Contacts of the strand formed by residues 184 - 189 (chain F) in PDB entry 1R5I


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 LEU 184 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96F  GLU*     4.3    15.0    -      -       +      +
     97F  PRO*     3.6    39.0    -      -       +      +
     99F  VAL*     4.2    17.9    -      -       +      +
    173F  CYS      3.6     0.6    -      -       -      +
    174F  GLN*     3.2     0.5    -      -       -      -
    175F  VAL*     2.8    42.5    +      -       +      +
    180F  VAL*     3.3    46.0    -      -       +      -
    182F  SER      3.7     1.1    -      -       -      +
    183F  PRO*     1.3    73.0    -      -       -      +
    185F  THR*     1.3    66.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 185 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172F  THR*     3.7    25.4    -      -       +      -
    173F  CYS      3.2     3.4    -      -       -      -
    174F  GLN*     3.8    25.6    -      -       +      +
    183F  PRO      4.3     6.0    +      -       -      +
    184F  LEU*     1.3    84.7    -      -       -      +
    186F  VAL*     1.3    68.7    +      -       -      +
    187F  GLU*     4.3     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 186 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99F  VAL*     3.4    43.7    -      -       +      +
    100F  THR*     4.6     1.3    -      -       -      -
    101F  VAL*     3.4    39.0    -      -       +      +
    131F  TRP*     5.1     0.3    -      -       -      -
    172F  THR*     3.4     2.5    -      -       -      -
    173F  CYS*     2.9    31.7    +      -       -      +
    185F  THR*     1.3    79.1    -      -       -      +
    187F  GLU*     1.3    72.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 187 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  VAL*     5.1     0.7    -      -       -      +
    170F  VAL*     3.3    12.0    -      -       +      +
    171F  TYR      3.3     4.5    -      -       -      +
    172F  THR*     3.5    23.3    -      -       +      +
    185F  THR*     6.0     1.8    -      -       -      -
    186F  VAL*     1.3    87.4    -      -       -      +
    188F  TRP*     1.3    67.2    +      -       -      +
    189F  ARG*     3.3    36.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 188 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  VAL*     3.9    38.4    -      -       +      -
    103F  PRO*     3.2    44.0    -      -       +      -
    115F  LEU*     3.7    36.5    -      -       +      +
    131F  TRP*     5.8     0.7    -      -       +      -
    165F  PRO*     4.9     7.4    -      -       +      +
    170F  VAL*     3.7     1.1    -      -       -      -
    171F  TYR*     3.0    36.4    +      +       +      +
    187F  GLU*     1.3    78.8    -      -       -      +
    189F  ARG*     1.3    78.7    +      -       -      +
    190F  ALA*     3.4     9.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 189 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169F  GLU      4.0     3.6    -      -       -      -
    170F  VAL*     3.2    36.8    -      -       -      +
    187F  GLU*     3.3    21.6    +      -       +      +
    188F  TRP*     1.3    85.0    +      -       -      +
    190F  ALA*     1.3    70.6    +      -       -      +
----------------------------------------------------------
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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