Contacts of the strand formed by residues 246 - 251 (chain A) in PDB entry 4NDH


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 PHE 246 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  TYR*     3.7    26.2    -      +       +      -
    202A  TRP*     3.7    26.9    -      +       -      -
    235A  ILE*     3.6    48.0    -      -       +      -
    239A  ALA*     4.0    13.2    -      -       +      -
    242A  SER*     4.9     0.9    -      -       -      -
    244A  LEU*     3.7    26.0    +      -       +      -
    245A  ARG*     1.3    85.4    +      -       -      +
    247A  ARG*     1.3    67.3    +      -       -      +
    248A  LEU*     4.6     4.3    -      -       +      +
    263A  VAL*     4.1     1.1    -      -       +      -
    264A  ILE      3.4    26.0    -      -       -      -
    265A  SER*     3.5    16.6    -      -       -      -
    266A  GLN*     4.1     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  ARG*     4.1    15.3    -      -       -      +
    246A  PHE*     1.3    79.4    -      -       -      +
    248A  LEU*     1.3    65.1    +      -       -      +
    262A  HIS      3.7     1.2    -      -       -      +
    263A  VAL*     3.7     1.9    -      -       -      -
    264A  ILE*     3.0    33.2    +      -       +      +
    266A  GLN*     3.3    36.4    +      -       +      +
    282A  PHE      3.3    24.2    +      -       -      -
    283A  ASN*     4.8     7.9    +      -       -      +
    284A  THR      5.3     2.2    +      -       -      -
    287A  PHE*     3.5    40.6    +      -       +      +
    289A  GLU*     2.9    36.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  HIS*     3.7    43.7    -      -       +      +
    231A  GLY*     4.1    10.1    -      -       -      -
    232A  GLU*     4.1    20.9    -      -       +      +
    235A  ILE*     4.0    20.9    -      -       +      -
    246A  PHE*     4.6     4.0    -      -       +      +
    247A  ARG*     1.3    84.7    -      -       -      +
    249A  GLY*     1.3    57.5    +      -       -      +
    261A  LEU*     4.3     7.2    -      -       +      -
    262A  HIS      3.2     6.3    -      -       -      +
    263A  VAL*     4.3    13.9    -      -       +      -
    287A  PHE*     3.9     3.0    -      -       -      -
    289A  GLU*     3.5    13.9    +      -       -      +
    290A  SER*     2.9    29.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  LEU*     1.3    75.6    -      -       -      +
    250A  TYR*     1.3    65.3    -      -       -      -
    261A  LEU*     3.4    10.4    -      -       -      +
    262A  HIS*     2.8    38.4    +      -       -      +
    287A  PHE*     3.4    16.2    -      -       -      -
    288A  LEU      3.1    12.1    -      -       -      -
    290A  SER      3.7     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  LEU*     3.7    29.8    -      -       +      -
    224A  LEU*     3.5    27.6    +      -       +      +
    227A  MET*     3.5    15.1    -      -       -      +
    249A  GLY*     1.3    76.5    -      -       -      -
    251A  HIS*     1.3    67.0    +      -       -      +
    259A  VAL*     4.2    13.7    -      -       +      -
    260A  HIS      3.2    31.0    -      -       -      -
    261A  LEU*     3.6    31.7    -      -       +      +
    262A  HIS*     4.7     2.7    -      -       -      -
    287A  PHE*     3.6     2.4    -      -       -      -
    288A  LEU*     2.7    43.5    +      -       +      +
    290A  SER*     4.1    15.3    +      -       -      -
    293A  VAL*     3.7    29.4    -      -       +      -
    294A  ILE*     6.1     1.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  LEU*     5.1     3.8    -      -       -      +
    250A  TYR*     1.3    78.3    -      -       -      +
    252A  ALA*     1.3    64.9    +      -       -      +
    253A  ILE      3.2     8.3    +      -       -      +
    254A  PRO*     4.0    12.1    -      -       +      +
    262A  HIS*     3.8    14.9    -      +       -      -
    281A  SER*     3.0    51.6    +      -       -      -
    282A  PHE*     3.5    30.6    -      +       -      -
    286A  TYR*     3.6    15.6    -      +       +      -
    287A  PHE*     4.0    10.1    -      +       -      -
    288A  LEU*     4.8     1.4    -      -       -      +
    401A  AMP      2.8    41.6    +      -       -      +
      1D    G      5.1     4.2    +      -       -      -
----------------------------------------------------------
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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