Contacts of the strand formed by residues 755 - 759 (chain B) in PDB entry 3LMG


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 755 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682B  ALA*     5.6     0.4    -      -       +      -
    744B  ILE*     3.7    29.3    +      -       +      +
    745B  GLY*     3.8    32.9    -      -       -      +
    747B  LEU      5.0     2.7    +      -       -      +
    753B  VAL      3.7     1.4    +      -       -      -
    754B  ARG*     1.3    76.1    -      -       -      +
    756B  LEU*     1.3    65.9    +      -       -      +
    757B  GLY*     3.1    17.1    +      -       -      +
    758B  LEU*     4.0    17.7    -      -       +      -
    766B  LEU*     3.6    46.0    -      -       +      -
    767B  VAL      3.9     3.1    -      -       -      +
    768B  THR*     3.8    19.5    -      -       +      -
    834B  PHE*     5.1     3.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 756 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    683B  ARG*     3.8    22.2    +      -       -      +
    685B  PHE*     4.3    12.7    -      -       +      -
    709B  TRP*     5.1    12.8    -      -       +      -
    718B  ILE*     5.7     3.1    -      -       +      -
    720B  VAL*     4.2    20.4    -      -       +      -
    754B  ARG*     3.3    35.7    +      -       -      +
    755B  LEU*     1.3    72.4    -      -       -      +
    757B  GLY*     1.3    57.1    +      -       -      +
    767B  VAL*     3.0    13.0    +      -       +      +
    768B  THR*     4.1     4.0    -      -       -      -
    769B  GLN*     3.7    42.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 757 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682B  ALA*     6.1     0.9    -      -       -      -
    683B  ARG*     3.6    16.4    -      -       -      -
    685B  PHE*     3.8    15.3    -      -       -      -
    755B  LEU*     3.1    14.1    -      -       -      +
    756B  LEU*     1.3    82.7    -      -       -      +
    758B  LEU*     1.3    62.2    +      -       -      +
    767B  VAL*     3.0    27.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 758 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682B  ALA*     4.8     7.4    -      -       +      -
    683B  ARG      3.2     9.2    +      -       -      +
    684B  ILE*     3.4    27.3    -      -       +      +
    685B  PHE*     2.9    25.8    +      -       -      -
    737B  VAL*     4.1     6.1    -      -       +      -
    741B  MET*     3.7    61.2    -      -       +      +
    742B  LEU*     6.5     0.2    -      -       +      -
    744B  ILE*     6.2     0.2    -      -       +      -
    755B  LEU*     4.0    13.5    -      -       +      -
    757B  GLY*     1.3    76.3    -      -       -      +
    759B  CYS*     1.3    62.7    +      -       -      +
    760B  PRO*     4.4     7.0    -      -       +      -
    764B  LEU*     5.3     4.3    -      -       +      -
    765B  GLN      3.4    10.5    -      -       -      +
    766B  LEU*     4.0    15.5    -      -       +      -
    767B  VAL*     5.1     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 759 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685B  PHE*     3.3    22.0    -      -       +      +
    686B  LYS      4.0     4.0    -      -       -      -
    687B  GLU*     3.9    24.9    -      -       -      -
    690B  LEU*     3.9    21.5    -      -       +      -
    758B  LEU*     1.3    77.0    -      -       -      +
    760B  PRO*     1.3    76.1    -      -       -      +
    761B  GLY      3.8     0.3    +      -       -      -
    763B  SER      3.9     2.4    -      -       -      +
    764B  LEU*     5.0     1.3    -      -       -      -
    765B  GLN*     2.9    54.8    +      -       +      +
----------------------------------------------------------
 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