66B  LYS*     3.4    32.8    -      -       +      -
    123B  PHE*     3.6    32.5    -      -       +      -
    124B  LEU      3.0     5.7    +      -       -      +
    125B  TYR*     3.5    37.0    -      -       +      -
    126B  MET*     2.8    34.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  VAL*     4.0    19.1    -      -       +      -
     49B  ILE*     1.3    76.8    -      -       -      +
     51B  GLU*     1.3    69.0    +      -       -      +
     62B  LEU*     3.6    29.3    -      -       +      +
     64B  LYS      4.4     0.3    -      -       -      +
     65B  THR*     3.1    18.8    +      -       -      +
     67B  PHE*     3.9    24.2    -      -       +      -
     69B  VAL*     6.0     0.2    -      -       +      -
     78B  LEU*     4.6    11.9    -      -       +      -
     82B  ILE*     3.8    32.8    -      -       +      -
     96B  LEU*     4.3    14.8    -      -       +      -
    126B  MET*     3.6    17.5    -      -       +      +
    128B  TYR*     3.8    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  THR*     3.4    16.8    -      -       -      +
     22B  PHE*     2.8    33.2    +      -       -      +
     23B  LYS      5.6     0.2    +      -       -      -
     25B  ARG*     4.7     1.4    +      -       -      -
     49B  ILE*     3.8    18.9    -      -       +      +
     50B  ILE*     1.3    81.1    -      -       -      +
     52B  ARG*     1.3    66.4    +      -       -      +
     62B  LEU*     5.2     0.9    -      -       -      -
     65B  THR*     3.6    14.1    -      -       +      +
    125B  TYR*     4.4     9.5    -      -       -      -
    126B  MET      3.0    11.7    +      -       -      +
    127B  VAL*     3.3    10.8    -      -       +      +
    128B  TYR*     3.1    31.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  GLU*     2.6    42.4    +      -       -      +
     51B  GLU*     1.3    76.8    -      -       -      +
     53B  TYR*     1.3    71.2    +      -       -      +
     54B  LYS*     3.1     6.1    +      -       -      -
     56B  GLU*     3.6    32.9    +      -       +      +
     59B  LEU      3.2    28.7    +      -       -      -
     60B  PRO*     3.8     6.3    -      -       -      +
     61B  VAL*     3.5    31.9    -      -       +      +
     62B  LEU*     5.9     0.6    -      -       -      +
    127B  VAL*     4.1     1.5    -      -       -      +
    128B  TYR*     3.5    32.6    -      -       +      +
----------------------------------------------------------
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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