Contacts of the strand formed by residues 1089 - 1093 (chain B) in PDB entry 1CM8


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 LEU1089 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1075B  LEU*     4.3    10.1    -      -       +      +
   1078B  LEU*     3.2    57.3    +      -       +      +
   1079B  LYS*     3.8    17.7    -      -       +      +
   1088B  GLY*     1.3    74.0    -      -       -      -
   1090B  LEU*     1.3    65.1    +      -       -      +
   1091B  ASP      4.3     7.4    -      -       -      +
   1092B  VAL*     5.0     2.2    -      -       +      -
   1107B  LEU*     4.2    20.2    -      -       +      -
   1108B  VAL      3.7    11.4    -      -       -      +
   1109B  MET*     3.9    15.9    -      -       +      -
   1351B  PHE*     3.6    25.7    -      -       +      -
   1353B  PRO      5.7     2.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1090 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1027B  TYR*     5.5     1.1    -      -       -      +
   1053B  VAL*     3.7    31.0    -      -       +      -
   1089B  LEU*     1.3    77.5    -      -       -      +
   1091B  ASP*     1.3    63.8    +      -       +      +
   1108B  VAL*     2.7    15.6    +      -       +      +
   1109B  MET      4.0     1.3    -      -       -      -
   1110B  PRO*     3.7    35.9    -      -       +      -
   1351B  PHE*     3.8     9.3    -      -       -      -
   1353B  PRO*     3.8    20.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP1091 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1024B  ARG*     2.8    36.3    +      -       -      -
   1027B  TYR*     2.7    37.4    +      -       -      +
   1048B  ARG*     5.8     0.2    -      -       -      -
   1089B  LEU*     3.6     4.1    -      -       -      +
   1090B  LEU*     1.3    83.5    +      -       -      +
   1092B  VAL*     1.3    73.6    +      -       -      +
   1093B  PHE*     3.7     2.4    -      -       -      -
   1107B  LEU*     4.0     0.2    -      -       -      -
   1108B  VAL*     2.8    37.9    +      -       +      +
   1351B  PHE*     3.4    15.3    -      -       -      -
   1353B  PRO*     5.0     7.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1092 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1024B  ARG*     4.0     3.3    +      -       -      -
   1075B  LEU*     3.9    16.8    -      -       +      -
   1089B  LEU*     5.0     2.5    -      -       +      -
   1091B  ASP*     1.3    84.0    +      -       -      +
   1093B  PHE*     1.3    66.2    +      -       -      +
   1105B  PHE*     4.0     8.3    -      -       +      -
   1106B  TYR      3.2    15.9    -      -       -      +
   1107B  LEU*     3.8    20.6    -      -       +      -
   1348B  VAL*     4.0    27.2    -      -       +      +
   1351B  PHE*     3.2    44.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE1093 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1011B  PHE*     3.6    17.0    -      +       +      -
   1022B  GLU      3.6     8.5    -      -       -      -
   1023B  VAL*     3.6    39.5    -      -       +      -
   1024B  ARG*     3.4    31.6    -      -       +      +
   1027B  TYR*     3.8    20.2    -      +       -      -
   1055B  ILE*     4.6     2.5    -      -       +      -
   1091B  ASP*     3.7    16.2    -      -       -      -
   1092B  VAL*     1.3    77.1    -      -       -      +
   1094B  THR*     1.3    65.6    +      -       -      +
   1095B  PRO*     4.3     0.4    -      -       +      -
   1105B  PHE*     3.3     6.4    -      -       -      +
   1106B  TYR*     2.7    67.4    +      +       +      -
   1108B  VAL*     3.8    13.0    -      -       +      -
   1348B  VAL*     4.4     5.6    -      -       -      -
----------------------------------------------------------
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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