Contacts of the strand formed by residues 207 - 214 (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 HIS 207 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161E  VAL*     3.4     8.7    -      -       -      +
    162E  ASN*     3.1    44.7    +      -       -      +
    163E  GLY      5.4     3.2    +      -       -      -
    205E  ARG      3.4     3.3    +      -       -      +
    206E  ASN*     1.3    72.5    -      -       -      +
    208E  PHE*     1.3    74.1    +      -       -      +
    209E  ARG*     4.4    16.4    -      -       +      +
    238E  GLU*     3.4    31.0    +      -       +      +
    239E  ALA      3.7     8.7    -      -       -      -
    240E  TRP*     3.5    41.3    -      +       -      +
----------------------------------------------------------
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Residues in contact with PHE 208 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127E  VAL*     5.5     1.2    -      -       -      +
    143E  LEU*     4.0    22.9    -      -       +      -
    159E  TRP*     5.0     7.9    -      -       +      -
    160E  TRP      3.6     5.4    -      -       -      +
    161E  VAL*     4.1    17.7    -      -       +      -
    194E  LEU*     4.2    11.4    -      -       +      -
    196E  VAL*     4.4    13.0    -      -       +      -
    200E  PHE*     3.7    29.4    -      +       -      -
    201E  TRP*     3.6    41.5    -      +       -      -
    206E  ASN*     3.5    33.9    -      -       +      -
    207E  HIS*     1.3    76.2    -      -       -      +
    209E  ARG*     1.3    60.5    +      -       -      +
    238E  GLU*     3.2     4.2    -      -       -      +
    239E  ALA      2.8    48.6    +      -       -      +
    241E  GLY*     3.9     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 209 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159E  TRP*     3.4    11.4    -      -       -      -
    160E  TRP*     2.9    61.8    +      -       +      +
    207E  HIS*     4.4    13.4    -      -       +      +
    208E  PHE*     1.3    74.8    -      -       -      +
    210E  CYS*     1.3    66.7    +      -       -      +
    211E  GLN*     2.5    37.9    +      -       +      +
    234E  ILE*     4.7     1.8    -      -       -      +
    236E  SER*     3.3    28.8    +      -       -      -
    237E  ALA      3.4     9.9    -      -       -      +
    238E  GLU*     4.4    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 210 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125E  VAL*     4.0     6.1    -      -       +      +
    127E  VAL*     3.8    16.5    -      -       +      +
    145E  CYS*     2.1    53.4    -      -       +      -
    157E  LEU*     4.1    22.7    -      -       -      -
    158E  SER      3.8     2.5    -      -       -      -
    159E  TRP*     4.0    10.7    -      -       +      -
    208E  PHE      4.4     0.2    +      -       -      -
    209E  ARG*     1.3    74.7    -      -       -      +
    211E  GLN*     1.3    60.6    -      -       -      +
    212E  VAL*     4.9     0.4    -      -       -      -
    236E  SER*     3.4     3.5    -      -       -      -
    237E  ALA      2.8    29.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 211 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156E  GLU      3.7     0.9    -      -       -      +
    157E  LEU*     3.5     5.2    -      -       -      +
    158E  SER*     2.8    52.4    +      -       -      +
    160E  TRP*     3.8    28.6    +      -       +      +
    209E  ARG*     2.5    46.1    +      -       +      +
    210E  CYS*     1.3    72.7    -      -       -      +
    212E  VAL*     1.3    64.2    +      -       -      +
    213E  GLN*     4.1     3.1    -      -       -      +
    234E  ILE*     3.6    40.3    -      -       +      +
    235E  VAL      3.9     2.9    -      -       -      -
    236E  SER*     4.5     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 212 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123E  PRO*     3.6    28.3    -      -       +      -
    125E  VAL*     3.7    27.4    -      -       +      -
    147E  ALA*     4.0    15.3    -      -       +      -
    155E  VAL*     4.1    13.9    -      -       +      -
    156E  GLU      3.5     3.1    -      -       -      +
    157E  LEU*     4.3    18.2    -      -       +      -
    210E  CYS*     4.9     2.0    -      -       -      -
    211E  GLN*     1.3    78.3    -      -       -      +
    213E  GLN*     1.3    71.0    +      -       -      +
    214E  PHE      3.6     0.9    +      -       -      -
    233E  GLN      3.8     0.3    -      -       -      +
    234E  ILE*     3.4     5.3    -      -       -      -
    235E  VAL*     2.9    40.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 213 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154E  HIS      3.9     0.2    -      -       -      +
    155E  VAL*     3.1     8.1    -      -       -      +
    156E  GLU*     2.9    47.1    +      -       +      +
    211E  GLN*     4.1     5.4    -      -       -      +
    212E  VAL*     1.3    71.5    -      -       -      +
    214E  PHE*     1.3    77.9    +      -       -      +
    215E  TYR*     3.7    31.7    -      -       +      +
    232E  THR*     3.5    18.2    -      -       -      +
    233E  GLN*     3.6    14.4    +      -       -      +
    234E  ILE*     3.5    27.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 214 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120E  VAL*     4.1     2.2    -      -       +      -
    121E  PHE      3.1    28.0    -      -       -      -
    122E  PRO*     3.9    15.0    -      -       +      -
    123E  PRO*     3.8    27.6    -      -       +      -
    150E  PHE*     4.3     2.5    -      -       +      -
    151E  TYR      3.5    13.0    -      -       -      -
    152E  PRO*     3.7    23.8    -      -       +      -
    154E  HIS      3.7     8.7    -      -       -      -
    155E  VAL*     4.0     8.7    -      -       +      -
    212E  VAL      3.6     1.3    +      -       -      +
    213E  GLN*     1.3    80.7    +      -       -      +
    215E  TYR*     1.3    77.0    +      -       -      +
    216E  GLY*     3.7    17.7    -      -       -      -
    230E  PRO      3.8    12.3    -      -       -      -
    231E  VAL      3.7    15.9    -      -       -      -
    232E  THR*     3.2     2.9    -      -       -      -
    233E  GLN*     2.8    40.0    +      -       +      +
    235E  VAL*     5.5     0.4    -      -       +      -
----------------------------------------------------------
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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