Contacts of the strand formed by residues 554 - 558 (chain A) in PDB entry 1N7D


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 LEU 554 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    521A  ILE*     5.9     2.9    -      -       +      -
    545A  ILE*     5.7     5.4    -      -       +      -
    546A  THR      4.5     4.3    -      -       -      +
    547A  LEU*     4.6     9.8    -      -       +      +
    552A  GLY      3.8     0.2    +      -       -      -
    553A  ARG      1.3    67.1    -      -       -      -
    555A  TYR*     1.3    54.1    -      -       -      +
    556A  TRP*     4.2     8.7    -      -       +      -
    565A  SER      4.0     0.9    -      -       -      -
    566A  SER*     2.2    43.1    -      -       -      -
    567A  ILE*     2.0    48.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 555 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    545A  ILE*     3.3     6.6    -      -       -      +
    546A  THR*     3.2    31.7    +      -       +      +
    547A  LEU*     5.8     0.4    -      -       -      -
    553A  ARG      3.8     2.2    +      -       -      +
    554A  LEU*     1.3    74.3    -      -       -      +
    556A  TRP*     1.3    56.6    +      -       -      +
    564A  ILE*     5.0     6.1    -      -       +      -
    565A  SER      3.5     4.7    -      -       -      -
    566A  SER*     4.1     6.3    -      -       -      +
    590A  LEU*     2.6    32.3    -      -       +      +
    592A  VAL*     4.1    15.0    -      -       +      -
    597A  VAL*     6.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 556 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    521A  ILE*     4.8    14.6    -      -       +      -
    535A  VAL*     4.3    26.9    -      -       +      -
    537A  GLU      6.0     1.3    -      -       -      -
    538A  ASN*     5.9     4.3    -      -       -      -
    539A  ILE*     4.9    10.0    -      -       +      +
    542A  PRO*     5.2     4.9    -      -       +      -
    543A  ASN      5.4     1.1    -      -       -      +
    544A  GLY      4.1     0.9    -      -       -      +
    545A  ILE*     3.5    25.4    -      -       +      -
    554A  LEU*     4.1     9.9    -      -       +      -
    555A  TYR*     1.3    76.6    -      -       -      +
    557A  VAL*     1.3    70.3    +      -       -      +
    558A  ASP*     2.7    41.7    +      -       -      -
    564A  ILE*     3.0    20.8    -      -       -      +
    565A  SER*     2.7    59.4    +      -       -      +
    566A  SER      4.1     0.2    -      -       -      -
    567A  ILE*     3.5    30.7    -      -       +      -
    574A  ARG*     4.3     9.6    -      -       +      -
    590A  LEU*     3.2     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 557 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    542A  PRO      3.4     0.5    -      -       -      -
    543A  ASN*     2.5    69.5    +      -       +      +
    544A  GLY      3.6     3.6    +      -       -      +
    556A  TRP*     1.3    78.9    -      -       -      +
    558A  ASP*     1.3    60.6    +      -       -      +
    563A  SER      4.0     2.0    -      -       -      +
    564A  ILE*     4.0    11.0    -      -       +      -
    587A  PRO*     3.1    36.6    -      -       +      -
    589A  SER      3.6     8.7    -      -       -      +
    590A  LEU*     3.1    31.0    -      -       +      -
    599A  TRP*     4.9     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 558 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    538A  ASN      4.6     3.5    -      -       -      +
    539A  ILE*     3.6    17.1    -      -       -      +
    541A  TRP      3.4     6.5    -      -       -      +
    542A  PRO*     4.0     2.8    -      -       -      +
    556A  TRP*     2.7    39.7    +      -       -      -
    557A  VAL*     1.3    75.4    -      -       -      +
    559A  SER*     1.3    61.6    +      -       -      +
    561A  LEU*     2.9    57.5    -      -       +      +
    563A  SER*     2.9    26.3    +      -       -      +
    564A  ILE      5.5     0.2    +      -       -      -
    565A  SER*     5.0     1.9    +      -       -      -
    587A  PRO*     3.5     6.1    -      -       -      +
----------------------------------------------------------
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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