Contacts of the strand formed by residues 107 - 111 (chain M) in PDB entry 3INU


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 THR 107 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6M  GLU*     3.5    25.0    +      -       -      +
      7M  SER*     4.1     6.8    +      -       -      -
      8M  GLY      3.1    30.1    +      -       -      +
      9M  GLY*     3.2    20.2    -      -       -      -
     20M  LEU*     4.1    11.7    -      -       +      -
     89M  VAL*     3.3     4.8    -      -       -      +
     90M  TYR*     2.7    37.9    +      -       -      +
    106M  GLY*     1.3    76.3    +      -       -      -
    108M  MET*     1.3    65.0    +      -       -      +
    109M  VAL*     3.5     1.7    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 108 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10M  GLY*     2.9    24.4    +      -       -      -
     41M  PRO*     3.8    22.7    -      -       +      -
     87M  THR*     3.8    23.8    -      -       +      -
     88M  ALA*     3.5    18.8    -      -       -      +
     89M  VAL*     4.0    17.6    -      -       +      +
    107M  THR*     1.3    75.4    -      -       -      +
    109M  VAL*     1.3    59.9    +      -       -      +
    110M  THR*     3.7    18.6    -      -       -      +
    150M  GLU*     3.7    37.4    -      -       +      +
    151M  PRO*     4.0    22.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 109 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9M  GLY*     3.8    18.6    -      -       -      -
     10M  GLY      3.6     2.9    -      -       -      +
     12M  VAL*     4.0    10.3    -      -       +      -
     18M  LEU*     3.5    25.8    -      -       +      -
     20M  LEU*     4.1    12.8    -      -       +      -
     82M  MET*     4.1    15.5    -      -       +      +
     86M  ASP      4.8     1.6    -      -       -      +
     87M  THR*     3.1     7.4    -      -       -      +
     88M  ALA      2.8    34.9    +      -       -      -
     90M  TYR*     3.9    28.5    -      -       +      -
    107M  THR      4.4     2.2    -      -       -      +
    108M  MET*     1.3    77.6    -      -       -      +
    110M  THR*     1.3    66.0    +      -       -      +
    111M  VAL*     4.5     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 110 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109L  THR*     6.2     0.7    -      -       +      -
     10M  GLY      3.0    12.6    +      -       -      -
     11M  LEU*     3.5     5.4    -      -       +      +
     12M  VAL*     3.1    25.0    +      -       -      -
     87M  THR*     3.8    12.3    -      -       +      +
    108M  MET*     3.7    23.4    -      -       +      +
    109M  VAL*     1.3    73.5    -      -       -      +
    111M  VAL*     1.3    64.0    +      -       -      +
    112M  SER*     4.3     6.7    -      -       -      -
    148M  PHE*     4.0    18.6    -      -       +      -
    149M  PRO*     3.6    34.7    -      -       +      +
    150M  GLU      4.3     0.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 111 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  VAL*     3.1    15.9    -      -       +      +
     13M  LYS      4.0     0.2    -      -       -      +
     14M  PRO*     3.6    30.7    -      -       +      -
     82M  LEU*     3.8    26.0    -      -       +      +
     83M  ARG      3.3    37.2    -      -       -      +
     84M  ALA*     4.0    10.3    -      -       -      +
     86M  ASP*     4.0    11.0    -      -       +      -
     87M  THR*     3.0    19.2    +      -       -      +
    109M  VAL*     4.5     5.4    -      -       +      -
    110M  THR*     1.3    73.0    -      -       -      +
    112M  SER*     1.3    61.2    +      -       -      +
    229M  SO4      4.5     5.4    +      -       -      -
----------------------------------------------------------
 Back to top of page


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