Contacts of the strand formed by residues 88 - 100 (chain Q) in PDB entry 4R2G


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 ALA 88 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38Q  ARG*     4.1     5.2    -      -       -      -
     39Q  GLN      3.4    25.6    -      -       -      +
     40Q  SER*     3.4    16.4    -      -       -      +
     41Q  PRO*     4.7     2.5    -      -       -      -
     86Q  ASP      3.3     4.0    +      -       -      +
     87Q  THR*     1.3    76.8    -      -       -      +
     89Q  ILE*     1.3    64.9    +      -       -      +
     90Q  TYR*     3.3    22.1    -      -       +      -
    108Q  ALA*     5.3     0.2    -      -       -      -
    109Q  VAL      2.9    31.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 89 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41P  GLY*     4.6    26.0    -      -       -      +
     39Q  GLN*     3.5    32.4    +      -       +      +
     88Q  ALA*     1.3    78.3    -      -       -      +
     90Q  TYR*     1.3    57.8    +      -       -      +
     91Q  PHE*     3.2    44.8    -      -       +      -
    105Q  LYS      5.1     0.9    -      -       -      +
    106Q  GLY*     4.2     2.9    -      -       -      -
    107Q  THR      3.4    21.8    -      -       -      +
    108Q  ALA*     4.1    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 90 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6Q  GLU*     4.0     3.1    -      -       -      +
     18Q  LEU*     4.1    19.7    -      -       +      +
     20Q  VAL*     4.3    20.4    -      -       +      -
     36Q  TRP*     4.3     5.8    -      +       +      -
     37Q  ILE      3.9     2.9    -      -       -      -
     38Q  ARG*     2.8    43.5    +      -       +      +
     48Q  ILE*     4.4     6.3    -      -       +      -
     80Q  LEU*     3.9    26.9    -      -       +      -
     82Q  LEU*     3.7    15.4    -      -       +      +
     86Q  ASP*     2.7    28.8    +      -       -      +
     88Q  ALA*     3.3    23.3    -      -       +      -
     89Q  ILE*     1.3    72.9    -      -       -      +
     91Q  PHE*     1.3    59.6    +      -       -      +
    106Q  GLY*     3.4     1.9    -      -       -      -
    107Q  THR*     2.8    42.1    +      -       +      +
    109Q  VAL*     4.0    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 91 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38P  HIS*     4.8     2.5    -      -       -      -
     41P  GLY      5.3     0.7    -      -       -      -
     42P  GLN      3.7    17.0    -      -       -      -
     43P  ALA*     3.5    25.1    -      -       +      -
     44P  PRO*     4.1     9.4    -      -       +      -
      6Q  GLU*     3.2     4.9    -      -       -      +
     36Q  TRP*     3.3     8.7    -      -       -      -
     37Q  ILE*     2.8    45.2    +      -       +      +
     38Q  ARG      4.7     2.5    -      -       -      -
     39Q  GLN*     4.3    15.7    -      -       +      -
     45Q  LEU*     5.0     2.0    -      -       +      -
     89Q  ILE*     3.2    46.0    -      -       +      -
     90Q  TYR*     1.3    74.4    -      -       -      +
     92Q  CYS*     1.3    61.4    +      -       -      +
    103Q  TRP*     3.9    25.6    -      +       +      -
    104Q  GLY      3.7    16.6    -      -       -      -
    105Q  LYS      3.5    15.9    -      -       -      -
    106Q  GLY*     3.8     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 92 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4Q  LEU*     3.5    10.1    -      -       -      -
      6Q  GLU*     2.5    20.8    +      -       -      +
     22Q  CYS*     2.0    56.3    -      -       +      -
     35Q  THR      3.2     6.7    -      -       -      +
     36Q  TRP*     3.8    21.0    -      -       +      -
     78Q  LEU*     4.5     9.2    -      -       +      -
     91Q  PHE*     1.3    77.7    -      -       -      +
     93Q  ALA*     1.3    65.1    +      -       -      +
    104Q  GLY      2.9    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 93 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4Q  LEU*     3.5     5.0    -      -       -      +
     34Q  TRP*     3.6     9.1    -      -       -      -
     35Q  THR*     2.9    35.2    +      -       +      +
