Contacts of the strand formed by residues 695 - 705 (chain A) in PDB entry 4QUM


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 695 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    664A  PHE*     4.4     2.7    -      -       +      -
    665A  ALA*     3.2    35.0    -      -       +      +
    670A  ASN*     3.4    47.1    -      -       +      +
    673A  LYS*     3.9    36.2    -      -       +      +
    674A  ASN*     2.8    28.6    +      -       -      -
    681A  PRO*     3.3    18.0    -      -       +      +
    686A  ARG*     3.5    26.7    -      -       -      +
    687A  VAL      5.4     0.4    -      -       -      -
    689A  LEU*     3.5    10.2    -      -       -      +
    694A  ASP*     1.3    79.4    -      -       -      +
    696A  ILE*     1.3    77.2    +      -       -      +
    697A  ASN*     3.8    10.5    -      -       -      -
    727A  GLN*     4.1     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 696 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673A  LYS*     5.8     1.3    -      -       -      -
    681A  PRO*     4.3     2.3    -      -       -      +
    686A  ARG*     4.8     1.9    -      -       -      +
    687A  VAL*     3.7    27.2    +      -       +      +
    689A  LEU*     3.8    18.4    -      -       +      -
    695A  TYR*     1.3    94.2    -      -       -      +
    697A  ASN*     1.3    71.1    +      -       +      +
    698A  ALA*     2.9    25.6    +      -       +      +
    717A  THR*     4.4     9.6    -      -       -      +
    718A  GLN*     6.0     2.2    -      -       +      +
    724A  THR*     5.1     7.4    -      -       +      +
    727A  GLN*     3.9    26.9    -      -       +      +
    728A  PHE*     4.0    20.6    -      -       +      +
    731A  VAL*     4.0    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 697 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673A  LYS      4.2     2.7    +      -       -      +
    674A  ASN*     2.8    30.1    +      -       -      +
    679A  VAL*     2.9    25.3    +      -       -      +
    681A  PRO*     3.8    11.1    -      -       -      +
    695A  TYR*     3.8     9.1    -      -       -      -
    696A  ILE*     1.3    74.0    -      -       -      +
    698A  ALA*     1.3    50.9    +      -       -      +
    717A  THR*     2.4    25.8    +      -       -      -
    718A  GLN*     3.3    42.5    +      -       -      +
    844A  ALA      5.7     0.2    -      -       -      -
    881A  ARG*     3.0    30.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 698 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681A  PRO*     3.9     2.8    -      -       -      +
    686A  ARG*     3.3     9.9    -      -       -      +
    687A  VAL*     3.0    41.9    +      -       +      -
    696A  ILE*     2.9    18.7    +      -       +      +
    697A  ASN*     1.3    77.5    +      -       -      +
    699A  SER*     1.3    63.6    +      -       -      +
    715A  ILE*     4.2     6.1    -      -       +      -
    716A  ALA      3.3     8.3    -      -       -      +
    717A  THR*     3.3    17.7    -      -       -      +
    731A  VAL*     5.6     1.3    -      -       +      -
    881A  ARG*     4.1     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 699 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681A  PRO*     3.7    12.8    -      -       -      +
    685A  THR*     3.3     9.4    +      -       -      -
    687A  VAL*     4.0     5.4    -      -       -      -
    698A  ALA*     1.3    75.2    +      -       -      +
    700A  TYR*     1.3    63.9    +      -       -      +
    701A  VAL*     3.6     1.4    +      -       -      +
    715A  ILE*     3.4     4.5    -      -       -      -
    716A  ALA      2.8    33.4    +      -       -      -
    880A  GLN      3.5    21.5    +      -       -      -
    881A  ARG*     2.9    40.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 700 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684A  THR      5.7     0.7    -      -       -      -
    685A  THR*     2.7    38.1    +      -       +      +
    686A  ARG      3.6    16.8    -      -       -      -
    687A  VAL*     3.7    17.7    -      -       +      +
