Contacts of the strand formed by residues 97 - 100 (chain H) in PDB entry 1A4J


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 97 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  GLY      3.6     0.3    -      -       -      +
     34H  MET*     3.7     4.9    -      -       -      -
     35H  ASN*     2.8    41.5    +      -       +      +
     37H  VAL*     3.6    24.0    -      -       +      -
     95H  PHE*     4.0     6.5    -      -       +      +
     96H  CYS*     1.3    78.6    -      -       -      +
     98H  GLN*     1.3    61.3    +      -       -      +
    106H  PHE*     3.5    43.3    -      -       +      -
    108H  TYR      3.3    14.4    -      -       -      +
    109H  TRP*     3.5    34.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 98 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2H  VAL*     2.9    35.4    -      -       +      +
      4H  LEU*     3.8    12.6    -      -       +      +
     24H  ALA*     3.6    24.4    -      -       -      +
     25H  SER*     5.9     0.2    +      -       -      -
     28H  THR*     4.5    12.3    +      -       -      +
     29H  PHE*     4.5     9.9    +      -       -      +
     32H  TYR*     3.7    36.8    -      -       +      +
     33H  GLY      3.6     3.4    -      -       -      +
     34H  MET*     4.2    18.9    -      -       +      +
     97H  VAL*     1.3    72.8    -      -       -      +
     99H  ALA*     1.3    60.8    +      -       -      +
    106H  PHE*     3.7     2.1    -      -       -      -
    107H  ASP*     3.0    24.1    +      -       -      +
    108H  TYR*     2.8    20.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 99 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32H  TYR*     3.1    12.6    -      -       -      -
     33H  GLY*     2.7    35.2    +      -       -      +
     35H  ASN*     3.4    25.4    -      -       -      +
     98H  GLN*     1.3    74.4    -      -       -      +
    100H  GLU*     1.3    62.9    +      -       -      +
    101H  ARG      4.1     0.9    +      -       -      -
    104H  ARG      5.7     0.9    -      -       -      -
    105H  THR      3.1    16.2    -      -       -      +
    106H  PHE*     4.2    12.3    -      -       +      -
    107H  ASP*     4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 100 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31H  ASN      4.9     6.3    -      -       -      +
     32H  TYR*     4.0    14.8    -      -       +      -
     99H  ALA*     1.3    74.7    -      -       -      +
    101H  ARG*     1.3    57.1    +      -       -      +
    102H  LEU*     3.0    36.9    +      -       -      +
    103H  ARG*     2.4    59.9    +      -       -      +
    104H  ARG*     2.7    34.5    +      -       -      -
    105H  THR*     3.2     3.4    +      -       -      +
    107H  ASP*     3.1    21.6    +      -       -      +
----------------------------------------------------------
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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