Contacts of the strand formed by residues 88 - 95 (chain D) in PDB entry 3QUM


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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  LYS*     4.0    12.3    -      -       +      -
     39D  GLN      3.9     3.8    -      -       -      -
     40D  ARG*     3.9    22.9    -      -       -      +
     41D  PRO*     4.8     4.0    -      -       -      -
     86D  ASP      3.5     3.0    +      -       -      +
     87D  SER*     1.3    78.5    -      -       -      +
     89D  VAL*     1.3    69.3    +      -       -      +
     90D  TYR*     3.7    18.8    -      -       +      -
    109D  THR*     3.4     5.4    -      -       -      -
    110D  VAL      3.0    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  LYS*     3.6     2.6    -      -       -      -
     39D  GLN*     3.2    36.5    +      -       +      +
     88D  ALA*     1.3    77.4    -      -       -      +
     90D  TYR*     1.3    75.1    +      -       -      +
     91D  TYR*     3.6    35.2    -      -       +      +
    106D  ALA      4.7     1.3    -      -       -      +
    107D  GLY*     3.7    21.3    -      -       -      -
    108D  THR      3.6     8.3    -      -       -      +
    109D  THR*     4.2    13.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  GLN*     3.1    11.8    -      -       -      +
     20D  MET*     3.9    18.4    -      -       +      -
     36D  TRP*     4.6     1.9    -      -       +      -
     37D  VAL      3.5     3.1    -      -       -      +
     38D  LYS*     3.6    31.8    +      -       +      +
     48D  ILE*     3.8    12.8    -      -       +      -
     80D  MET*     3.8    22.7    -      -       +      -
     82D  LEU*     3.7    29.6    -      -       +      +
     86D  ASP*     2.7    36.1    +      -       -      +
     88D  ALA*     3.7    19.3    -      -       +      -
     89D  VAL*     1.3    90.2    -      -       -      +
     91D  TYR*     1.3    61.9    +      -       -      +
    108D  THR*     2.8    36.1    +      -       -      +
    110D  VAL*     4.3    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 91 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  GLN*     4.1     2.6    +      -       -      -
     42C  GLN      3.6    14.1    +      -       -      -
     43C  PRO*     3.2    31.0    -      -       +      -
     44C  PRO*     4.3     2.9    -      -       +      -
      6D  GLN*     3.5     6.7    -      -       -      +
     36D  TRP*     3.4     7.8    -      -       -      +
     37D  VAL*     2.9    39.9    +      -       +      +
     39D  GLN*     3.7    30.0    +      -       +      -
     45D  LEU*     5.4     0.7    -      -       +      -
     89D  VAL*     3.6    30.8    -      -       +      +
     90D  TYR*     1.3    75.3    -      -       -      +
     92D  CYS*     1.3    62.1    +      -       -      +
    104D  TRP*     3.5    33.0    -      +       +      -
    105D  GLY      3.5    18.2    -      -       -      -
    106D  ALA      3.8    13.5    +      -       -      -
    107D  GLY*     3.9     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 92 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  LEU*     3.7     2.3    -      -       -      +
      6D  GLN*     3.3    13.6    +      -       -      +
     22D  CYS*     2.0    58.8    -      -       -      -
     34D  MET*     5.4     5.6    -      -       +      -
     35D  HIS      3.0    17.0    -      -       -      +
     36D  TRP*     3.4    25.6    -      -       +      +
     37D  VAL      4.9     0.2    -      -       -      +
     91D  TYR*     1.3    75.3    -      -       -      +
     93D  ALA*     1.3    61.0    +      -       -      +
    104D  TRP*     5.7     0.2    -      -       -      -
    105D  GLY      2.9    24.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 93 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  LEU*     3.9     5.8    -      -       -      -
     34D  MET*     3.9     2.9    -      -       -      -
     35D  HIS*     2.9    41.4    +      -       +      +
     37D  VAL*     6.1     1.4    -      -       +      +
     92D  CYS*     1.3    76.6    -      -       -      +
     94D  ARG*     1.3    56.2    +      -       -      +
    101D  PHE*     4.4    10.3    -      -       +      -
    103D  VAL      3.0    20.4    -      -       -      +
    104D  TRP*     3.5    36.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  VAL*     3.9    22.7    -      -       -      +
      4D  LEU*     4.7     4.0    -      -       +      -
     27D  TYR*     3.5    52.5    -      -       -      +
     32D  TYR*     3.7    46.5    +      -       +      -
     33D  TRP      4.2     6.1    -      -       -      +
     34D  MET*     4.4    15.0    -      -       +      -
     93D  ALA*     1.3    76.7    -      -       -      +
     95D  SER*     1.3    64.0    +      -       -      +
    101D  PHE*     3.3     4.9    -      -       -      -
    102D  ASP*     2.4    74.4    +      -       -      +
    103D  VAL*     3.1    17.1    +      -       +      +
    110Q  GLU*     5.0     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  TYR*     3.4     8.3    -      -       -      +
     33D  TRP*     3.3    20.6    +      -       -      +
     35D  HIS*     2.8    33.1    -      -       -      -
     94D  ARG*     1.3    81.3    -      -       -      +
     96D  GLY*     1.3    55.6    +      -       -      +
     98D  LEU*     4.6     2.3    +      -       -      -
     99D  TYR      3.4    22.4    -      -       -      -
    101D  PHE*     3.9     6.1    -      -       -      -
    102D  ASP*     3.6     4.3    -      -       -      -
     84Q  GLN*     2.5    29.3    +      -       -      +
----------------------------------------------------------
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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