Contacts of the strand formed by residues 1072 - 1078 (chain B) in PDB entry 6ZGI


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 GLU1072 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    713B  ALA*     3.9    13.8    -      -       +      +
    714B  ILE      3.3    10.5    -      -       -      +
    715B  PRO*     4.0     2.7    -      -       +      -
    716B  THR*     5.0     0.2    -      -       -      -
   1070B  ALA      4.1     3.1    +      -       -      +
   1071B  GLN*     1.3    74.7    -      -       -      +
   1073B  LYS*     1.3    61.2    +      -       -      +
   1321B  NAG      3.2    35.6    -      -       +      +
    892C  ALA*     4.6    12.7    -      -       -      +
    893C  ALA      3.9     9.3    -      -       -      +
    894C  LEU*     3.1    35.1    -      -       +      +
    895C  GLN*     5.1     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS1073 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    713B  ALA*     3.2     5.6    -      -       -      -
    714B  ILE      2.9    31.5    +      -       -      +
    716B  THR*     4.4    12.8    -      -       +      -
   1072B  GLU*     1.3    75.3    -      -       -      +
   1074B  ASN*     1.3    67.8    +      -       -      +
   1075B  PHE*     3.4    42.6    -      -       +      -
   1098B  ASN*     6.3     0.6    -      -       -      +
   1110B  TYR*     4.8    10.6    +      -       -      -
   1321B  NAG      4.4     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN1074 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711B  SER*     4.9     5.2    -      -       -      +
    712B  ILE      3.5     3.4    -      -       -      +
    713B  ALA*     4.1     6.2    -      -       -      +
   1073B  LYS*     1.3    80.8    -      -       -      +
   1075B  PHE*     1.3    71.6    +      -       -      +
   1321B  NAG      1.4    65.7    +      -       -      +
    895C  GLN*     3.0    24.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1075 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711B  SER*     3.4     6.4    +      -       -      -
    712B  ILE*     2.9    38.5    +      -       +      +
    714B  ILE*     3.6    32.8    -      -       +      -
    716B  THR*     5.7     0.2    -      -       +      -
   1073B  LYS*     3.4    59.5    -      -       +      -
   1074B  ASN*     1.3    75.2    -      -       -      +
   1076B  THR*     1.3    61.3    +      -       -      +
   1096B  VAL*     3.9    23.6    -      -       +      -
   1097B  SER      3.8    21.8    -      -       -      +
   1098B  ASN*     4.7     8.3    -      -       +      -
   1110B  TYR*     3.6    39.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR1076 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710B  ASN*     3.6    24.7    -      -       -      +
    711B  SER*     5.6     0.9    -      -       -      -
   1075B  PHE*     1.3    73.9    -      -       -      +
   1077B  THR*     1.3    61.8    +      -       -      +
   1096B  VAL*     3.4     4.2    -      -       -      +
   1097B  SER*     2.9    53.2    +      -       -      -
   1099B  GLY*     4.9     4.0    +      -       -      -
   1102B  TRP*     4.0     6.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR1077 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710B  ASN*     3.8    18.8    +      -       -      +
    711B  SER      3.9    18.6    -      -       -      +
    712B  ILE*     4.1    18.8    -      -       +      -
   1076B  THR*     1.3    75.9    -      -       -      +
   1078B  ALA*     1.3    67.6    +      -       -      +
   1094B  VAL*     3.9     2.6    -      -       -      +
   1095B  PHE      2.7    21.5    +      -       -      -
   1102B  TRP*     3.9     7.0    -      -       -      -
   1133B  VAL*     5.5     0.3    -      -       -      +
    897C  PRO*     4.0    11.9    -      -       +      -
    900C  MET*     3.5    36.6    -      -       -      +
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Residues in contact with ALA1078 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1077B  THR*     1.3    84.0    +      -       -      +
   1079B  PRO*     1.3    74.8    -      -       +      +
   1080B  ALA      4.0     6.3    -      -       -      +
   1081B  ILE*     5.2     0.4    -      -       +      -
   1090B  PRO*     6.0     0.2    -      -       -      +
   1095B  PHE*     3.7    21.2    +      -       +      +
   1102B  TRP*     3.7    21.5    -      -       +      -
   1131B  GLY      4.2     0.9    -      -       -      +
   1133B  VAL*     3.7    30.1    -      -       +      -
    900C  MET*     4.3     8.2    -      -       -      +
----------------------------------------------------------
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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