Contacts of the strand formed by residues 702 - 706 (chain A) in PDB entry 5HG1


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 702 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    517A  CYS*     3.4    30.6    +      -       -      +
    673A  GLU*     4.6     3.4    +      -       -      -
    687A  MET*     3.6    27.8    -      -       +      -
    688A  GLU      3.0    11.0    -      -       -      +
    689A  GLU*     2.5    47.2    +      -       -      -
    690A  MET*     4.2     5.1    -      -       -      +
    701A  GLY*     1.3    78.2    -      -       -      -
    703A  MET*     1.3    60.3    +      -       -      +
    849A  ARG*     3.2    46.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 703 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513A  PRO*     3.7    24.9    -      -       +      -
    515A  TYR*     3.5    41.1    -      -       +      +
    516A  VAL      3.8     9.6    -      -       -      +
    517A  CYS*     3.4    21.8    -      -       -      -
    687A  MET*     4.1     2.7    -      -       -      -
    688A  GLU*     2.7    41.3    +      -       -      +
    690A  MET*     3.9    26.1    -      -       -      +
    693A  VAL*     4.6    11.9    -      -       +      -
    696A  VAL*     4.6    10.5    -      -       +      -
    702A  ARG*     1.3    74.3    -      -       -      +
    704A  CYS*     1.3    73.7    +      -       -      +
    705A  VAL*     3.6     1.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 704 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    514A  THR*     2.5    37.6    +      -       -      +
    516A  VAL*     3.0    18.4    +      -       +      +
    659A  VAL*     3.8    14.4    -      -       -      -
    662A  MET*     3.7    18.4    -      -       +      -
    685A  CYS*     3.6    35.7    -      -       -      -
    686A  TYR      3.3    10.1    -      -       -      -
    687A  MET*     3.6    17.8    -      -       -      -
    703A  MET*     1.3    79.6    -      -       -      +
    705A  VAL*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 705 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    499A  LEU*     4.6     4.5    -      -       +      -
    511A  MET*     3.7    25.6    -      -       +      +
    512A  LEU      3.1    13.0    -      -       -      +
    513A  PRO*     4.4     6.5    -      -       +      -
    514A  THR*     3.9     0.9    -      -       -      -
    685A  CYS*     3.3    19.0    -      -       -      +
    686A  TYR*     3.0    41.7    +      -       +      +
    688A  GLU*     4.1    12.6    -      -       +      -
    693A  VAL*     4.2    15.7    -      -       +      -
    703A  MET*     3.8    10.1    -      -       +      +
    704A  CYS*     1.3    80.1    -      -       -      +
    706A  ASN*     1.3    62.5    +      -       -      +
    707A  MET*     3.3     4.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 706 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  MET*     4.4     0.2    -      -       -      -
    512A  LEU*     2.7    48.2    +      -       +      +
    514A  THR*     3.3    19.2    -      -       +      +
    604A  PHE      5.5     1.4    +      -       -      -
    606A  CYS      5.7     2.2    +      -       -      +
    656A  ASN*     3.0    38.0    -      -       +      +
    658A  THR*     4.4     1.1    -      -       -      -
    659A  VAL*     4.8     1.1    -      -       +      -
    683A  ASN*     2.6    28.8    +      -       -      -
    685A  CYS*     4.2     8.1    -      -       -      -
    705A  VAL*     1.3    69.4    -      -       -      +
    707A  MET*     1.3    62.3    +      -       -      +
    708A  GLU*     3.1    18.0    +      -       -      +
----------------------------------------------------------
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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