Contacts of the strand formed by residues 15 - 21 (chain E) 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 CYS 15 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244D  PRO*     5.1     2.2    -      -       -      -
     11E  LEU*     4.5    12.8    -      -       -      -
     12E  PRO*     3.3    21.8    -      -       +      +
     14E  PRO*     1.3    77.8    -      -       -      +
     16E  ARG*     1.3    64.5    +      -       -      +
     17E  VAL*     4.4     8.3    -      -       -      -
     46E  GLU      3.4     3.3    +      -       -      +
     47E  ILE*     3.6    23.1    -      -       -      -
     48E  SER*     2.9    26.2    +      -       -      -
     73E  ASP*     3.3    24.2    -      -       +      +
    145E  ARG*     3.7    16.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 16 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243D  GLU*     2.6    38.5    +      -       -      -
     15E  CYS*     1.3    76.3    -      -       -      +
     17E  VAL*     1.3    68.1    +      -       -      +
     48E  SER*     3.3    27.4    +      -       -      +
     49E  PHE      6.3     0.2    -      -       -      -
     50E  THR*     6.4     0.4    -      -       +      -
     71E  ARG      3.6    21.1    -      -       -      +
     72E  TRP*     3.9    12.6    -      -       +      -
     73E  ASP*     2.9    43.4    +      -       -      +
     56F  ARG*     5.5     5.1    -      -       -      +
     62F  GLU*     3.7    23.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 17 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  LEU*     5.3     0.2    -      -       +      -
     15E  CYS*     4.4     9.0    -      -       -      -
     16E  ARG*     1.3    83.6    -      -       -      +
     18E  LEU*     1.3    59.9    +      -       -      +
     19E  VAL*     3.9    13.5    -      -       +      -
     42E  LEU*     6.0     1.3    -      -       +      -
     47E  ILE*     3.6    24.7    -      -       +      -
     48E  SER      2.9    12.2    +      -       -      +
     49E  PHE*     3.2     4.9    -      -       +      -
     50E  THR      3.1    24.4    +      -       -      -
     72E  TRP*     3.7     8.4    -      -       -      -
     74E  ALA*     3.6    24.2    -      -       +      +
     76E  VAL*     3.0    35.0    -      -       +      -
    142E  LEU*     4.9     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 18 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17E  VAL*     1.3    70.1    -      -       -      +
     19E  VAL*     1.3    57.3    +      -       -      +
     20E  LEU*     3.6    27.9    +      -       +      +
     50E  THR*     3.8    16.8    -      -       -      +
     52E  MET*     3.7    30.7    -      -       +      -
     63E  LEU*     6.5     0.2    -      -       +      -
     64E  VAL*     5.7     2.7    -      -       +      -
     67E  GLU*     4.2    16.8    -      -       +      +
     72E  TRP*     3.6    41.1    -      -       +      +
     74E  ALA      3.0    10.7    +      -       -      -
     75E  LEU*     3.5    27.0    -      -       +      +
     76E  VAL      2.7    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 19 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17E  VAL*     3.9    14.1    -      -       +      -
     18E  LEU*     1.3    73.6    -      -       -      +
     20E  LEU*     1.3    57.3    +      -       -      +
     21E  LEU*     3.6     9.0    +      -       +      -
     34E  PHE*     4.0    21.8    -      -       +      -
     42E  LEU*     5.2     3.4    -      -       +      -
     49E  PHE*     4.0    17.9    -      -       +      -
     50E  THR      3.0    13.3    +      -       -      +
     51E  LEU*     3.4    25.7    -      -       +      +
     52E  MET      2.8    31.6    +      -       -      +
     76E  VAL*     3.2    29.4    -      -       +      +
     78E  MET*     4.6     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 20 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18E  LEU*     3.6    31.6    -      -       +      +
     19E  VAL*     1.3    69.0    -      -       -      +
     21E  LEU*     1.3    58.9    +      -       -      +
     52E  MET*     3.4    35.7    -      -       +      +
     54E  THR*     4.4     5.6    -      -       +      -
     60E  ALA*     4.6    13.0    -      -       +      +
     63E  LEU*     5.1     4.5    -      -       +      -
     64E  VAL*     3.7    30.3    -      -       +      -
     75E  LEU*     5.6     4.0    -      -       +      -
     76E  VAL      2.8    12.7    +      -       -      +
     77E  VAL*     3.5     2.9    -      -       +      -
     78E  MET      2.9    25.6    +      -       -      -
     83E  LEU*     3.3    17.7    -      -       +      +
     87E  VAL*     3.7    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 21 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19E  VAL*     4.4     0.9    -      -       +      -
     20E  LEU*     1.3    73.9    -      -       -      +
     22E  ASN*     1.3    62.9    +      -       -      +
     23E  PRO*     3.3    35.4    -      -       +      +
     30E  ALA*     3.9    11.2    -      -       +      +
     31E  LEU*     3.9    21.8    -      -       +      +
     34E  PHE*     3.8    24.7    -      -       +      -
     51E  LEU*     3.7    31.6    -      -       +      -
     52E  MET      3.1     6.5    +      -       -      -
     53E  LEU*     3.3    14.0    -      -       +      -
     54E  THR*     3.0    23.4    +      -       -      +
     78E  MET*     3.6    23.8    -      -       +      +
----------------------------------------------------------
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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