Contacts of the helix formed by residues 3100 - 3107 (chain A) in PDB entry 3CMT


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 ASP3100 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3098A  ALA      3.5     3.0    +      -       -      +
   3099A  LEU*     1.3    78.8    -      -       -      +
   3101A  PRO*     1.4    70.7    -      -       -      +
   3102A  ILE*     3.2    23.0    +      -       -      +
   3103A  TYR*     3.0    27.3    +      -       +      +
   3104A  ALA*     2.9    21.0    +      -       -      +
   3502A  ADP      3.8     8.3    +      -       -      -
   4037A  VAL*     3.9    24.9    +      -       +      +
   4060A  ARG*     4.5     4.9    -      -       -      +
   4250A  LYS      4.5    13.6    -      -       -      +
   4251A  ILE*     4.3     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO3101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3099A  LEU      3.4     7.1    -      -       -      +
   3100A  ASP*     1.4    86.7    -      -       -      +
   3102A  ILE*     1.3    69.5    +      -       +      +
   3104A  ALA*     3.1     4.3    +      -       +      +
   3105A  ARG*     2.9    25.8    +      -       -      +
   3111A  ILE*     3.5    15.9    -      -       +      +
   4029A  LEU*     3.6    36.6    -      -       +      +
   4030A  GLY*     5.9     0.2    -      -       -      -
   4032A  ASP      5.5     0.7    -      -       -      +
   4035A  MET*     3.3    42.0    -      -       +      +
   4036A  ASP*     4.4     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE3102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3100A  ASP*     3.2    15.4    +      -       -      +
   3101A  PRO*     1.3    91.1    -      -       +      +
   3103A  TYR*     1.3    63.4    +      -       -      +
   3105A  ARG*     3.3    31.1    +      -       -      +
   3106A  LYS*     3.1    43.4    +      -       -      +
   4036A  ASP*     4.4    15.9    -      -       -      +
   4037A  VAL      5.9     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR3103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3074A  THR*     3.9    16.8    +      -       -      +
   3077A  LEU*     4.9     7.0    -      -       +      -
   3100A  ASP*     3.0    20.8    +      -       +      +
   3102A  ILE*     1.3    76.9    -      -       -      +
   3104A  ALA*     1.3    67.2    +      -       -      +
   3106A  LYS*     3.0    14.5    +      -       +      +
   3107A  LEU*     3.0    55.9    +      -       +      +
   3262A  ILE*     4.9     2.3    -      -       -      +
   3263A  LEU      4.7     1.0    +      -       -      -
   3264A  TYR*     4.1     4.7    -      -       -      -
   3265A  GLY*     3.4    37.5    +      -       -      -
   3502A  ADP      3.3    70.3    +      +       -      +
----------------------------------------------------------
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Residues in contact with ALA3104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3077A  LEU*     4.2    34.7    -      -       +      +
   3099A  LEU*     4.5     3.1    -      -       +      -
   3100A  ASP      2.9    10.8    +      -       -      +
   3101A  PRO*     3.4    11.7    -      -       +      +
   3103A  TYR*     1.3    77.7    -      -       -      +
   3105A  ARG*     1.3    61.2    +      -       -      +
   3107A  LEU*     3.2     8.3    +      -       -      +
   3108A  GLY      3.4     0.5    +      -       -      -
   3109A  VAL*     3.0    27.3    +      -       +      +
   3111A  ILE*     3.6    16.4    -      -       +      -
   3114A  LEU*     6.3     0.2    -      -       +      -
   4029A  LEU*     4.4     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG3105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3101A  PRO      2.9     8.4    +      -       -      +
   3102A  ILE*     3.5    33.2    +      -       -      +
   3104A  ALA*     1.3    73.7    -      -       -      +
   3106A  LYS*     1.3    62.0    +      -       -      +
   3108A  GLY*     2.8    22.3    +      -       -      -
   3109A  VAL      3.7    13.0    -      -       -      +
   3111A  ILE*     3.5    27.5    -      -       +      +
   3112A  ASP*     5.9     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS3106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3102A  ILE*     3.1    33.9    +      -       +      +
   3103A  TYR*     3.0    20.5    +      -       +      +
   3105A  ARG*     1.3    78.0    -      -       -      +
   3107A  LEU*     1.3    57.5    +      -       +      +
   3108A  GLY*     3.3     3.5    +      -       -      -
   3265A  GLY*     3.6    39.1    -      -       -      +
   3266A  GLU*     4.0     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU3107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3074A  THR*     3.9    21.3    -      -       +      +
   3077A  LEU*     3.8    32.8    -      -       +      -
   3078A  GLN*     3.0    25.1    +      -       -      +
   3081A  ALA*     3.9     5.9    -      -       -      +
   3085A  ARG*     5.5     0.7    +      -       -      -
   3103A  TYR*     3.0    52.5    +      -       +      +
   3104A  ALA*     3.6     7.2    -      -       -      +
   3105A  ARG      3.1     0.8    -      -       -      -
   3106A  LYS*     1.3    75.4    -      -       -      +
   3108A  GLY*     1.3    59.5    +      -       -      +
   3109A  VAL*     3.5     1.3    -      -       +      -
   3266A  GLU      3.7    10.4    -      -       -      +
   3267A  GLY*     3.5    33.4    -      -       -      +
----------------------------------------------------------
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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