Contacts of the strand formed by residues 252 - 259 (chain B) in PDB entry 2NVX


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 SER 252 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242B  SER*     2.5    38.3    +      -       -      +
    250B  PHE*     3.5     3.0    +      -       -      -
    251B  ILE*     1.3    71.4    -      -       -      +
    253B  THR*     1.3    61.0    +      -       -      +
    254B  LEU*     3.6     2.6    +      -       -      +
    274B  PRO*     3.0    24.1    -      -       -      +
    359B  GLU*     2.9    38.0    +      -       -      -
    361B  LEU      5.0     0.5    +      -       -      -
    362B  PRO*     3.6    14.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 253 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239B  GLU*     5.2    11.7    -      -       +      +
    240B  ILE      3.8     4.3    -      -       -      +
    241B  ARG*     3.9    31.9    -      -       +      -
    251B  ILE*     3.6    18.4    +      -       +      +
    252B  SER*     1.3    74.2    +      -       -      +
    254B  LEU*     1.3    59.0    +      -       -      +
    255B  GLN*     4.3     3.5    +      -       -      +
    272B  THR      4.4     4.5    -      -       -      +
    273B  LEU      5.3     0.3    -      -       -      -
    274B  PRO*     4.9    10.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 254 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  ALA      3.5     4.7    -      -       -      +
    239B  GLU*     3.5     3.7    -      -       -      +
    240B  ILE*     3.3    41.9    +      -       +      +
    242B  SER*     5.1     1.8    -      -       -      +
    252B  SER*     3.6     5.6    +      -       -      +
    253B  THR*     1.3    75.1    -      -       -      +
    255B  GLN*     1.3    69.3    +      -       -      +
    256B  VAL*     4.3     7.0    -      -       +      -
    271B  ALA*     5.0     3.4    -      -       +      -
    272B  THR      3.1    25.6    -      -       -      +
    273B  LEU*     4.0    22.9    -      -       +      -
    274B  PRO*     5.1     3.4    -      -       +      -
    360B  PHE*     4.2    14.6    -      -       +      -
    361B  LEU*     4.1    16.6    -      -       +      +
    378B  LEU*     5.2     1.3    -      -       +      -
    381B  MET*     3.6    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 255 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228B  LYS*     6.2     1.6    -      -       -      +
    237B  VAL*     4.1    22.2    -      -       +      +
    238B  ALA      3.5     2.7    -      -       -      -
    239B  GLU*     4.0    25.1    +      -       +      +
    253B  THR*     4.3     3.8    +      -       -      +
    254B  LEU*     1.3    80.4    -      -       -      +
    256B  VAL*     1.3    62.4    +      -       -      +
    257B  LYS*     3.7    25.3    +      -       +      +
    271B  ALA*     3.3     5.9    -      -       -      +
    272B  THR*     2.8    49.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 256 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237B  VAL*     3.5     2.2    -      -       -      -
    238B  ALA*     2.8    44.7    +      -       +      +
    254B  LEU*     4.3     9.2    -      -       +      -
    255B  GLN*     1.3    76.5    -      -       -      +
    257B  LYS*     1.3    59.6    +      -       -      +
    269B  ILE*     4.3     9.4    -      -       +      -
    270B  LYS      3.9     4.0    -      -       -      +
    271B  ALA*     4.2     8.3    -      -       +      -
    282B  ILE*     4.9     2.0    -      -       +      -
    378B  LEU*     4.7     4.9    -      -       +      -
    381B  MET*     4.0    28.3    -      -       +      -
    382B  ILE*     3.6    31.9    -      -       +      +
    385B  LEU*     3.6    20.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 257 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  ILE*     3.5    38.8    -      -       +      -
    236B  HIS      3.7     5.4    -      -       -      +
    237B  VAL*     4.2    14.1    -      -       +      -
    255B  GLN*     3.7    28.0    +      -       +      +
    256B  VAL*     1.3    75.0    -      -       -      +
    258B  LEU*     1.3    60.2    +      -       -      +
    259B  TYR*     3.9    13.9    +      -       +      +
    269B  ILE*     3.1    17.2    -      -       -      +
    270B  LYS      2.9    27.5    +      -       -      +
    272B  THR*     2.9    27.8    +      -       -      +
    279B  ASP*     3.3    19.8    +      -       -      -
    385B  LEU*     4.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 258 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  ILE*     4.3     1.5    -      -       -      +
    235B  SER*     3.0    27.2    +      -       -      +
    236B  HIS*     2.9    25.8    +      -       +      +
    257B  LYS*     1.3    72.9    -      -       -      +
    259B  TYR*     1.3    74.6    +      -       -      +
    267B  ARG*     3.9    27.6    -      -       +      +
    268B  THR      3.2    19.7    -      -       -      +
    269B  ILE*     3.3    17.7    -      -       +      -
    313B  MET*     5.8     3.1    -      -       -      +
    385B  LEU*     3.7    17.7    -      -       +      -
    386B  LEU*     4.1    14.8    -      -       +      -
    389B  ALA*     3.8    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233B  PRO*     3.5    18.2    -      -       +      -
    234B  ILE*     3.3    31.6    -      -       +      +
    257B  LYS*     4.3    17.2    +      -       +      +
    258B  LEU*     1.3    83.9    -      -       -      +
    260B  GLY*     1.3    70.6    +      -       -      +
    267B  ARG*     3.8    11.0    -      -       -      +
    268B  THR*     3.3    30.2    +      -       +      +
    270B  LYS*     3.7    42.6    -      -       +      +
    279B  ASP*     2.3    34.2    +      -       -      +
----------------------------------------------------------
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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