Contacts of the strand formed by residues 495 - 500 (chain B) in PDB entry 1D0N


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 VAL 495 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413B  ASP*     5.7     1.3    -      -       -      +
    453B  TYR*     4.9     4.5    -      -       +      +
    461B  GLN      2.7    16.4    +      -       -      +
    462B  ILE*     4.0    22.0    -      -       +      -
    463B  ILE*     2.8    28.8    +      -       -      +
    493B  THR      5.2     0.4    -      -       -      +
    494B  PRO*     1.3    76.6    -      -       -      +
    496B  GLN*     1.3    62.9    +      -       -      +
    718B  THR*     3.3    31.0    -      -       +      -
    719B  VAL      3.7     7.0    -      -       -      +
    720B  VAL*     4.3     6.7    -      -       +      +
    721B  LYS      6.0     0.2    -      -       -      +
    724B  PHE      4.3    10.3    -      -       -      +
    726B  PRO*     3.9    36.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 496 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463B  ILE*     3.8     4.5    -      -       +      +
    480B  ALA      5.0     1.2    +      -       -      -
    483B  THR*     3.6    34.1    -      -       +      +
    484B  ALA*     4.2    19.8    -      -       -      +
    487B  ASP*     2.9    29.9    -      -       +      +
    494B  PRO      3.9     0.4    +      -       -      +
    495B  VAL*     1.3    74.5    -      -       -      +
    497B  SER*     1.3    60.7    +      -       -      +
    498B  ARG      4.3     0.2    +      -       -      -
    697B  LEU*     4.1    27.0    -      -       +      +
    717B  ILE      3.8     1.2    -      -       -      +
    718B  THR*     3.5     0.7    -      -       -      -
    719B  VAL*     2.7    56.6    +      -       +      +
    721B  LYS*     4.3     7.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 497 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462B  ILE*     4.8     4.7    -      -       -      -
    463B  ILE      2.9    11.9    +      -       -      +
    464B  TYR*     3.6    31.9    -      -       -      -
    465B  ASN*     2.8    30.2    +      -       -      +
    495B  VAL      4.1     0.4    +      -       -      -
    496B  GLN*     1.3    76.7    -      -       -      +
    498B  ARG*     1.3    64.6    +      -       -      +
    499B  VAL*     3.9     4.9    +      -       -      +
    505B  PRO*     5.1     1.7    -      -       -      +
    716B  PRO*     4.9     4.5    -      -       -      +
    717B  ILE      3.3     4.9    +      -       -      -
    718B  THR*     3.1    25.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 498 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465B  ASN*     3.7     9.6    -      -       +      +
    467B  GLN*     4.3    28.1    +      -       -      +
    496B  GLN      4.3     0.4    +      -       -      -
    497B  SER*     1.3    72.5    +      -       -      +
    499B  VAL*     1.3    66.7    +      -       -      +
    500B  VAL*     3.6    24.3    -      -       -      +
    697B  LEU*     4.3    31.5    -      -       +      +
    701B  LYS*     4.2    29.0    -      -       -      +
    713B  ARG      3.5    22.6    +      -       -      -
    714B  ARG*     4.4     1.0    +      -       -      +
    715B  THR      3.5    19.4    +      -       -      -
    716B  PRO*     3.5     4.6    -      -       -      +
    717B  ILE*     2.9    40.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 499 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464B  TYR*     4.2    20.4    -      -       +      -
    465B  ASN      2.9    16.3    +      -       -      +
    466B  TRP*     3.3    28.7    -      -       +      +
    467B  GLN*     2.9    28.4    +      -       -      +
    497B  SER*     4.1    11.4    -      -       -      +
    498B  ARG*     1.3    81.0    -      -       -      +
    500B  VAL*     1.3    71.5    +      -       -      +
    503B  LYS      4.4     3.6    -      -       -      +
    504B  GLU*     4.3     4.9    -      -       -      -
    505B  PRO*     4.0    27.8    -      -       +      -
    508B  LEU*     4.3     5.2    -      -       +      -
    716B  PRO*     4.6     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 500 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467B  GLN*     3.7    20.0    -      -       +      +
    468B  GLY      5.7     0.2    -      -       -      -
    469B  ALA*     5.5     7.4    -      -       +      +
    498B  ARG*     3.6    33.2    -      -       -      +
    499B  VAL*     1.3    85.8    -      -       -      +
    501B  GLN*     1.3    72.2    +      -       +      +
    503B  LYS*     3.0    19.5    +      -       -      +
    504B  GLU*     4.1     0.2    -      -       -      +
    714B  ARG*     3.8    43.1    +      -       +      -
----------------------------------------------------------
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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