Contacts of the strand formed by residues 88 - 94 (chain K) 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 K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38K  LYS*     4.4     6.7    -      -       +      -
     39K  GLN      3.3     4.5    -      -       -      +
     40K  ARG*     3.1    39.0    -      -       +      +
     41K  PRO*     4.3     7.2    -      -       -      -
     86K  ASP      3.0     7.1    +      -       -      +
     87K  SER*     1.3    76.4    -      -       -      +
     89K  VAL*     1.3    67.4    +      -       -      +
     90K  TYR*     3.6    12.8    -      -       +      -
    108K  SER*     4.3     3.6    -      -       -      -
    109K  VAL      3.3    23.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 89 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38K  LYS*     3.5     2.1    -      -       -      -
     39K  GLN*     2.8    42.9    +      -       +      +
     41K  PRO*     6.4     0.9    -      -       +      -
     88K  ALA*     1.3    80.3    -      -       -      +
     90K  TYR*     1.3    64.6    +      -       -      +
     91K  PHE*     3.9    26.4    +      -       +      -
    105K  GLN      5.3     0.7    -      -       -      +
    106K  GLY*     4.4     4.9    -      -       -      -
    107K  THR      3.9    22.9    -      -       -      +
    108K  SER*     3.9    17.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 90 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6K  GLN*     2.9    19.1    -      -       -      +
     20K  ILE*     5.3    11.2    -      -       +      +
     36K  TRP*     5.1     4.4    -      -       +      -
     37K  VAL      3.2     9.0    -      -       -      +
     38K  LYS*     3.7    34.1    +      -       +      -
     48K  ILE*     3.9    23.6    -      -       +      -
     63K  PHE*     5.5     1.6    -      +       -      -
     80K  MET*     3.9    19.5    -      -       +      -
     82K  LEU*     3.5    31.2    -      -       +      +
     86K  ASP*     2.8    32.3    +      -       -      +
     88K  ALA      3.6    18.8    -      -       -      -
     89K  VAL*     1.3    74.6    -      -       -      +
     91K  PHE*     1.3    63.5    +      -       -      +
    107K  THR*     3.2    24.6    +      -       -      +
    109K  VAL*     4.3    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 91 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6K  GLN*     3.6     3.6    -      -       -      +
     36K  TRP*     3.3     7.2    -      -       -      -
     37K  VAL*     2.8    55.5    +      -       +      +
     39K  GLN*     3.1    35.2    -      -       +      -
     45K  LEU*     5.1     1.3    -      -       +      -
     89K  VAL*     3.9    21.3    -      -       +      -
     90K  TYR*     1.3    75.3    -      -       -      +
     92K  CYS*     1.3    63.1    +      -       -      +
    103K  TRP*     3.8    23.1    -      +       +      -
    104K  GLY      3.7    17.3    -      -       -      -
    105K  GLN      3.8    16.6    -      -       -      -
    106K  GLY*     4.0     4.7    -      -       -      -
     38M  GLN*     4.2     3.4    -      -       -      -
     42M  GLN      4.4     4.3    -      -       -      -
     43M  SER*     3.8    23.6    -      -       -      -
     44M  PRO*     3.9    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 92 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4K  LEU*     4.3     8.5    -      -       -      -
      6K  GLN*     2.6    37.6    -      -       -      +
     22K  CYS*     2.1    44.6    -      -       -      -
     34K  MET*     3.5    15.5    -      -       +      -
     35K  ASN      3.2     7.6    -      -       -      +
     36K  TRP*     3.7    20.7    -      -       +      -
     91K  PHE*     1.3    78.5    -      -       -      +
     93K  ALA*     1.3    65.6    +      -       -      +
    103K  TRP*     3.7     1.6    -      -       -      -
    104K  GLY      3.5    19.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 93 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4K  LEU*     4.4     1.3    -      -       -      -
     34K  MET*     3.4     7.3    -      -       -      -
     35K  ASN*     2.6    44.9    +      -       -      +
     37K  VAL*     5.5     2.7    -      -       +      -
     91K  PHE      5.0     0.9    -      -       -      +
     92K  CYS*     1.3    80.2    -      -       -      +
     94K  ARG*     1.3    58.6    +      -       -      +
    100K  PHE*     4.5    14.4    -      -       +      +
    102K  TYR      3.1    13.5    -      -       -      +
    103K  TRP*     3.9    30.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 94 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2K  VAL*     4.6     6.6    -      -       -      +
      4K  LEU*     4.5     4.7    -      -       +      +
     27K  TYR*     3.4    53.1    -      -       -      +
     32K  SER*     3.3    22.8    +      -       -      -
     33K  TRP      3.5    12.3    -      -       -      +
     34K  MET*     4.3     7.2    -      -       +      -
     35K  ASN*     4.3     0.2    -      -       -      -
     93K  ALA*     1.3    73.4    -      -       -      +
     95K  ASP*     1.3    72.0    +      -       -      +
     96K  GLY*     5.0     1.3    -      -       -      -
    100K  PHE      4.2     3.1    -      -       -      -
    101K  ASP*     2.4    66.2    +      -       -      +
    102K  TYR*     2.9    39.0    +      -       +      +
----------------------------------------------------------
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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