Contacts of the strand formed by residues 250 - 254 (chain A) in PDB entry 2VZ3


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 THR 250 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  THR*     4.7     3.6    -      -       -      +
    224A  HIS*     4.0     0.2    -      -       -      -
    240A  VAL*     3.8    29.6    -      -       +      -
    241A  VAL      3.3     5.8    -      -       -      +
    242A  THR*     3.7     6.8    -      -       +      +
    249A  LYS*     1.3    81.0    +      -       -      +
    251A  SER*     1.3    69.7    +      -       -      +
    252A  LEU*     4.0    11.4    -      -       +      -
    262A  PRO*     4.3     1.6    -      -       -      +
    263A  GLY*     2.9    30.5    +      -       -      +
    264A  PRO*     2.7    31.3    +      -       +      +
    265A  ASP*     4.6     0.2    -      -       -      +
    266A  MET*     3.9     3.8    -      -       -      +
    302A  TYR*     5.2     0.9    -      -       +      -
    309A  TRP*     2.9    19.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  THR*     2.7    35.8    +      -       -      -
    224A  HIS*     2.7    26.6    +      -       -      +
    226A  MET*     3.7    19.4    -      -       -      -
    239A  ILE      3.4     1.7    -      -       -      +
    240A  VAL*     3.7     1.9    -      -       -      -
    241A  VAL*     2.8    34.2    +      -       -      +
    250A  THR*     1.3    73.5    -      -       -      +
    252A  LEU*     1.3    62.9    +      -       -      +
    253A  TYR      4.2     0.2    -      -       -      -
    260A  TRP*     3.9     6.3    -      -       -      -
    261A  ILE      4.0     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  ASP*     5.0     0.4    -      -       -      +
    238A  GLN*     3.5    28.7    -      -       +      +
    239A  ILE      3.3     2.5    -      -       -      +
    240A  VAL*     3.8    25.1    -      -       +      -
    250A  THR*     4.0    12.3    -      -       +      -
    251A  SER*     1.3    81.0    -      -       -      +
    253A  TYR*     1.3    59.6    +      -       -      +
    254A  ASP      3.9     0.7    +      -       -      -
    259A  SER      3.8     0.3    -      -       -      +
    260A  TRP*     3.2     7.4    -      -       -      -
    261A  ILE*     2.7    57.1    +      -       +      +
    262A  PRO      4.1    14.6    -      -       -      +
    263A  GLY*     4.1    10.3    -      -       -      -
    264A  PRO*     5.3     0.4    -      -       +      -
    302A  TYR*     3.6    25.1    -      -       +      +
    307A  LYS*     6.1     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  GLU*     2.9    41.1    +      -       +      -
    184A  LEU*     3.9    10.5    -      -       +      -
    217A  ARG*     5.2     0.7    -      -       -      -
    237A  GLY      4.3     0.2    -      -       -      +
    238A  GLN*     3.4     6.4    -      -       -      -
    239A  ILE*     2.8    64.2    +      -       +      +
    252A  LEU*     1.3    72.1    -      -       -      +
    254A  ASP*     1.3    67.9    +      -       -      +
    255A  SER*     3.5    25.9    +      -       -      -
    258A  ASP*     2.8    40.8    +      -       -      +
    259A  SER      3.7     7.4    -      -       -      -
    260A  TRP*     3.6    46.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASP 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  ASN      4.9     2.1    -      -       -      +
    237A  GLY      4.7     2.8    -      -       -      +
    238A  GLN*     3.0    38.0    +      -       -      +
    252A  LEU      3.9     0.8    +      -       -      -
    253A  TYR*     1.3    74.4    -      -       -      +
    255A  SER*     1.3    57.5    +      -       -      +
    256A  SER*     2.8    28.2    +      -       -      -
    257A  SER*     2.9    28.0    +      -       -      +
    258A  ASP*     2.9    24.9    +      -       -      -
    259A  SER*     2.9    21.8    +      -       -      +
    261A  ILE*     4.3     7.4    -      -       +      -
----------------------------------------------------------
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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