Contacts of the strand formed by residues 131 - 136 (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 ALA 131 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  PRO*     3.3    12.6    -      -       +      +
    103B  VAL      3.1    20.8    +      -       -      -
    124B  PHE*     4.0     4.7    -      -       -      -
    129B  THR*     3.1    10.1    -      -       -      +
    130B  PRO*     1.4    82.4    -      -       +      +
    132B  MET*     1.3    67.9    +      -       -      +
    353B  GLN*     4.9     3.6    -      -       -      +
    356B  TRP*     3.8    25.6    -      -       +      -
    357B  ILE      3.2    15.5    -      -       -      +
    358B  SER*     4.2     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  VAL*     3.3    19.3    -      -       +      +
    105B  LEU*     3.5    35.7    -      -       +      -
    119B  MET      3.9     6.1    -      -       -      +
    120B  THR*     4.1    21.3    -      -       -      -
    123B  MET*     3.8    20.9    -      -       +      -
    124B  PHE*     3.6    26.5    -      -       +      -
    129B  THR*     4.8     2.2    -      -       +      -
    131B  ALA*     1.3    79.8    -      -       -      +
    133B  TYR*     1.3    61.6    +      -       -      +
    134B  VAL*     4.0    23.8    -      -       +      -
    356B  TRP*     3.4     5.2    -      -       -      -
    357B  ILE*     2.9    44.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  VAL      3.1     4.9    +      -       -      +
    104B  LEU*     3.4     9.6    -      -       +      -
    105B  LEU*     2.8    32.6    +      -       -      +
    132B  MET*     1.3    77.7    -      -       -      +
    134B  VAL*     1.3    84.1    +      -       -      +
    135B  ALA*     3.9    13.9    -      -       +      -
    346B  LEU*     5.1     1.8    -      -       +      -
    352B  PHE*     3.5    23.1    -      +       +      -
    355B  MET*     3.1    43.3    -      -       +      +
    356B  TRP*     3.4    21.5    -      -       +      -
    357B  ILE*     5.1     0.7    -      -       +      -
    373B  LYS      3.7    17.5    +      -       -      -
    374B  CYS*     3.7    31.5    -      -       -      -
    375B  PHE*     4.5    12.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  LEU*     3.4    11.2    -      -       +      +
    107B  GLU*     3.4    40.0    -      -       +      +
    116B  ARG*     4.4     9.6    +      -       +      +
    119B  MET*     3.9    25.4    -      -       +      -
    120B  THR*     4.8     0.2    -      -       -      +
    132B  MET*     4.0    21.1    -      -       +      -
    133B  TYR*     1.3    84.9    -      -       -      +
    135B  ALA*     1.3    58.4    +      -       -      +
    370B  VAL*     3.8    23.6    -      -       +      -
    374B  CYS*     3.7    22.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  LEU*     4.4    15.2    -      -       +      +
    105B  LEU      3.4     5.1    +      -       -      -
    106B  THR*     3.2     6.6    -      -       -      -
    107B  GLU*     2.7    33.3    +      -       -      -
    133B  TYR*     3.9    20.3    -      -       +      -
    134B  VAL*     1.3    74.4    -      -       -      +
    136B  ILE*     1.3    57.6    +      -       -      +
    139B  VAL*     6.1     1.8    -      -       +      -
    140B  LEU*     3.4    26.2    -      -       +      -
    346B  LEU*     5.3     3.4    -      -       +      -
    375B  PHE*     6.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  GLU*     3.3    26.4    +      -       +      +
    108B  ALA      4.4     6.5    -      -       -      +
    109B  PRO*     3.8    27.4    -      -       +      -
    110B  LEU      5.3     0.2    -      -       -      +
    135B  ALA*     1.3    71.0    -      -       -      +
    137B  GLN*     1.3    63.8    +      -       -      +
    138B  ALA*     3.9    10.5    -      -       +      +
    139B  VAL*     3.5    24.3    +      -       +      +
    140B  LEU*     2.9    19.8    -      -       -      +
    161B  HIS*     4.2    24.5    -      -       +      +
    163B  VAL*     5.4     0.9    -      -       +      -
    175B  ILE*     5.6     2.9    -      -       +      -
    374B  CYS      6.1     0.4    -      -       -      +
    375B  PHE*     4.2    31.4    -      -       +      -
----------------------------------------------------------
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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