Contacts of the strand formed by residues 682 - 689 (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 SER 682 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    677A  ILE      3.0    13.0    +      -       -      -
    678A  VAL*     4.1     6.7    -      -       -      +
    681A  GLY*     1.3    74.1    -      -       -      -
    683A  ASN*     1.3    61.8    +      -       -      +
    709A  TRP*     3.0    29.3    +      -       -      -
    710A  GLY*     3.8    10.4    +      -       -      -
    742A  GLU*     3.2    10.5    +      -       -      +
    745A  ILE*     3.1    28.5    -      -       -      +
    746A  SER*     3.5    15.7    +      -       -      -
   1001A  62C      3.4    10.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 683 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    656A  ASN*     3.5     7.9    -      -       -      +
    658A  THR*     3.3    13.9    -      -       +      +
    676A  LEU*     3.4     3.1    -      -       -      +
    677A  ILE*     2.8    33.6    +      -       -      +
    682A  SER*     1.3    75.6    +      -       -      +
    684A  ALA*     1.3    79.6    +      -       -      +
    706A  ASN*     2.6    27.9    +      -       -      -
    708A  GLU*     3.0    15.9    +      -       -      -
    709A  TRP*     2.9    33.4    +      -       -      -
   1001A  62C      3.2    34.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 684 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    658A  THR*     3.4     6.5    -      -       -      +
    674A  VAL*     5.3     1.3    -      -       +      -
    675A  GLY      3.0    13.5    -      -       -      +
    676A  LEU*     4.0     9.9    -      -       +      -
    683A  ASN*     1.3    88.3    +      -       -      +
    685A  CYS*     1.3    62.9    +      -       -      +
    706A  ASN*     4.2     0.2    -      -       -      -
    707A  MET*     2.9    38.5    +      -       -      +
    709A  TRP*     3.9    29.7    -      -       +      -
    838A  MET*     4.5     6.3    -      -       +      -
    841A  VAL*     5.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 685 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    658A  THR*     3.6    15.7    -      -       -      +
    659A  VAL*     3.5    35.0    -      -       +      -
    662A  MET*     4.2     6.5    -      -       -      -
    674A  VAL*     3.1     7.0    -      -       -      +
    675A  GLY*     2.7    45.2    +      -       -      -
    684A  ALA*     1.3    74.5    -      -       -      +
    686A  TYR*     1.3    59.9    +      -       -      +
    704A  CYS*     3.6    19.1    -      -       -      -
    705A  VAL      3.3    20.2    -      -       -      +
    706A  ASN*     4.2     2.5    -      -       -      -
    707A  MET*     4.5     2.0    -      -       -      -
    841A  VAL*     5.4     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 686 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    495A  MET*     3.2    20.1    -      -       +      +
    499A  LEU*     3.9     0.2    -      -       -      +
    511A  MET*     3.0    26.9    -      -       +      +
    662A  MET*     4.9     0.2    -      -       -      -
    673A  GLU      3.2     9.9    -      -       -      +
    674A  VAL*     4.1     1.1    -      -       +      -
    685A  CYS*     1.3    74.3    -      -       -      +
    687A  MET*     1.3    65.8    +      -       -      +
    688A  GLU*     2.6    29.0    +      -       -      -
    704A  CYS*     3.3     5.9    -      -       -      -
    705A  VAL*     3.0    51.0    +      -       +      -
    707A  MET*     4.5     6.3    -      -       +      -
    841A  VAL*     4.0    18.2    -      -       +      -
    844A  ARG*     3.2    20.7    +      -       +      -
    845A  ILE*     3.3    41.7    -      -       +      -
    848A  ASN*     4.9     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 687 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516A  VAL*     4.2     9.9    -      -       +      +
    517A  CYS      4.3    13.0    -      -       -      +
    519A  THR      6.3     0.4    -      -       -      +
    662A  MET*     3.9    15.3    -      -       -      -
    672A  CYS      5.6     0.4    -      -       -      +
    673A  GLU*     3.2    28.8    +      -       +      +
    686A  TYR*     1.3    76.2    -      -       -      +
    688A  GLU*     1.3    62.8    +      -       -      +
    689A  GLU*     4.8     1.2    -      -       -      +
    702A  ARG*     3.6    30.5    -      -       +      -
    703A  MET      3.5     1.8    -      -       -      -
    704A  CYS*     3.6    31.9    -      -       -      +
    845A  ILE*     4.3    12.0    -      -       -      +
    848A  ASN*     5.5     1.0    +      -       -      -
    849A  ARG*     3.8    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 688 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    499A  LEU*     3.8     8.5    -      -       +      -
    686A  TYR*     2.6    40.1    +      -       +      -
    687A  MET*     1.3    74.2    -      -       -      +
    689A  GLU*     1.3    83.2    +      -       -      +
    692A  ASN*     3.1    14.4    +      -       +      -
    693A  VAL*     3.9    14.4    -      -       +      -
    702A  ARG*     3.0    10.9    -      -       -      +
    703A  MET      2.7    36.5    +      -       -      +
    705A  VAL*     4.1    13.9    -      -       +      -
    844A  ARG*     2.6    30.4    +      -       -      -
    848A  ASN*     2.9    16.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 689 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    687A  MET      4.8     0.7    -      -       -      +
    688A  GLU*     1.3    82.0    -      -       -      +
    690A  MET*     1.3    57.1    +      -       -      +
    691A  ARG*     3.9    34.9    +      -       +      +
    692A  ASN*     2.7    39.9    +      -       -      +
    693A  VAL*     3.2    11.3    +      -       -      +
    701A  GLY      3.5     6.8    -      -       -      +
    702A  ARG*     2.5    43.2    +      -       -      -
    848A  ASN*     3.9    18.5    +      -       +      +
    849A  ARG*     3.5    17.2    +      -       -      +
----------------------------------------------------------
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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