Contacts of the strand formed by residues 49 - 56 (chain K) in PDB entry 6R90


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 49 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31K  LEU*     4.0    20.6    -      -       +      -
     33K  ILE*     5.1     0.7    -      -       +      -
     42K  TYR*     3.7    44.4    -      -       +      -
     43K  VAL      3.4     7.0    -      -       -      +
     44K  VAL*     4.8     0.7    -      -       -      -
     45K  THR*     4.0     3.1    +      -       -      -
     48K  GLY*     1.3    79.7    -      -       -      +
     50K  ARG*     1.3    59.7    +      -       -      +
     51K  PRO*     3.9     6.1    -      -       -      +
    317K  LEU*     4.3    15.3    -      -       +      -
    323K  PHE*     4.4    12.8    -      -       +      -
    333K  LEU*     3.8    25.8    -      -       +      +
    351K  GLU*     5.2     2.9    +      -       -      +
    353K  PHE*     4.0    20.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 50 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28K  ASP*     6.4     0.2    -      -       -      -
     42K  TYR*     3.4     2.9    -      -       -      -
     43K  VAL*     3.0    71.6    +      -       +      +
     45K  THR*     4.2    12.5    -      -       +      +
     49K  LEU*     1.3    72.8    -      -       -      +
     51K  PRO*     1.3    76.3    +      -       +      +
     52K  VAL*     3.3    10.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 51 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41K  ILE      4.3     0.2    -      -       -      +
     42K  TYR*     3.5    29.8    -      -       +      -
     49K  LEU      3.9     7.4    -      -       -      +
     50K  ARG*     1.3    91.9    +      -       +      +
     52K  VAL*     1.3    60.4    +      -       -      +
     53K  LYS      5.3     1.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 52 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24K  THR*     5.3     6.1    -      -       +      -
     41K  ILE*     3.0    15.1    +      -       +      +
     42K  TYR      4.3     0.4    -      -       -      -
     43K  VAL*     3.3    38.6    -      -       +      +
     50K  ARG*     3.4    20.9    -      -       -      +
     51K  PRO*     1.3    74.8    -      -       -      +
     53K  LYS*     1.3    71.7    +      -       +      +
     91K  TYR*     3.8    23.1    -      -       +      +
     93K  GLN*     5.4     1.3    -      -       -      +
     98K  ILE*     4.1    14.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 53 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40K  GLU*     3.5     2.3    -      -       -      +
     41K  ILE*     2.8    49.5    +      -       +      +
     42K  TYR*     6.0     0.2    -      -       -      -
     51K  PRO*     5.3     0.8    -      -       -      +
     52K  VAL*     1.3    87.0    -      -       +      +
     54K  GLU*     1.3    70.1    +      -       -      +
     55K  VAL*     3.8    29.2    -      -       +      -
     91K  TYR*     5.6     3.8    -      -       +      -
     98K  ILE*     4.4    35.3    +      -       +      -
    100K  ILE*     6.1     4.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 54 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11K  LYS*     2.6    29.6    +      -       -      +
     38K  ARG*     2.5    46.0    +      -       +      +
     39K  LEU      3.4     4.5    -      -       -      +
     40K  GLU*     3.7    29.8    -      -       +      +
     53K  LYS*     1.3    85.3    +      -       -      +
     55K  VAL*     1.3    72.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 55 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38K  ARG*     3.3     1.9    -      -       -      +
     39K  LEU*     2.9    61.2    +      -       +      +
     41K  ILE*     4.7     3.4    -      -       +      -
     53K  LYS*     3.8    28.5    -      -       +      -
     54K  GLU*     1.3    91.5    -      -       -      +
     56K  GLY*     1.3    67.4    +      -       -      +
     57K  MET*     4.9     7.0    -      -       +      -
    100K  ILE*     5.3    13.5    -      -       +      -
   1065K  VAL*     5.5    11.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 56 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37K  THR      3.5     4.9    -      -       -      -
     38K  ARG*     3.2    31.7    -      -       -      +
     55K  VAL*     1.3    79.8    -      -       -      +
     57K  MET*     1.3    65.7    +      -       -      +
     58K  TYR*     5.5     3.5    -      -       -      -
   1065K  VAL*     4.7     7.8    -      -       -      +
----------------------------------------------------------
 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