Contacts of the strand formed by residues 8 - 12 (chain B) in PDB entry 3LUE


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 8 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ALA*     1.3    73.5    -      -       -      +
      9B  VAL*     1.3    62.8    +      -       -      +
     10B  VAL*     3.7     5.4    +      -       +      +
     20B  GLY      3.1    11.7    -      -       -      +
     21B  PHE*     3.2    32.3    -      -       +      -
     90B  PHE*     3.3    40.2    -      -       +      -
     94B  LEU*     4.7    10.3    -      -       +      -
     96B  VAL*     3.3    16.2    -      -       +      -
     97B  ALA      5.5     0.4    -      -       -      +
     98B  PRO*     5.7     1.3    -      -       +      -
    101B  HIS*     3.7    34.5    -      -       +      +
    102B  PRO      3.1     5.8    +      -       -      +
    103B  VAL*     3.6    11.9    -      -       +      +
    104B  LEU      3.2    20.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  LEU*     1.3    72.1    -      -       -      +
     10B  VAL*     1.3    63.7    +      -       -      +
     11B  ASP*     5.7     0.2    -      -       +      -
     19B  ALA*     3.2     5.0    -      -       -      -
     20B  GLY      2.9    27.3    +      -       -      -
     22B  ALA*     4.2    16.4    -      -       +      +
    104B  LEU*     3.7    31.0    -      -       +      +
    106B  THR*     5.1     4.5    -      -       +      -
    340B  TRP*     3.2    28.4    +      -       +      +
    343B  GLY*     3.8    14.6    -      -       -      +
    344B  SER*     3.4    33.0    -      -       -      +
    347B  ALA*     4.8     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  LEU*     4.5    10.3    -      -       +      +
      9B  VAL*     1.3    76.4    -      -       -      +
     11B  ASP*     1.3    62.9    +      -       -      +
     12B  ASN*     3.6    24.2    +      -       -      +
     17B  CYS*     5.9     3.8    -      -       +      -
     18B  LYS      3.7     3.4    -      -       -      +
     19B  ALA*     4.4     3.1    -      -       +      +
     86B  TRP*     3.7    18.8    -      -       +      +
     89B  THR*     3.9    27.8    -      -       +      +
     90B  PHE*     4.5    16.6    -      -       +      -
    103B  VAL*     5.5     1.8    -      -       +      -
    104B  LEU      3.0     7.9    +      -       -      +
    105B  LEU*     3.4    18.1    -      -       +      -
    106B  THR*     2.9    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  VAL*     4.1     0.8    -      -       +      -
     10B  VAL*     1.3    73.3    -      -       -      +
     12B  ASN*     1.3    65.5    +      -       -      +
     13B  GLY*     3.7     1.0    +      -       -      -
     17B  CYS*     3.3    10.2    -      -       -      +
     18B  LYS*     2.8    64.9    +      -       +      +
    106B  THR*     2.7    26.0    +      -       +      +
    137B  GLN*     4.1     7.1    -      -       -      +
    339B  VAL*     3.4    33.3    -      -       +      +
    340B  TRP*     4.1    13.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  VAL*     3.6    21.2    +      -       -      +
     11B  ASP*     1.3    74.6    +      -       -      +
     13B  GLY*     1.3    61.4    +      -       -      +
     14B  SER      4.3     0.3    +      -       -      -
     17B  CYS*     4.3     6.3    -      -       -      -
     71B  ILE*     4.0    22.8    -      -       +      +
     74B  GLY*     5.0     3.1    -      -       -      +
     76B  VAL*     6.0     1.3    -      -       +      -
     82B  MET*     3.2    11.3    -      -       +      +
     86B  TRP*     2.9    41.4    +      -       -      -
    105B  LEU*     4.3     4.6    -      -       -      +
    106B  THR*     3.4    25.7    +      -       -      +
    119B  MET*     5.7     0.6    -      -       -      -
    137B  GLN*     4.0    17.8    +      -       -      -
    157B  ASP*     5.9     0.2    -      -       -      +
----------------------------------------------------------
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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