Contacts of the strand formed by residues 45 - 52 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  ARG*     2.9    20.3    +      -       -      -
     42C  HIS*     3.1    45.8    +      -       +      +
     44C  THR*     1.3    86.8    +      -       -      +
     46C  ILE*     1.3    63.5    +      -       -      +
     47C  PRO*     3.6     5.4    -      -       -      +
     68C  LEU*     3.8    32.8    -      -       +      +
     69C  VAL      3.4     6.5    -      -       -      +
     70C  PRO*     3.8    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 46 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  ARG*     4.2     7.9    -      -       -      +
     44C  THR      5.2     0.4    -      -       -      +
     45C  LYS*     1.3    77.9    -      -       -      +
     47C  PRO*     1.3    69.7    -      -       +      +
     48C  VAL*     3.4    13.5    -      -       +      +
     67C  PHE      3.2     4.7    -      -       -      +
     68C  LEU*     4.1     2.2    -      -       -      -
     69C  VAL      2.6    44.3    +      -       -      +
     71C  ASP*     4.1    10.5    -      -       +      -
    110C  ILE*     3.8    27.8    -      -       +      -
    111C  SER*     3.8    26.0    -      -       -      +
    114C  TYR*     3.4    47.8    -      -       +      -
    124C  LEU*     4.5     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 47 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  VAL*     4.6     5.2    -      -       +      -
     38C  ILE*     4.3    20.4    -      -       +      -
     39C  ARG*     4.2    18.4    -      -       -      +
     45C  LYS      3.6     8.5    -      -       -      +
     46C  ILE*     1.3    87.1    -      -       +      +
     48C  VAL*     1.3    65.8    +      -       -      +
     67C  PHE      3.3     6.1    -      -       -      +
     68C  LEU*     4.2     6.3    -      -       +      -
    114C  TYR*     4.2     7.8    -      -       +      +
    122C  GLY      3.8    19.1    -      -       -      +
    123C  PHE*     4.0    23.1    -      -       +      -
    124C  LEU*     3.2    23.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 48 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  ILE*     3.4    17.7    -      -       +      +
     47C  PRO*     1.3    80.5    -      -       -      +
     49C  ILE*     1.3    67.7    +      -       -      +
     50C  ILE*     3.8    21.8    -      -       +      -
     65C  THR      3.6     1.0    -      -       -      +
     66C  LYS*     3.4     3.3    -      -       -      -
     67C  PHE*     2.6    49.0    +      -       +      +
     69C  VAL*     3.8     7.6    -      -       +      -
     78C  LEU*     5.0     1.6    -      -       +      -
    110C  ILE*     3.7    25.6    -      -       +      -
    123C  PHE*     4.3     1.2    -      -       -      -
    124C  LEU*     3.2    13.2    -      -       +      +
    126C  MET*     3.6    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 49 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  PHE*     3.4    40.4    -      -       +      -
     48C  VAL*     1.3    74.1    -      -       -      +
     50C  ILE*     1.3    63.4    +      -       -      +
     51C  GLU*     3.7    32.8    -      -       +      +
     65C  THR*     3.4     9.4    -      -       +      +
     66C  LYS*     3.6    21.3    -      -       +      -
    123C  PHE*     3.5    32.1    -      -       +      -
    124C  LEU      2.8     8.1    +      -       -      +
    125C  TYR*     3.7    24.5    -      -       +      -
    126C  MET*     2.9    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 50 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  VAL*     3.8    18.4    -      -       +      -
     49C  ILE*     1.3    78.3    -      -       -      +
     51C  GLU*     1.3    67.4    +      -       -      +
     62C  LEU*     3.9    20.1    -      -       +      +
     64C  LYS      4.1     5.4    -      -       -      +
     65C  THR*     3.0    23.7    +      -       -      +
     67C  PHE*     3.8    28.5    -      -       +      -
     78C  LEU*     4.4    11.0    -      -       +      -
     82C  ILE*     3.6    36.6    -      -       +      -
     96C  LEU*     4.7     7.9    -      -       +      -
    126C  MET*     3.5    15.5    -      -       +      +
    128C  TYR*     4.0    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 51 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  THR*     3.5    19.8    -      -       +      +
     22C  PHE*     2.8    33.4    +      -       -      +
     23C  LYS      5.3     0.2    +      -       -      -
     25C  ARG*     4.6     3.5    +      -       -      -
     49C  ILE*     3.7    24.2    -      -       +      +
     50C  ILE*     1.3    81.5    -      -       -      +
     52C  ARG*     1.3    65.9    +      -       -      +
     62C  LEU*     6.1     0.2    -      -       -      -
     65C  THR*     4.0     7.7    -      -       +      +
    125C  TYR*     4.5     8.0    -      -       -      -
    126C  MET      3.0    10.9    +      -       -      +
    127C  VAL*     3.1    14.4    -      -       +      +
    128C  TYR*     2.9    31.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 52 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  GLU*     2.9    39.0    +      -       -      +
     51C  GLU*     1.3    78.9    -      -       -      +
     53C  TYR*     1.3    69.4    +      -       -      +
     54C  LYS*     3.5     3.1    +      -       -      -
     56C  GLU*     3.5    37.0    +      -       +      +
     57C  LYS      6.3     0.2    -      -       -      -
     59C  LEU      3.1    28.7    +      -       -      -
     60C  PRO*     3.9     7.7    -      -       -      +
     61C  VAL*     3.8    33.0    -      -       +      +
    127C  VAL*     4.4     0.8    -      -       -      +
    128C  TYR*     3.4    30.2    +      -       +      +
----------------------------------------------------------
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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