Contacts of the strand formed by residues 180 - 189 (chain A) in PDB entry 4YLP


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 VAL 180 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  LEU*     3.3    26.7    -      -       +      +
     48A  LEU*     2.7    30.1    -      -       +      +
     51A  MET*     3.6    17.3    -      -       +      -
    178A  SER*     3.2    21.8    +      -       -      +
    179A  PRO*     1.3    71.9    -      -       +      +
    181A  GLU*     1.3    57.4    +      -       -      +
    182A  ARG      5.1     0.4    -      -       -      +
    183A  ILE*     3.7    39.3    -      -       +      -
    205A  MET*     5.5     4.7    -      -       +      -
    206A  GLU      4.6     1.8    -      -       -      +
    207A  THR*     2.7    17.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LEU*     5.2     4.6    -      -       -      +
    179A  PRO      3.2     6.0    +      -       -      +
    180A  VAL*     1.3    72.8    -      -       -      +
    182A  ARG*     1.3    63.2    +      -       +      +
    206A  GLU*     2.9    17.6    +      -       +      +
    207A  THR*     4.5     7.4    -      -       -      -
    208A  ASN*     4.7     5.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LEU*     5.9     0.7    -      -       -      -
    180A  VAL*     3.7     1.1    -      -       -      +
    181A  GLU*     1.3    85.8    -      -       +      +
    183A  ILE*     1.3    67.2    +      -       -      +
    184A  ALA*     6.3     1.3    -      -       +      +
    204A  GLU*     4.0     7.1    +      -       -      +
    205A  MET*     3.6     1.7    -      -       -      -
    206A  GLU*     2.9    68.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  ARG*     3.5    38.7    +      -       +      +
     47A  LEU*     3.1    54.5    -      -       +      -
     48A  LEU*     3.6    26.2    -      -       +      -
    180A  VAL*     3.7    17.5    -      -       +      -
    182A  ARG*     1.3    82.1    -      -       -      +
    184A  ALA*     1.3    69.2    +      -       -      +
    203A  ILE*     5.6     1.8    -      -       +      -
    204A  GLU      3.6     8.5    -      -       -      +
    205A  MET*     4.3    12.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  ARG*     5.0     7.4    -      -       -      +
    182A  ARG*     6.3     1.1    -      -       +      +
    183A  ILE*     1.3    79.5    -      -       -      +
    185A  TYR*     1.3    64.9    +      -       -      +
    203A  ILE*     3.7     5.5    -      -       -      +
    204A  GLU*     2.9    49.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  HIS*     3.2    30.5    +      +       -      +
     40A  GLY*     3.3    47.8    -      -       -      +
     41A  ASN*     3.8    22.5    +      -       -      -
     43A  LEU*     5.3     2.0    -      -       +      -
     44A  ARG*     5.5     7.6    -      -       +      -
    184A  ALA*     1.3    81.1    -      -       -      +
    186A  ASN*     1.3    75.8    +      -       -      +
    187A  VAL*     4.1    22.9    -      -       +      -
    201A  LEU*     4.4     7.9    -      -       +      -
    202A  VAL      3.2    10.1    -      -       -      +
    203A  ILE*     5.1     5.2    -      -       +      -
    204A  GLU*     5.8     1.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  TYR*     1.3    81.6    -      -       -      +
    187A  VAL*     1.3    63.3    +      -       -      +
    188A  GLU*     3.4    24.2    +      -       -      +
    201A  LEU*     4.7     0.7    -      -       -      -
    202A  VAL*     2.8    51.9    +      -       +      +
    204A  GLU*     4.0    18.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  GLY*     3.5    32.3    -      -       -      +
     37A  HIS*     3.9    20.2    -      -       +      +
    185A  TYR*     4.1    14.1    -      -       +      -
    186A  ASN*     1.3    71.5    +      -       -      +
    188A  GLU*     1.3    59.5    +      -       -      +
    199A  ASP*     2.7    33.9    -      -       +      +
    200A  LYS      3.6     4.7    -      -       -      +
    201A  LEU*     3.5    11.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  ASN*     3.4    25.3    +      -       +      +
    187A  VAL*     1.3    77.7    -      -       -      +
    189A  ALA*     1.3    65.2    +      -       -      +
    199A  ASP*     3.4     6.5    -      -       -      +
    200A  LYS*     2.9    39.4    +      -       +      +
    202A  VAL*     3.7    31.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  GLU*     1.3    76.0    -      -       -      +
    190A  ALA*     1.3    59.3    +      -       -      +
    191A  ARG      4.2     0.7    +      -       -      -
    196A  THR      6.1     1.1    -      -       -      +
    198A  LEU      4.2     6.5    -      -       -      +
    199A  ASP*     4.4     4.0    -      -       -      +
    200A  LYS*     3.9    11.5    -      -       -      -
----------------------------------------------------------
 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