     37Q  ILE*     4.9     2.2    -      -       +      -
     92Q  CYS*     1.3    78.3    -      -       -      +
     94Q  THR*     1.3    67.3    +      -       -      +
     95Q  ALA      3.5     0.2    +      -       -      -
    100Q  MET*     4.2    12.3    -      -       -      +
    102Q  VAL      3.1    17.3    -      -       -      +
    103Q  TRP*     3.9    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 94 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2Q  VAL*     4.5     1.7    -      -       -      +
      4Q  LEU*     4.1     2.7    -      -       -      +
     32Q  TYR*     4.1    16.1    -      -       +      -
     33Q  TYR      3.8     7.2    -      -       -      +
     34Q  TRP*     3.7    20.6    -      -       -      -
     93Q  ALA*     1.3    75.2    -      -       -      +
     95Q  ALA*     1.3    64.2    +      -       -      +
     96Q  ARG*     3.2    41.1    -      -       +      +
    100Q  MET*     3.3    27.0    +      -       -      -
    101Q  ASP*     3.3    13.8    +      -       -      +
    102Q  VAL*     2.9    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 95 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33Q  TYR*     3.1    47.9    +      -       +      +
     34Q  TRP      4.7     0.7    -      -       -      +
     35Q  THR*     3.8    24.9    -      -       +      -
     47Q  TRP*     5.8     1.1    -      -       +      -
     50Q  TYR*     5.1     5.6    -      -       +      -
     93Q  ALA      3.5     0.4    +      -       -      -
     94Q  THR*     1.3    74.5    -      -       -      +
     96Q  ARG*     1.3    68.4    +      -       -      +
    100Q  TYR*     3.5    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 96 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2Q  VAL*     5.6     0.2    -      -       -      +
     32Q  TYR*     4.6    14.6    -      -       -      -
     33Q  TYR*     5.5     0.4    -      -       -      -
     94Q  THR*     3.2    22.3    -      -       +      +
     95Q  ALA*     1.3    77.2    -      -       -      +
     97Q  ARG*     1.3    60.9    -      -       -      +
     98Q  GLY      3.5     2.0    +      -       -      -
    100Q  TYR*     2.9    76.5    +      -       +      +
    101Q  ASP*     2.6    40.5    +      -       -      +
    102Q  VAL*     4.1     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 97 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  MAN      4.3     9.5    +      -       -      -
     33Q  TYR*     3.7    34.0    +      -       +      -
     54Q  ARG*     5.2    11.0    -      -       -      +
     95Q  ALA      4.2     0.6    +      -       -      -
     96Q  ARG*     1.3    71.2    -      -       -      +
     98Q  GLY*     1.3    59.2    +      -       -      +
     99Q  GLN      4.2     0.2    +      -       -      -
    100Q  TYR*     3.3    98.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 98 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  MAN      4.5     5.2    -      -       -      -
     96Q  ARG      3.5     4.2    +      -       -      -
     97Q  ARG*     1.3    75.2    -      -       -      +
     99Q  GLN*     1.3    60.3    +      -       -      +
    100Q  TYR*     2.9    69.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 99 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  MAN      5.9     2.3    -      -       -      -
      9G  MAN      3.0    48.0    +      -       -      +
     98Q  GLY*     1.3    75.0    -      -       -      +
    100Q  TYR*     1.3   154.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 100 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4G  MAN      2.9    38.3    +      -       -      -
      5G  MAN      2.9    51.9    +      -       -      -
     30P  SER*     4.5     6.6    -      -       -      -
     31P  ARG      2.9    22.4    +      -       -      +
     32P  ALA*     4.2     3.8    -      -       +      -
     50P  ASN*     4.6     3.1    -      -       -      -
     66P  ASP*     2.8    29.6    +      -       -      +
     99Q  GLN*     1.3    69.3    -      -       -      +
    100Q  PHE*     1.3   159.8    +      -       -      +
----------------------------------------------------------
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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