Contacts of the strand formed by residues 78 - 83 (chain 2) in PDB entry 6Q8W


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 TYR 78 (chain 2).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     762  GLY      4.2     2.0    -      -       -      -
     772  LYS*     1.3   100.3    -      -       +      +
     792  HIS*     1.3    60.0    +      -       -      +
     802  LEU*     3.5    11.6    +      -       +      +
    1162  LEU*     2.7    62.2    +      -       +      +
    1172  PHE*     3.6    15.1    -      +       +      -
    1182  SER      3.2    15.1    +      -       -      +
    1362  VAL*     3.9    23.1    -      -       +      -
    1372  ASN*     3.3     3.6    -      -       -      +
    1572  LEU*     4.2    38.5    +      -       +      +
    1602  GLY*     5.0     8.3    -      -       -      -
    1612  LYS      5.1     2.9    +      -       -      -
    1632  LEU*     6.3     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 79 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     712  GLN*     3.7    22.6    +      -       +      -
     752  THR*     2.8    34.3    +      -       +      +
     772  LYS      3.9     0.2    -      -       -      -
     782  TYR*     1.3    67.4    -      -       -      +
     802  LEU*     1.3    63.4    +      -       -      +
     812  GLN*     3.2    32.7    +      -       +      +
    1082  PRO      5.0     3.4    -      -       -      -
    1182  SER*     3.1    12.7    -      -       -      -
    1192  VAL      3.8    22.9    -      -       -      -
    1202  GLN*     3.2    31.6    +      -       +      +
    1352  GLN      3.4     4.2    -      -       -      +
    1372  ASN*     2.4    39.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     782  TYR*     3.8    20.9    -      -       +      +
     792  HIS*     1.3    70.4    -      -       -      +
     812  GLN*     1.3    60.6    +      -       -      +
     822  VAL*     3.8     5.6    +      -       +      +
    1002  LEU*     4.4    34.3    -      -       +      -
    1042  LEU*     4.6     6.7    -      -       +      -
    1172  PHE*     4.0    24.0    -      -       +      -
    1182  SER      2.9    19.4    +      -       -      +
    1192  VAL*     3.6     4.5    -      -       +      -
    1202  GLN*     3.2    26.0    +      -       -      +
    1342  ILE*     5.0    12.3    -      -       +      -
    1352  GLN      3.8     3.6    -      -       -      -
    1362  VAL*     4.2    20.6    -      -       +      -
    1532  LEU*     5.2     6.3    -      -       +      -
    1542  LEU*     4.7     6.1    -      -       +      -
    1572  LEU*     4.8     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 81 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1371  GLU*     5.3     2.9    -      -       -      +
     692  TYR*     4.5    18.1    -      -       -      -
     792  HIS*     3.4    29.3    +      -       +      +
     802  LEU*     1.3    72.1    -      -       -      +
     822  VAL*     1.3    61.5    +      -       -      +
     832  CYS      3.9     0.5    +      -       -      -
    1202  GLN*     3.6    13.0    +      -       -      +
    1222  VAL*     3.9    26.4    -      -       +      +
    1252  LEU*     4.3     5.6    -      -       +      +
    1342  ILE*     3.3     6.8    -      -       -      +
    1352  GLN*     2.9    66.0    +      -       +      +
    1372  ASN*     3.6    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     802  LEU      4.3     7.6    -      -       -      +
     812  GLN*     1.3    74.6    -      -       -      +
     832  CYS*     1.3    72.7    +      -       -      +
     842  ALA*     3.5     1.4    +      -       +      -
     932  ALA*     5.0     3.6    -      -       +      +
     962  LEU*     4.2    24.7    -      -       +      -
     972  TRP*     4.0    36.1    -      -       +      -
    1002  LEU*     4.4    13.5    -      -       +      -
    1202  GLN      3.0    12.0    +      -       -      +
    1212  LYS*     3.5     6.7    -      -       +      +
    1222  VAL*     2.6    34.8    +      -       -      +
    1332  VAL      4.2     3.6    -      -       -      +
    1342  ILE*     4.2    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 83 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     812  GLN      3.9     1.8    +      -       -      -
     822  VAL*     1.3    83.2    -      -       -      +
     842  ALA*     1.3    61.9    -      -       -      +
     852  THR*     3.6    22.2    -      -       -      -
     882  CYS*     3.8    26.2    -      -       -      +
     932  ALA*     3.6    14.6    -      -       -      +
     962  LEU*     5.9     0.2    -      -       -      +
    1222  VAL      3.2     6.1    -      -       -      -
    1232  GLU      3.7     9.9    -      -       -      -
    1242  CYS*     3.9     2.7    -      -       -      -
    1252  LEU*     3.8    29.2    -      -       +      +
    1322  PRO*     5.7     1.0    -      -       -      +
    1332  VAL*     3.4    25.8    +      -       +      +
----------------------------------------------------------
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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