Contacts of the strand formed by residues 461 - 467 (chain A) in PDB entry 2DH3


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 ARG 461 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453A  ILE*     5.2     6.7    -      -       +      +
    454A  ARG      3.5     4.5    -      -       -      +
    455A  HIS*     3.4    30.4    -      -       +      +
    457A  ASP      5.8     0.7    -      -       -      -
    459A  ASN      3.6     5.3    +      -       -      +
    460A  GLU*     1.3    75.0    -      -       -      +
    462A  PHE*     1.3    65.1    +      -       -      +
    485A  SER*     4.0    13.9    +      -       -      -
    486A  ALA      3.9     9.9    +      -       -      -
    487A  SER      3.2    21.6    +      -       -      -
    488A  LEU*     5.4     0.2    -      -       -      +
    489A  PRO*     4.8     2.2    -      -       -      +
    524A  ARG*     3.4     4.3    -      -       -      -
    525A  PHE*     2.8    73.7    +      -       +      +
    526A  PRO      2.9    27.9    +      -       -      -
    527A  TYR*     3.0    38.7    +      -       -      +
    529A  ALA*     4.7     3.0    -      -       -      +
    327B  ASN*     3.1    21.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 462 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428A  GLN*     4.0     2.7    -      -       +      -
    432A  GLU*     3.7    49.4    -      -       +      -
    434A  SER*     4.0    13.7    -      -       -      -
    435A  LEU*     4.1    22.4    -      -       +      -
    452A  TYR      3.9     0.3    -      -       -      +
    453A  ILE*     3.4     6.9    -      -       -      +
    454A  ARG*     2.9    43.7    +      -       +      +
    460A  GLU*     3.8    19.1    -      -       +      -
    461A  ARG*     1.3    77.9    -      -       -      +
    463A  LEU*     1.3    59.8    +      -       -      +
    464A  VAL*     5.3     1.6    -      -       +      -
    495A  LEU*     4.0    19.3    -      -       +      -
    522A  LEU*     4.3    21.3    -      -       +      -
    523A  LEU      3.3    11.9    -      -       -      +
    524A  ARG*     4.0    24.2    -      -       +      -
    525A  PHE*     4.5     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 463 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  PHE*     3.7    14.6    -      -       +      -
    452A  TYR      3.5     6.5    -      -       -      +
    453A  ILE*     3.6    23.8    -      -       +      -
    462A  PHE*     1.3    74.3    -      -       -      +
    464A  VAL*     1.3    79.1    +      -       -      +
    465A  VAL*     4.4    10.1    -      -       +      -
    477A  LEU*     3.9    19.1    -      -       +      -
    488A  LEU*     5.5     0.7    -      -       +      -
    510A  LEU*     3.6    36.3    -      -       +      -
    513A  LEU*     5.9     0.7    -      -       +      -
    521A  LEU      3.8     1.0    -      -       -      +
    522A  LEU*     3.5     4.9    -      -       -      +
    523A  LEU*     2.7    49.1    +      -       +      +
    525A  PHE*     3.7    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 464 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  LEU*     4.5     5.8    -      -       +      -
    358A  THR*     3.7    18.8    -      -       +      +
    451A  SER*     3.1    24.2    -      -       -      -
    452A  TYR*     3.0    56.6    +      -       +      +
    454A  ARG*     5.4     3.6    -      -       +      -
    462A  PHE*     5.3     2.5    -      -       +      -
    463A  LEU*     1.3    78.9    -      -       -      +
    465A  VAL*     1.3    71.7    +      -       -      +
    466A  LEU*     3.8    26.9    -      -       +      -
    521A  LEU      3.5     7.0    -      -       -      +
    522A  LEU*     4.1    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 465 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449A  LEU*     4.2    15.3    -      -       +      -
    450A  PHE      3.9     0.7    -      -       -      -
    451A  SER*     3.5    19.1    -      -       -      +
    463A  LEU*     4.4    16.4    -      -       +      -
    464A  VAL*     1.3    81.4    -      -       -      +
    466A  LEU*     1.3    61.5    +      -       -      +
    467A  ASN      4.2     0.2    -      -       -      -
    475A  ALA*     4.2    21.3    -      -       +      -
    477A  LEU*     4.5    11.2    -      -       +      -
    513A  LEU*     4.6    10.3    -      -       +      -
    515A  LEU*     4.3    13.2    -      -       +      +
    519A  GLU      4.0     1.4    -      -       -      +
    520A  GLY*     3.3     4.9    -      -       -      -
    521A  LEU*     3.0    46.9    +      -       +      +
    523A  LEU*     4.8     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 466 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  LEU*     3.7    23.3    -      -       +      +
    354A  LEU*     3.6    36.1    -      -       +      -
    355A  MET*     3.7    35.2    -      -       +      -
    449A  LEU*     3.3    10.1    -      -       -      -
    450A  PHE*     3.2    50.7    +      -       +      +
    452A  TYR*     4.4     1.3    -      -       +      -
    464A  VAL*     3.8    14.8    -      -       +      -
    465A  VAL*     1.3    77.0    -      -       -      +
    467A  ASN*     1.3    60.8    +      -       -      +
    468A  PHE*     3.7    21.5    -      -       +      -
    519A  GLU      4.0     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 467 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  LEU*     3.3     9.9    -      -       -      +
    448A  GLY      4.8     0.9    -      -       -      +
    449A  LEU*     3.8    12.3    -      -       +      +
    465A  VAL      4.2     0.4    -      -       -      -
    466A  LEU*     1.3    71.4    -      -       -      +
    468A  PHE*     1.3    62.3    +      -       -      +
    469A  GLY*     3.1    18.8    +      -       -      +
    471A  VAL      3.0    24.9    +      -       -      +
    473A  LEU*     3.7    24.0    -      -       -      +
    515A  LEU*     3.7    18.8    +      -       +      +
    516A  GLU      3.6    17.9    +      -       -      +
    517A  PRO*     4.2     1.2    -      -       -      +
    518A  HIS*     3.2    23.1    -      -       -      -
    519A  GLU      3.0    21.2    +      -       -      +
----------------------------------------------------------
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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