Contacts of the strand formed by residues 12 - 16 (chain E) in PDB entry 2VLK


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 TYR 12 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  PRO*     3.3    18.5    -      -       -      +
     11E  LYS*     1.3   124.7    +      -       +      +
     13E  LEU*     1.3    62.6    +      -       -      +
    109E  THR*     4.9     0.2    -      -       -      -
    110E  ARG*     3.5    29.8    -      -       +      -
    153E  ASP      5.0     0.2    -      -       -      -
    154E  HIS*     3.6    42.2    -      +       +      +
    155E  VAL      3.7    11.2    +      -       -      -
    156E  GLU*     3.5    13.0    -      -       +      +
    215E  TYR*     3.3    57.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 13 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  PRO*     3.8    26.9    -      -       +      -
     12E  TYR*     1.3    76.2    -      -       -      +
     14E  PHE*     1.3    60.4    +      -       -      +
     15E  ARG*     3.4    35.2    -      -       -      +
     21E  VAL*     4.2    10.8    -      -       +      -
     22E  THR      4.9     3.4    -      -       -      +
     23E  LEU*     3.6    31.9    -      -       +      -
    109E  THR*     4.1    13.7    -      -       +      -
    110E  ARG      2.9    10.0    +      -       -      +
    111E  LEU*     4.1    13.9    -      -       +      -
    112E  THR      3.0    23.7    +      -       -      -
    154E  HIS*     3.2    10.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 14 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13E  LEU*     1.3    77.2    -      -       -      +
     15E  ARG*     1.3    90.6    +      -       -      +
    112E  THR*     3.3    22.4    -      -       +      -
    114E  THR*     3.2    42.4    -      -       +      -
    117E  LEU*     4.1     8.7    -      -       +      -
    120E  VAL*     3.3    30.5    -      -       +      -
    151E  TYR*     3.9    14.6    -      +       -      -
    152E  PRO*     3.8    22.4    -      -       +      -
    154E  HIS*     4.7     6.3    -      -       +      +
    215E  TYR      5.6     0.9    -      -       -      +
    216E  GLY      5.2    13.2    -      -       -      +
    217E  LEU*     4.1    20.2    -      -       +      -
    221E  ASP*     5.3     4.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 15 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13E  LEU*     3.4    31.8    -      -       -      +
     14E  PHE*     1.3   108.0    +      -       -      +
     16E  LYS*     1.3    66.5    +      -       -      +
     19E  GLN*     3.8    34.5    +      -       +      +
     20E  ASN      4.8     2.4    +      -       -      -
     21E  VAL*     3.7    32.4    -      -       +      +
    111E  LEU*     4.6     6.1    -      -       +      -
    112E  THR      3.0     7.9    +      -       -      +
    113E  VAL*     3.1    17.4    -      -       +      -
    114E  THR*     3.0    29.6    +      -       -      +
    220E  ASN*     5.9     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 16 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15E  ARG*     1.3    75.0    -      -       -      +
     17E  GLU*     1.3    80.8    +      -       +      +
     18E  GLY      3.3     0.2    +      -       -      -
     19E  GLN*     3.1    45.6    +      -       +      +
    113E  VAL*     3.9     2.2    -      -       -      +
    114E  THR*     3.8     9.4    -      -       -      -
    115E  GLU      4.7    13.0    -      -       -      +
    116E  ASP*     5.4     2.0    -      -       -      +
    117E  LEU*     3.9    39.3    -      -       +      +
----------------------------------------------------------
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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