Contacts of the strand formed by residues 198 - 205 (chain X) in PDB entry 3RCI


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 ILE 198 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52X  VAL*     3.4    28.3    -      -       +      -
     53X  ASP      3.3     4.5    -      -       -      +
     54X  ALA*     4.8     3.1    -      -       +      -
     59X  LEU*     4.9     1.1    -      -       +      -
     94X  THR*     3.1     9.0    -      -       -      -
     95X  PHE*     2.9    50.9    +      -       +      +
     98X  VAL*     4.1     2.7    -      -       +      -
    184X  ILE*     3.7    38.8    -      -       +      +
    187X  PHE*     4.1    19.3    -      -       +      -
    194X  THR*     3.6    30.5    +      -       +      -
    196X  LYS      3.4    12.4    +      -       -      +
    197X  LYS*     1.3    72.6    -      -       -      +
    199X  VAL*     1.3    58.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 199 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52X  VAL*     3.2     4.7    -      -       -      -
     53X  ASP*     2.8    40.9    +      -       +      +
     92X  GLY*     4.0    14.1    -      -       -      +
     93X  SER      3.5     9.9    -      -       -      +
     94X  THR*     4.2     6.1    -      -       +      -
    197X  LYS*     3.9    40.6    -      -       +      +
    198X  ILE*     1.3    76.6    -      -       -      +
    200X  ILE*     1.3    74.4    +      -       -      +
    201X  THR*     3.2    20.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 200 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50X  LEU*     4.2    15.7    -      -       +      -
     51X  ASP      3.3     6.3    -      -       -      +
     52X  VAL*     4.6     5.4    -      -       +      -
     90X  TYR*     4.0    20.9    -      -       +      +
     91X  LYS      3.8     0.2    -      -       -      -
     92X  GLY*     2.8    30.3    +      -       -      -
     93X  SER*     2.8    24.5    +      -       -      +
     94X  THR      5.1     0.2    -      -       -      +
     95X  PHE*     3.8    31.6    -      -       +      -
    106X  ALA*     4.4     7.9    -      -       +      -
    154X  PHE*     4.3    19.7    -      -       +      -
    199X  VAL*     1.3    69.4    -      -       -      +
    201X  THR*     1.3    59.2    +      -       -      +
    202X  ASP      3.4    21.8    -      -       -      +
    203X  CYS*     4.0    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 201 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51X  ASP*     2.8    23.1    +      -       -      +
     53X  ASP*     3.2    46.9    +      -       +      +
     91X  LYS*     3.4    23.0    -      -       -      +
     92X  GLY*     4.7     2.1    +      -       -      +
    199X  VAL*     3.2    15.5    +      -       +      +
    200X  ILE*     1.3    73.7    -      -       -      +
    202X  ASP*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 202 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49X  TYR*     3.0    24.2    +      -       -      -
     51X  ASP*     2.8    42.1    +      -       +      +
     61X  ARG*     5.1     0.9    +      -       -      -
     91X  LYS*     2.9    31.8    +      -       -      +
    200X  ILE*     3.3     5.7    -      -       -      +
    201X  THR*     1.3    83.0    +      -       -      +
    203X  CYS*     1.3    82.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 203 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49X  TYR*     3.1    30.1    +      -       -      +
     50X  LEU*     3.8    15.0    -      -       +      -
     81X  LEU      4.5     0.7    -      -       -      -
     82X  CYS*     3.2    30.7    -      -       -      +
     83X  THR*     4.9     1.2    -      -       -      +
     90X  TYR*     3.9    13.5    -      -       -      -
     91X  LYS*     3.4    37.6    -      -       -      +
    200X  ILE*     4.0     1.8    -      -       +      -
    202X  ASP*     1.3    89.5    +      -       -      +
    204X  GLY*     1.3    58.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 204 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48X  VAL*     3.2     8.3    -      -       -      +
     49X  TYR*     2.9    42.5    +      -       -      -
     82X  CYS*     3.4    19.6    +      -       -      +
     83X  THR*     4.4     3.6    -      -       -      -
    203X  CYS*     1.3    80.0    -      -       -      +
    205X  GLN*     1.3    59.9    +      -       -      -
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Residues in contact with GLN 205 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46X  PRO*     3.8     8.7    -      -       -      +
     47X  LEU      3.5     5.6    -      -       -      +
     48X  VAL*     4.1     6.3    -      -       +      -
     49X  TYR*     3.9     3.4    -      -       -      -
     79X  ARG*     3.0    46.9    +      -       -      +
     83X  THR*     3.8    16.3    -      -       +      +
    204X  GLY*     1.3    74.1    -      -       -      -
    206X  LEU*     1.3    66.2    +      -       -      +
    207X  SER*     2.9    38.0    +      -       -      +
----------------------------------------------------------
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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