Contacts of the strand formed by residues 204 - 209 (chain B) in PDB entry 1L0N


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 MET 204 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  GLY      4.5     2.1    -      -       -      +
     33B  LEU*     3.6    13.8    -      -       +      -
     34B  VAL*     3.5    18.4    +      -       -      +
     49B  LEU*     3.7    24.0    -      -       +      -
     50B  PHE      3.3     4.3    -      -       -      -
     51B  ILE*     4.0    22.9    -      -       +      -
    127B  THR*     6.0     0.9    -      -       -      +
    128B  THR*     5.6     2.5    -      -       +      -
    199B  PHE*     3.6    26.5    -      -       -      +
    200B  THR      3.2    24.9    -      -       -      +
    201B  SER      3.0     6.5    +      -       -      +
    202B  ALA      3.5     0.6    -      -       -      -
    203B  ARG*     1.3    82.2    -      -       -      +
    205B  ALA*     1.3    62.7    +      -       -      +
    224B  LEU*     3.6    40.6    -      -       +      +
    226B  ILE*     5.5     2.5    -      -       -      -
    387B  LEU*     4.0     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU*     4.8     0.4    -      -       -      -
     34B  VAL*     3.5    11.9    -      -       +      +
     48B  GLY      3.6     1.7    -      -       -      +
     49B  LEU*     3.4     5.8    -      -       -      +
     50B  PHE*     2.7    46.7    +      -       +      +
    204B  MET*     1.3    77.8    -      -       -      +
    206B  LEU*     1.3    59.5    +      -       -      +
    207B  ILE*     3.8     5.3    +      -       +      -
    386B  ALA*     3.8    22.2    -      -       +      -
    387B  LEU*     3.6    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU*     5.0     1.9    -      -       +      +
     34B  VAL      3.1    11.8    +      -       -      +
     35B  ILE*     3.5    13.0    -      -       +      +
     36B  ALA      3.2    19.8    +      -       -      +
     47B  ILE*     4.1    23.1    -      -       +      -
     48B  GLY      3.8     3.8    -      -       -      +
     49B  LEU*     3.9    19.1    -      -       +      -
    120B  MET*     5.0     4.9    -      -       -      -
    123B  LEU*     4.5    11.7    -      -       +      -
    124B  LEU*     5.4     2.0    -      -       +      -
    205B  ALA*     1.3    70.1    -      -       -      +
    207B  ILE*     1.3    60.6    +      -       -      +
    216B  LEU*     3.7    44.3    -      -       +      +
    219B  VAL*     3.9    16.8    -      -       +      -
    220B  ALA*     4.1     6.3    -      -       +      -
    224B  LEU*     4.0    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  VAL*     5.1     0.7    -      -       +      -
     35B  ILE      5.0     0.2    -      -       -      -
     36B  ALA*     3.1    30.7    -      -       +      +
     47B  ILE*     3.4     7.3    -      -       -      +
     48B  GLY      2.9    32.9    +      -       -      +
     50B  PHE*     3.7    28.0    -      -       +      -
    205B  ALA*     4.3     5.4    -      -       +      +
    206B  LEU*     1.3    78.2    -      -       -      +
    208B  GLY*     1.3    64.4    +      -       -      +
    209B  LEU*     5.4     1.8    -      -       +      -
    216B  LEU*     4.0     2.0    -      -       -      -
    378B  PHE*     6.1     0.4    -      -       +      -
    379B  LEU*     3.7    23.7    -      -       +      +
    382B  VAL*     4.0    28.5    -      -       +      +
    383B  GLY*     3.8    13.0    -      -       -      -
    386B  ALA*     4.4    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  ALA      2.8    11.9    +      -       -      +
     37B  SER*     3.2     2.9    -      -       -      -
     38B  LEU      3.0    24.9    +      -       -      -
     46B  ARG      3.5     5.8    -      -       -      -
     47B  ILE*     4.0     2.9    -      -       -      -
    207B  ILE*     1.3    77.2    -      -       -      +
    209B  LEU*     1.3    66.6    +      -       -      +
    210B  GLY      4.1     0.2    -      -       -      -
    211B  VAL*     3.8    13.0    -      -       -      -
    216B  LEU*     3.5    15.9    -      -       -      +
    379B  LEU*     4.4     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 209 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  LEU*     3.7    13.9    -      -       +      +
     40B  ASN*     3.5    25.4    -      -       -      +
     44B  ALA      4.9     0.7    -      -       -      -
     45B  SER*     3.1     5.5    -      -       -      -
     46B  ARG*     2.6    53.8    +      -       +      +
    207B  ILE*     5.4     1.3    -      -       +      -
    208B  GLY*     1.3    83.7    -      -       -      +
    210B  GLY*     1.3    62.1    +      -       -      +
    211B  VAL*     3.3     1.8    -      -       -      +
    375B  SER*     3.7    36.6    -      -       -      +
    378B  PHE*     3.6    35.7    -      -       +      -
    379B  LEU*     3.8    12.6    -      -       +      -
----------------------------------------------------------
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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