Contacts of the strand formed by residues 95 - 99 (chain A) in PDB entry 1L1G


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 ALA 95 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  VAL      3.8     0.2    -      -       -      +
     41A  MET*     3.6     4.3    -      -       -      +
     42A  THR*     2.9    36.5    +      -       +      +
     43A  ALA      4.1     3.1    -      -       -      +
     44A  ALA*     3.8    20.2    -      -       -      +
     47A  VAL*     3.9    18.8    -      -       +      -
     77A  ILE*     4.9     0.2    -      -       +      -
     78A  VAL      3.3    12.8    -      -       -      +
     79A  VAL*     4.0     6.3    -      -       +      -
     94A  ILE*     1.3    78.7    -      -       -      +
     96A  LEU*     1.3    65.1    +      -       -      +
     97A  LEU*     4.7     3.4    -      -       +      -
    232A  TRP*     4.2     2.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ILE*     3.8    26.5    -      -       +      -
     39A  TRP*     3.7    18.5    -      -       +      -
     40A  VAL      3.3     2.9    -      -       -      +
     41A  MET*     3.9    17.5    -      -       +      -
     76A  LYS      3.9     0.3    -      -       -      +
     77A  ILE*     3.7     1.9    -      -       -      -
     78A  VAL*     2.8    41.4    +      -       -      +
     95A  ALA*     1.3    81.2    -      -       -      +
     97A  LEU*     1.3    62.9    +      -       -      +
    232A  TRP*     3.7    18.8    -      -       +      -
    233A  ILE*     3.8    25.4    -      -       +      +
    236A  VAL*     3.6    33.4    -      -       +      -
    237A  ILE*     4.4     6.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LEU*     3.6    33.2    -      -       +      -
     39A  TRP*     3.3     8.0    -      -       -      -
     40A  VAL*     2.8    50.4    +      -       +      +
     42A  THR*     3.9    27.4    -      -       +      -
     47A  VAL*     4.2     7.2    -      -       +      -
     53A  PHE*     5.7     0.4    -      -       +      -
     55A  VAL*     4.2     7.6    -      -       +      -
     74A  VAL*     4.1    21.8    -      -       +      -
     76A  LYS      3.4     3.1    -      -       -      -
     77A  ILE*     4.0    28.0    -      -       +      -
     95A  ALA*     4.7     1.6    -      -       +      -
     96A  LEU*     1.3    81.5    -      -       -      +
     98A  ARG*     1.3    60.6    +      -       -      +
     99A  LEU*     3.7     3.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ASN*     3.3    24.0    -      -       -      +
     39A  TRP*     3.7    25.7    -      -       +      -
     74A  VAL*     3.8     1.9    -      -       -      -
     75A  GLN*     2.6    63.5    +      -       -      +
     76A  LYS*     2.8    44.5    +      -       +      +
     97A  LEU*     1.3    71.7    -      -       -      +
     99A  LEU*     1.3    67.0    +      -       -      +
    240A  ASN*     3.1    44.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LEU*     4.1    18.2    -      -       +      -
     37A  GLN      3.8    20.4    -      -       -      +
     38A  ASN*     2.8    29.0    +      -       -      +
     39A  TRP      4.1     0.4    -      -       -      +
     40A  VAL*     4.0    12.3    -      -       +      -
     55A  VAL*     3.9    32.3    -      -       +      -
     72A  VAL*     3.9    19.7    -      -       +      -
     73A  GLY      3.6     8.3    -      -       -      +
     74A  VAL*     4.5     4.7    -      -       +      -
     75A  GLN*     3.8     5.5    -      -       -      +
     97A  LEU      4.1     6.1    -      -       -      +
     98A  ARG*     1.3    88.2    -      -       -      +
    100A  ALA*     1.3    67.2    +      -       -      +
    101A  GLN      3.2    16.1    +      -       -      +
    103A  VAL*     4.3     4.0    -      -       +      -
----------------------------------------------------------
 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