Contacts of the strand formed by residues 21 - 29 (chain B) in PDB entry 2VBJ


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 GLY 21 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  PHE      3.8     0.6    +      -       -      -
     17B  VAL*     2.9    28.4    +      -       -      -
     19B  ALA      3.5     0.2    -      -       -      -
     20B  ASP*     1.3    82.1    -      -       -      +
     22B  SER*     1.3    63.0    +      -       -      -
     44B  GLN      3.2    12.3    -      -       -      -
     45B  VAL*     4.1     6.5    -      -       -      -
     98B  LYS*     3.1    21.1    +      -       -      -
     15E    A      3.4     8.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  VAL*     4.9     2.0    -      -       -      +
     21B  GLY*     1.3    73.7    -      -       -      -
     23B  ILE*     1.3    64.2    +      -       -      +
     24B  ILE*     3.2    28.5    -      -       -      +
     42B  THR      3.7     1.6    -      -       -      +
     43B  PHE*     3.6     4.7    -      -       -      -
     44B  GLN*     2.8    40.8    +      -       -      +
     98B  LYS*     4.1     2.4    -      -       -      +
     15E    A      3.4    19.8    -      -       -      +
     16E    A      2.8    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  VAL*     4.9     4.9    -      -       +      -
     22B  SER*     1.3    77.5    +      -       -      +
     24B  ILE*     1.3    59.7    +      -       -      +
     42B  THR      3.6     6.1    -      -       -      +
     43B  PHE*     4.1    16.8    -      -       +      -
     88B  LEU*     4.2    17.5    -      -       +      -
     95B  LEU*     4.4     6.7    -      -       +      -
     98B  LYS*     4.0    29.6    -      -       +      +
    101B  GLN*     4.1    16.6    -      -       +      +
    102B  ALA*     3.9    26.2    -      -       +      +
    105B  VAL*     3.4    32.3    -      -       +      -
    132B  ILE*     3.6     9.2    -      -       +      +
    136B  ASN*     2.9    25.9    +      -       -      +
     16E    A      4.4     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  SER*     3.2    28.3    -      -       -      +
     23B  ILE*     1.3    74.6    -      -       -      +
     25B  ALA*     1.3    61.6    +      -       -      +
     26B  GLN*     3.9    26.9    -      -       +      +
     40B  LYS      3.8     0.5    -      -       -      +
     41B  LEU*     3.4     4.7    -      -       -      +
     42B  THR*     2.8    52.1    +      -       +      +
     44B  GLN*     3.9    25.1    -      -       +      +
    105B  VAL*     5.3     0.9    -      -       -      +
    136B  ASN*     4.5     2.7    -      -       -      +
     16E    A      3.7    26.5    -      -       +      +
     17E    A      3.6    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  ILE      4.1     2.4    +      -       -      -
     24B  ILE*     1.3    76.4    -      -       -      +
     26B  GLN*     1.3    64.0    +      -       -      +
     40B  LYS      3.4     3.8    -      -       -      -
     41B  LEU*     3.7    16.4    -      -       +      -
    105B  VAL*     5.0     0.2    -      -       +      -
    129B  VAL*     3.5    28.2    -      -       +      +
    132B  ILE*     3.5    39.5    -      -       +      +
    133B  ALA*     5.2     2.9    -      -       -      +
    136B  ASN*     5.1     0.6    -      -       -      +
    141B  ARG*     5.2     3.6    +      -       -      -
     17E    A      4.2    11.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  ILE*     3.9    17.6    -      -       +      +
     25B  ALA*     1.3    80.0    -      -       -      +
     27B  ILE*     1.3    65.9    +      -       -      +
     28B  GLU*     4.1     1.8    -      -       +      -
     39B  LEU*     3.4     9.5    -      -       -      +
     40B  LYS*     2.7    65.0    +      -       +      +
     42B  THR*     4.6     6.6    +      -       -      -
    129B  VAL*     4.2     2.8    -      -       -      +
    141B  ARG*     6.2     0.4    -      -       -      +
     17E    A      3.8    21.7    -      -       -      +
     18E    A      2.8    62.6    +      -       -      +
     19E    G      5.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  GLN*     1.3    77.7    -      -       -      +
     28B  GLU*     1.3    61.2    +      -       -      +
     29B  PRO*     3.9     0.2    -      -       -      +
     37B  HIS*     3.8    16.4    -      -       +      -
     38B  ARG      3.5     6.1    -      -       -      +
     39B  LEU*     3.8    15.5    -      -       +      -
    126B  CYS*     3.8    28.3    -      -       +      +
    129B  VAL*     3.9     8.2    -      -       +      +
    141B  ARG*     4.0    10.8    -      -       -      +
    143B  THR*     3.3    37.0    +      -       +      +
    144B  THR*     3.6    33.9    -      -       -      +
    145B  SER      3.7     3.6    -      -       -      +
    148B  VAL*     3.5    24.7    -      -       +      -
     18E    A      4.3     9.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  GLN*     4.1     2.2    -      -       +      -
     27B  ILE*     1.3    72.4    -      -       -      +
     29B  PRO*     1.3    73.1    -      -       +      +
     30B  ASN*     3.4     0.6    +      -       +      -
     37B  HIS*     3.2     3.4    -      -       -      -
     38B  ARG*     2.9    56.2    +      -       +      +
     40B  LYS*     4.6    15.7    -      -       +      +
     19E    G      5.7     6.1    -      -       +      +
     20E    G      6.2     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  ILE      3.9     0.9    -      -       -      +
     28B  GLU*     1.3    88.1    -      -       +      +
     30B  ASN*     1.3    65.2    +      -       -      +
     36B  LYS      3.5     0.9    -      -       -      +
     37B  HIS*     3.5    22.6    -      -       +      +
    143B  THR*     3.6    29.2    -      -       +      +
    147B  THR*     5.7     2.5    -      -       +      -
     19E    G      4.6    12.3    -      -       -      +
----------------------------------------------------------
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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