Contacts of the strand formed by residues 36 - 42 (chain H) in PDB entry 6CMO


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 SER 36 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32H  PHE*     6.3     0.2    -      -       -      -
     35H  SER*     1.3    75.9    -      -       -      +
     37H  ILE*     1.3    71.9    +      -       -      +
     38H  HIS*     2.7    25.6    +      -       -      -
     53H  SER*     4.4     0.2    -      -       -      -
     54H  ILE      3.4    16.4    -      -       -      -
     55H  TYR*     3.7    10.3    -      -       -      -
     56H  SER*     5.6     0.2    -      -       -      -
    101H  ARG*     3.5     2.9    -      -       -      +
    102H  TYR      2.7    39.1    +      -       -      -
    104H  TRP*     3.2    23.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 37 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7H  LEU*     4.5     8.5    -      -       +      -
     25H  CYS*     4.7     5.4    -      -       +      +
     27H  ALA*     5.9     0.4    -      -       +      -
     30H  PHE*     4.4    21.3    -      -       +      -
     32H  PHE*     3.5    30.5    -      -       +      -
     35H  SER*     4.6     2.0    -      -       -      +
     36H  SER*     1.3    84.5    -      -       -      +
     38H  HIS*     1.3    64.0    +      -       -      +
     39H  TRP*     4.3    18.0    -      -       -      +
     53H  SER*     3.4     4.2    +      -       -      -
     54H  ILE*     3.0    36.3    +      -       +      +
     82H  ALA*     4.8    11.4    -      -       +      -
     99H  CYS*     3.8    25.6    -      -       -      -
    100H  ALA      3.3     6.5    -      -       -      +
    101H  ARG*     4.3    13.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 38 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  SER*     2.7    27.6    +      -       -      -
     37H  ILE*     1.3    74.4    -      -       -      +
     39H  TRP*     1.3    63.5    +      -       -      +
     40H  VAL*     5.4     2.5    -      -       +      -
     50H  TRP*     3.7    16.3    +      -       +      +
     52H  ALA      3.9     2.2    -      -       -      -
     53H  SER*     3.1    31.5    +      -       -      -
     55H  TYR*     4.1     9.0    -      +       -      -
     98H  TYR      3.2     4.3    -      -       -      +
     99H  CYS*     3.7     3.1    -      -       -      -
    100H  ALA*     2.7    46.4    +      -       +      +
    102H  TYR*     3.4    30.6    -      -       +      +
    104H  TRP*     3.9     5.0    +      +       -      -
    118H  MET*     3.9    12.6    -      -       +      -
     97L  ILE*     4.0    22.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 39 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9H  GLU*     4.2    18.2    -      -       +      -
     10H  SER      5.3     0.2    -      -       -      -
     23H  LEU*     4.5    15.0    -      -       +      -
     24H  SER*     3.6    30.7    -      -       -      -
     25H  CYS*     3.6    31.4    -      -       +      -
     37H  ILE*     4.3    14.7    -      -       +      +
     38H  HIS*     1.3    82.8    -      -       -      +
     40H  VAL*     1.3    60.9    +      -       -      +
     50H  TRP*     3.4    16.8    -      -       -      -
     51H  VAL*     3.4    18.5    -      -       +      +
     52H  ALA      3.2    15.2    +      -       -      +
     53H  SER*     5.4     1.1    -      -       -      -
     54H  ILE*     4.9    13.4    -      -       +      +
     82H  ALA*     5.0     4.1    -      -       +      +
     83H  TYR      5.4     0.4    -      -       -      -
     84H  LEU*     3.5    37.3    -      -       +      +
     97H  TYR*     3.9    35.0    -      +       +      -
     98H  TYR      3.5    15.0    -      -       -      -
     99H  CYS*     4.6     2.5    -      -       +      -
    125H  THR*     6.4     0.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 40 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  HIS*     5.4     4.3    -      -       +      -
     39H  TRP*     1.3    80.4    -      -       -      +
     41H  ARG*     1.3    62.2    +      -       -      +
     48H  LEU*     3.7    22.2    -      -       +      -
     49H  GLU      3.3    10.3    -      -       -      +
     50H  TRP*     3.9    16.4    -      -       +      +
     51H  VAL*     4.4     0.4    -      -       -      -
     96H  VAL      3.3    13.6    -      -       -      +
     97H  TYR*     3.4    18.0    -      -       -      -
     98H  TYR*     3.6    29.7    +      -       +      +
    100H  ALA*     5.8     1.3    -      -       +      -
    118H  MET*     6.3     1.1    -      -       +      -
    121H  TRP*     4.2    15.7    -      -       +      -
     99L  PHE*     3.7    27.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 41 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40H  VAL*     1.3    72.7    -      -       -      +
     42H  GLN*     1.3    58.9    +      -       -      +
     43H  ALA*     3.8    10.1    +      -       -      +
     48H  LEU*     3.5     4.9    -      -       -      +
     49H  GLU*     2.6    73.9    +      -       +      +
     51H  VAL*     3.7    26.8    -      -       +      +
     67H  VAL*     5.7     4.7    -      -       -      +
     71H  PHE*     6.4     2.0    -      -       -      -
     92H  GLU      3.1    26.1    +      -       -      -
     93H  ASP*     3.6    27.7    +      -       -      +
     94H  THR      4.0     7.7    +      -       -      -
     95H  ALA*     3.7    12.3    -      -       +      +
     96H  VAL      3.9     1.8    -      -       -      -
     97H  TYR*     3.6    29.5    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 42 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41H  ARG*     1.3    70.3    -      -       -      +
     43H  ALA*     1.3    90.1    +      -       -      +
     44H  PRO*     3.8     7.5    -      -       -      +
     45H  GLY      4.6     2.6    -      -       -      +
     46H  LYS      3.6     9.9    +      -       -      -
     47H  GLY      3.8     3.1    -      -       -      +
     48H  LEU*     3.7    31.2    -      -       +      -
     95H  ALA*     3.3     6.9    -      -       -      +
     96H  VAL*     3.1    55.3    +      -       +      +
     98H  TYR*     5.0    13.7    -      -       +      +
----------------------------------------------------------
 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