Contacts of the strand formed by residues 192 - 198 (chain M) 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 TYR 192 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117M  ILE*     5.8     1.0    -      -       -      +
    132M  VAL*     5.1    12.6    -      -       +      -
    148M  TRP*     6.2     4.5    -      +       +      -
    149M  LYS      4.0     3.6    -      -       -      -
    150M  ILE*     4.5    20.0    -      -       +      +
    179M  LEU*     5.0    11.2    -      -       +      -
    181M  LEU*     4.0    21.9    -      -       +      +
    186M  TYR*     2.5    58.7    +      +       -      -
    189M  HIS*     3.9    33.6    +      -       +      -
    190M  ASN      3.9     7.6    -      -       -      -
    191M  SER*     1.3    78.3    +      -       -      +
    193M  THR*     1.3    54.7    +      -       -      +
    208M  SER*     2.8    26.9    -      -       -      -
    209M  PHE*     3.4    41.4    +      +       +      -
----------------------------------------------------------
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Residues in contact with THR 193 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117M  ILE*     5.4     0.7    -      -       -      -
    147M  LYS      4.1     0.2    -      -       -      +
    148M  TRP*     3.6    12.1    -      -       -      -
    149M  LYS*     2.9    65.9    +      -       +      +
    150M  ILE      4.8     0.4    -      -       -      +
    151M  ASP*     6.1     0.9    -      -       -      -
    191M  SER*     4.2    11.4    -      -       -      +
    192M  TYR*     1.3    75.6    -      -       -      +
    194M  CYS*     1.3    70.6    +      -       -      +
    195M  GLU*     4.9     1.2    -      -       -      +
    206M  VAL*     4.1    13.1    -      -       +      +
    207M  LYS      3.5     1.0    +      -       -      -
    208M  SER*     3.1    25.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 194 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115M  VAL*     5.2     5.2    -      -       -      -
    117M  ILE*     3.0    25.9    -      -       +      +
    134M  CYS*     2.1    44.0    -      -       -      -
    136M  LEU*     5.2     3.6    -      -       -      -
    146M  VAL*     4.3    13.9    -      -       -      -
    147M  LYS      4.4     0.7    -      -       -      -
    148M  TRP*     4.0     9.9    -      -       +      -
    193M  THR*     1.3    76.6    +      -       -      +
    195M  GLU*     1.3    64.2    +      -       -      +
    196M  ALA*     5.3     1.6    -      -       -      -
    205M  ILE      3.8     0.4    -      -       -      +
    206M  VAL*     3.4     4.5    -      -       -      -
    207M  LYS*     2.9    33.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 195 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145M  ASN      3.9     1.0    -      -       -      +
    146M  VAL*     3.1     6.8    -      -       -      +
    147M  LYS*     2.9    66.6    +      -       +      +
    149M  LYS*     2.7    40.2    +      -       +      +
    193M  THR*     4.9     0.7    -      -       -      +
    194M  CYS*     1.3    79.0    -      -       -      +
    196M  ALA*     1.3    64.0    +      -       -      +
    197M  THR*     4.2     4.1    +      -       -      +
    204M  PRO*     4.1    18.2    -      -       +      +
    205M  ILE      3.2     2.5    -      -       -      +
    206M  VAL*     3.7    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 196 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113M  PRO*     5.9     1.7    -      -       +      +
    115M  VAL*     4.6     5.8    -      -       +      -
    136M  LEU*     3.8    18.8    -      -       +      -
    144M  ILE*     4.4     7.4    -      -       +      -
    145M  ASN      3.8     3.1    -      -       -      -
    146M  VAL*     3.7    20.4    -      -       +      -
    194M  CYS*     4.3     2.2    -      -       -      -
    195M  GLU*     1.3    77.0    -      -       -      +
    197M  THR*     1.3    58.1    -      -       -      +
    198M  HIS*     5.1     0.6    -      -       -      +
    205M  ILE*     2.6    58.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 197 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144M  ILE*     3.6     3.3    -      -       -      +
    145M  ASN*     3.4    34.1    +      -       -      -
    147M  LYS*     6.1     1.2    -      -       -      -
    195M  GLU*     4.2     4.9    +      -       -      +
    196M  ALA*     1.3    75.1    +      -       -      +
    198M  HIS*     1.3    75.3    +      -       -      +
    201M  SER      3.7     9.2    -      -       -      +
    202M  THR      4.7     4.9    -      -       -      +
    203M  SER      3.3    24.7    -      -       -      +
    204M  PRO*     3.4    22.1    -      -       +      +
    205M  ILE*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 198 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111M  ALA      3.8     4.6    +      -       -      -
    113M  PRO*     4.2    25.4    -      -       +      -
    139M  PHE*     4.2     9.5    -      +       -      +
    141M  PRO*     3.0    63.1    -      -       +      +
    143M  ASP      3.0    21.1    +      -       -      -
    144M  ILE*     3.9    12.3    -      -       +      +
    196M  ALA      5.1     1.1    -      -       -      +
    197M  THR*     1.3    83.6    -      -       -      +
    199M  LYS*     1.3    69.1    +      -       -      +
    200M  THR*     2.7    34.1    +      -       -      +
    201M  SER*     2.7    26.4    +      -       -      +
    203M  SER      4.7     0.6    +      -       -      -
    205M  ILE*     5.7     2.4    -      -       +      +
----------------------------------------------------------
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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