Contacts of the strand formed by residues 106 - 111 (chain E) in PDB entry 1L3R


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 106 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34E  SER*     5.7     0.7    -      -       -      +
     92E  LYS*     4.2    11.4    -      -       +      +
     95E  LEU*     3.8    31.3    +      -       +      +
     96E  GLN*     3.7    36.3    -      -       +      +
    104E  VAL      3.8     2.8    +      -       -      -
    105E  LYS*     1.3    70.4    -      -       -      +
    107E  GLU*     1.3    64.8    +      -       -      +
    108E  PHE      3.3    26.5    -      -       -      +
    109E  SER*     4.5    13.2    -      -       -      -
    118E  MET*     3.8    16.4    -      -       +      -
    119E  VAL      3.5    18.2    -      -       -      +
    120E  MET*     4.2     8.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 107 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  THR*     4.4     2.3    +      -       -      -
     69E  TYR*     3.5    34.8    -      -       +      +
    105E  LYS*     3.4    12.0    +      -       -      +
    106E  LEU*     1.3    76.8    -      -       -      +
    108E  PHE*     1.3    91.1    +      -       +      +
    119E  VAL      2.6    17.1    +      -       -      +
    120E  MET      4.7     1.8    -      -       -      -
    121E  GLU*     4.5    13.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 108 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  THR*     3.4    31.6    -      -       -      +
     38E  ALA*     3.8    17.3    -      -       +      -
     43E  PHE*     3.9    11.9    -      +       -      -
     62E  HIS*     4.5    16.8    -      +       -      -
     69E  TYR*     3.9    24.5    -      +       -      -
    106E  LEU*     3.3     9.1    -      -       -      +
    107E  GLU*     1.3   106.6    -      -       +      +
    109E  SER*     1.3    65.6    +      -       -      +
    119E  VAL*     2.8    49.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 109 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34E  SER*     4.5     9.7    +      -       -      -
     35E  GLN*     4.6     0.7    -      -       -      -
     36E  ASN*     3.5     8.2    +      -       -      -
     37E  THR*     3.1    29.0    +      -       -      +
     92E  LYS*     4.0    36.7    +      -       -      +
     96E  GLN*     6.0     0.2    -      -       -      +
    106E  LEU*     4.5     8.8    -      -       -      +
    108E  PHE*     1.3    79.1    -      -       -      +
    110E  PHE*     1.3    64.6    +      -       -      +
    117E  TYR      3.2    14.6    -      -       -      -
    118E  MET*     4.6     1.3    -      -       -      -
    350E  PHE*     4.5     3.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 110 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36E  ASN*     4.0    17.5    -      -       -      +
     38E  ALA*     3.2    34.1    -      -       +      +
     39E  GLN*     3.5     6.1    -      -       -      -
     40E  LEU*     3.2    35.4    -      -       +      -
     43E  PHE*     4.0    20.4    -      +       -      -
     71E  MET*     3.7    21.1    -      -       +      -
    109E  SER*     1.3    81.6    -      -       -      +
    111E  LYS*     1.3    67.8    +      -       -      +
    112E  ASP*     5.4     0.9    -      -       +      -
    117E  TYR*     2.7    68.9    +      +       +      +
    119E  VAL*     4.1     5.6    -      -       +      -
    350E  PHE*     3.4    11.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 111 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35E  GLN*     4.0     2.6    -      -       -      +
     36E  ASN*     5.1     5.2    +      -       -      +
     76E  LYS*     5.3     4.5    -      -       -      +
    110E  PHE*     1.3    86.6    -      -       -      +
    112E  ASP*     1.3    66.7    +      -       -      +
    115E  ASN      3.3    15.9    -      -       -      +
    116E  LEU*     3.9    15.3    -      -       +      -
    117E  TYR*     4.0     2.7    -      -       -      -
    341E  GLU*     5.8     3.1    -      -       -      -
    344E  GLY      5.4     0.2    +      -       -      -
    347E  PHE*     2.8    27.3    +      -       +      +
    348E  THR*     3.0    18.4    +      -       -      +
    350E  PHE*     2.7    35.1    +      -       +      +
----------------------------------------------------------
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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