Contacts of the strand formed by residues 180 - 187 (chain L) in PDB entry 1A4J


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 180 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172H  PHE*     3.4     6.0    -      -       -      -
    140L  LEU*     3.6     3.8    -      -       -      +
    141L  LEU*     2.8    50.7    +      -       +      +
    144L  PHE*     3.9    19.7    -      -       +      -
    147L  ARG      5.7     1.8    -      -       -      +
    149L  ALA*     5.2     6.7    -      -       +      +
    151L  VAL*     4.0    24.5    -      -       +      -
    166L  GLU*     3.8    30.1    -      -       +      +
    167L  SER      3.2    13.9    -      -       -      +
    168L  VAL*     4.2    13.9    -      -       +      -
    179L  SER*     1.3    77.7    -      -       -      +
    181L  SER*     1.3    74.2    +      -       -      +
    182L  SER*     4.1     3.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 181 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172H  PHE*     3.5    23.6    -      -       -      +
    185H  SER*     3.7    17.9    +      -       -      -
    187H  VAL*     5.9     1.1    -      -       -      -
    138L  VAL*     4.6    10.1    -      -       -      -
    139L  CYS      3.3     7.0    -      -       -      -
    140L  LEU*     4.6     2.2    -      -       -      +
    165L  GLN      4.0     0.5    +      -       -      +
    166L  GLU*     3.1     3.6    -      -       -      +
    167L  SER*     2.8    43.9    +      -       -      -
    180L  LEU*     1.3    76.4    -      -       -      +
    182L  SER*     1.3    59.5    +      -       -      +
    183L  THR*     4.6     5.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 182 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138L  VAL*     3.5     0.9    -      -       -      -
    139L  CYS*     2.8    41.5    +      -       -      -
    151L  VAL*     4.2    21.4    +      -       -      +
    153L  TRP*     3.1    28.5    +      -       -      -
    164L  SER*     4.2     6.8    +      -       -      -
    165L  GLN      3.5     5.0    +      -       -      -
    166L  GLU*     3.9    19.4    +      -       -      +
    180L  LEU*     4.1     5.8    -      -       -      +
    181L  SER*     1.3    73.7    -      -       -      +
    183L  THR*     1.3    62.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 183 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147H  LEU*     5.4     8.6    -      -       +      +
    185H  SER*     5.0     3.5    +      -       -      -
    136L  SER*     4.0    24.7    -      -       -      +
    137L  VAL      3.3     9.2    -      -       -      +
    138L  VAL*     4.0    17.3    -      -       +      +
    153L  TRP*     4.5     0.2    -      -       -      -
    164L  SER*     3.1     7.9    -      -       -      -
    165L  GLN*     2.7    41.3    +      -       -      -
    181L  SER*     4.6     6.9    +      -       -      -
    182L  SER*     1.3    75.1    +      -       -      +
    184L  LEU*     1.3    64.5    +      -       -      +
    185L  THR*     3.9    10.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 184 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135L  ALA      3.6     1.7    -      -       -      +
    136L  SER*     3.5     3.5    -      -       -      -
    137L  VAL*     2.7    44.7    +      -       +      +
    153L  TRP*     3.7    46.3    -      -       +      -
    155L  VAL*     4.1    22.9    -      -       +      -
    160L  GLN*     4.2     6.1    -      -       +      -
    163L  ASN*     3.5    40.6    -      -       -      +
    164L  SER*     4.0     4.9    -      -       -      -
    183L  THR*     1.3    72.1    -      -       -      +
    185L  THR*     1.3    60.5    +      -       -      +
    186L  LEU*     4.1    21.3    +      -       +      -
    197L  TYR*     4.3     8.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 185 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149H  LYS*     3.8    18.2    -      -       -      +
    177H  GLN*     5.2     2.2    -      -       -      +
    134L  THR*     5.2     6.1    -      -       +      -
    135L  ALA      3.7     2.9    -      -       -      +
    136L  SER*     3.5    24.9    -      -       -      +
    163L  ASN*     3.1    26.6    +      -       -      +
    164L  SER*     5.0     0.9    -      -       -      -
    165L  GLN*     5.4     2.8    +      -       -      +
    183L  THR*     4.1    11.5    +      -       +      +
    184L  LEU*     1.3    71.6    -      -       -      +
    186L  LEU*     1.3    75.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 186 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134L  THR*     3.8     5.7    -      -       -      +
    135L  ALA*     3.0    34.3    +      -       -      +
    137L  VAL*     4.9     4.0    -      -       +      -
    155L  VAL*     5.0     3.1    -      -       +      -
    160L  GLN*     4.4     5.2    -      -       -      +
    163L  ASN*     3.4    29.4    -      -       +      +
    184L  LEU*     4.1    17.9    -      -       +      +
    185L  THR*     1.3    80.2    -      -       -      +
    187L  SER*     1.3    68.4    +      -       -      +
    190L  ASP*     4.5     9.4    -      -       +      +
    191L  TYR*     4.1    17.7    -      -       +      +
    197L  TYR*     3.6    36.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 187 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133L  GLY      3.8     8.5    -      -       -      -
    134L  THR*     4.8     2.5    -      -       -      +
    186L  LEU*     1.3    78.9    -      -       -      +
    188L  LYS*     1.3    58.5    +      -       -      +
    189L  ALA*     3.7     7.0    +      -       -      +
    190L  ASP*     3.1    34.6    +      -       -      +
    191L  TYR*     2.9    26.7    +      -       -      +
----------------------------------------------------------
 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