Contacts of the strand formed by residues 187 - 193 (chain u) in PDB entry 5GJQ


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 PHE 187 (chain u).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23u  ALA*     4.7     0.4    -      -       +      -
     24u  ALA      3.6    12.6    -      -       -      +
     25u  ASP*     3.7     7.6    -      -       -      +
     26u  MET*     4.0     5.6    -      -       -      -
    169u  VAL*     5.1     0.7    -      -       +      -
    170u  GLU*     5.2     8.3    -      -       +      -
    173u  MET*     3.7    35.0    -      -       +      -
    184u  TYR      5.1     0.7    -      -       -      +
    185u  ASN      3.4    10.3    -      -       -      +
    186u  ARG*     1.3    77.9    -      -       -      +
    188u  GLN*     1.3    73.5    -      -       -      +
    189u  ILE*     3.7    28.3    -      -       +      -
    201u  GLY      3.9     0.9    -      -       -      +
    202u  PRO*     3.7     4.5    -      -       -      +
    203u  LEU*     2.9    65.0    +      -       +      +
    204u  SER      3.9     7.9    -      -       -      -
    205u  THR*     3.6    30.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 188 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22u  ILE      3.9     0.2    -      -       -      +
     23u  ALA*     3.3     5.7    -      -       -      +
     24u  ALA      3.0    35.6    +      -       -      +
     26u  MET*     3.4    36.0    -      -       +      +
     40u  SER*     2.7    35.3    +      -       -      -
     41u  ARG      4.1     3.8    +      -       -      -
     42u  ILE*     4.0    16.8    +      -       +      +
    187u  PHE*     1.3    75.9    -      -       -      +
    189u  ILE*     1.3    64.6    -      -       -      +
    190u  ALA      4.3     0.2    -      -       -      -
    199u  ILE*     4.0    22.5    -      -       +      +
    200u  GLU      3.9    12.7    +      -       -      +
    201u  GLY*     5.0     6.4    -      -       -      -
    202u  PRO*     5.5     1.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 189 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21u  VAL*     3.5    24.2    -      -       +      -
     22u  ILE      3.4     2.7    -      -       -      -
     23u  ALA*     4.1    11.2    -      -       +      -
    166u  ARG*     4.0    43.5    -      -       +      +
    169u  VAL*     3.9    15.9    -      -       +      -
    170u  GLU*     5.5     2.0    -      -       +      +
    187u  PHE*     3.7    27.5    +      -       +      -
    188u  GLN*     1.3    78.9    -      -       -      +
    190u  ALA*     1.3    62.7    +      -       -      +
    191u  THR*     4.0    10.3    -      -       -      +
    198u  GLU      3.9     0.5    -      -       -      +
    199u  ILE*     3.6     3.4    -      -       -      -
    200u  GLU*     2.9    37.6    +      -       +      +
    203u  LEU*     4.1     8.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 190 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21u  VAL*     3.4     2.6    -      -       -      +
     22u  ILE      2.8    34.7    +      -       -      +
     42u  ILE*     3.9    22.4    -      -       +      +
     50u  MET*     3.3    25.7    -      -       -      +
    188u  GLN      4.3     0.2    -      -       -      -
    189u  ILE*     1.3    72.6    -      -       -      +
    191u  THR*     1.3    63.0    +      -       -      +
    197u  VAL*     4.8     0.9    -      -       +      -
    198u  GLU      3.2     9.0    -      -       -      +
    199u  ILE*     4.0    17.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 191 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16u  PHE*     3.7    27.4    -      -       +      -
     20u  VAL      3.3    11.0    -      -       -      +
     21u  VAL*     4.3     4.8    -      -       +      +
     50u  MET*     4.3     1.1    -      -       -      -
    162u  GLN*     3.8    19.7    +      -       +      +
    166u  ARG*     6.1     0.2    -      -       -      -
    189u  ILE*     4.0    13.3    -      -       -      +
    190u  ALA*     1.3    79.3    +      -       -      +
    192u  VAL*     1.3    65.3    +      -       -      +
    193u  THR*     4.1     6.9    +      -       +      +
    196u  GLY      3.4     1.6    -      -       -      +
    197u  VAL*     3.3     4.4    -      -       -      +
    198u  GLU*     2.9    39.8    +      -       -      +
    200u  GLU*     4.1    12.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 192 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16u  PHE*     4.3     0.3    -      -       -      -
     19u  GLY*     2.9     6.6    -      -       -      -
     20u  VAL*     2.9    51.1    +      -       +      +
     47u  ASN      4.3     2.5    -      -       -      +
     48u  SER*     4.1    18.8    -      -       -      +
     49u  THR*     4.2     5.8    -      -       -      +
     50u  MET*     3.6    14.8    -      -       +      -
    113u  GLY      4.2     0.2    -      -       -      +
    114u  GLY*     4.0    16.8    -      -       -      +
    115u  TYR*     4.2    10.1    -      -       +      +
    191u  THR*     1.3    73.7    -      -       -      +
    193u  THR*     1.3    61.9    +      -       -      +
    196u  GLY      3.3     3.1    -      -       -      +
    197u  VAL*     3.3    35.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 193 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16u  PHE*     4.2     9.6    -      -       +      -
     18u  GLY      3.6    16.2    -      -       -      +
     47u  ASN      4.9     2.8    -      -       -      +
     48u  SER*     6.0     0.3    -      -       -      -
    115u  TYR*     3.7    14.9    -      -       -      +
    162u  GLN*     3.9    30.3    -      -       -      +
    191u  THR*     4.1     4.0    +      -       +      -
    192u  VAL*     1.3    80.9    -      -       -      +
    194u  GLU*     1.3    67.6    +      -       -      +
    195u  LYS*     3.2    22.8    +      -       -      +
    196u  GLY*     3.0    18.0    +      -       -      +
----------------------------------------------------------
 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