    688A  LEU*     4.1    10.6    +      -       +      +
    699A  SER*     1.3    72.9    -      -       -      +
    701A  VAL*     1.3    65.1    +      -       -      +
    702A  ASN*     4.2    15.7    -      -       -      +
    714A  TYR      3.8     4.5    -      -       -      -
    715A  ILE*     4.0    21.5    -      -       +      -
    735A  GLN*     3.1    33.0    +      -       -      -
    837A  PRO*     5.8     2.2    -      -       +      -
    880A  GLN*     3.5    20.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 701 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    699A  SER      3.9     9.0    -      -       -      +
    700A  TYR*     1.3    81.2    -      -       -      +
    702A  ASN*     1.3    61.6    +      -       -      +
    703A  MET*     4.4    14.6    -      -       +      -
    714A  TYR*     2.8    57.1    +      -       +      +
    716A  ALA*     3.9    17.9    -      -       +      -
    853A  VAL*     4.7     1.6    -      -       +      -
    877A  MET*     4.5     7.4    -      -       +      +
    880A  GLN*     3.5    18.4    -      -       +      +
    881A  ARG*     4.0    22.0    -      -       +      +
    884A  MET*     4.3    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 702 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    700A  TYR*     4.6    16.2    -      -       -      +
    701A  VAL*     1.3    78.4    +      -       -      +
    703A  MET*     1.3    61.2    +      -       -      +
    704A  GLU*     3.9    10.6    -      -       -      +
    711A  VAL*     3.9    14.1    -      -       +      -
    712A  ASN      3.7     2.2    -      -       -      -
    713A  LYS*     3.3    34.9    -      -       -      +
    714A  TYR      4.0     2.1    +      -       -      +
    876A  LYS*     3.5     9.2    -      -       -      -
    880A  GLN*     2.6    35.3    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    701A  VAL*     4.4     2.9    -      -       +      -
    702A  ASN*     1.3    78.9    -      -       -      +
    704A  GLU*     1.3    64.2    +      -       -      +
    705A  ILE*     3.8     5.7    +      -       +      +
    710A  LEU      3.9     0.2    -      -       -      +
    711A  VAL*     3.4     2.5    -      -       -      -
    712A  ASN*     2.9    42.0    +      -       +      +
    714A  TYR*     4.0    11.7    -      -       +      -
    853A  VAL*     3.6    20.4    -      -       +      -
    857A  THR*     3.9    22.9    -      -       +      +
    873A  ILE*     3.6    44.2    -      -       +      +
    876A  LYS*     3.9    20.4    -      -       +      +
    877A  MET*     3.6    21.8    -      -       +      -
    880A  GLN*     4.2     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 704 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    702A  ASN*     4.4    11.7    -      -       -      +
    703A  MET*     1.3    74.9    -      -       -      +
    705A  ILE*     1.3    64.5    +      -       -      +
    706A  PRO*     3.3    20.4    -      -       +      +
    710A  LEU      3.4     7.4    -      -       -      +
    711A  VAL*     4.2    20.4    -      -       +      +
    857A  THR*     5.9     0.9    -      -       -      +
    876A  LYS*     3.3    35.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 705 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703A  MET*     4.4     5.4    -      -       +      +
    704A  GLU*     1.3    75.2    -      -       -      +
    706A  PRO*     1.3    68.8    -      -       +      +
    707A  ALA*     4.6     1.3    -      -       +      +
    708A  ALA*     2.9    19.0    +      -       +      +
    710A  LEU*     2.7    44.1    +      -       +      +
    712A  ASN*     4.5     7.0    -      -       -      +
    857A  THR*     4.2    24.2    -      -       +      +
    860A  CYS*     3.5    33.4    -      -       +      -
    861A  LEU*     3.6    28.9    -      -       +      -
    864A  ARG*     5.2     1.6    -      -       -      -
    866A  LEU*     3.9    18.8    -      -       +      -
----------------------------------------------------------
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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