Contacts of the strand formed by residues 131 - 136 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102H  PRO*     3.3    13.6    -      -       +      +
    103H  VAL      3.1    20.5    +      -       -      -
    124H  PHE*     4.0     4.7    -      -       -      -
    129H  THR*     3.1     9.7    -      -       -      +
    130H  PRO*     1.4    83.0    -      -       +      +
    132H  MET*     1.3    67.9    +      -       -      +
    353H  GLN*     4.9     4.3    -      -       -      +
    356H  TRP*     3.8    24.2    -      -       +      -
    357H  ILE      3.2    14.8    -      -       -      +
    358H  SER*     4.2     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 132 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103H  VAL*     3.3    18.8    -      -       +      +
    105H  LEU*     3.5    35.2    -      -       +      -
    119H  MET      3.9     5.4    -      -       -      +
    120H  THR*     4.1    21.1    -      -       -      -
    123H  MET*     3.8    21.1    -      -       +      -
    124H  PHE*     3.6    26.2    -      -       +      -
    129H  THR*     4.8     1.8    -      -       +      -
    131H  ALA*     1.3    79.8    -      -       -      +
    133H  TYR*     1.3    62.2    +      -       -      +
    134H  VAL*     4.0    24.0    -      -       +      -
    356H  TRP*     3.4     5.2    -      -       -      -
    357H  ILE*     2.9    45.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 133 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103H  VAL      3.1     5.4    +      -       -      +
    104H  LEU*     3.4     9.6    -      -       +      -
    105H  LEU*     2.8    32.6    +      -       -      +
    132H  MET*     1.3    76.2    -      -       -      +
    134H  VAL*     1.3    83.3    +      -       -      +
    135H  ALA*     3.9    13.5    -      -       +      -
    346H  LEU*     5.1     2.0    -      -       +      -
    352H  PHE*     3.5    22.4    -      +       +      -
    355H  MET*     3.1    45.0    -      -       +      +
    356H  TRP*     3.4    21.8    -      -       +      -
    357H  ILE*     5.1     0.7    -      -       +      -
    373H  LYS      3.7    18.2    +      -       -      -
    374H  CYS*     3.7    32.0    -      -       -      -
    375H  PHE*     4.5    12.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105H  LEU*     3.4    12.8    -      -       +      +
    107H  GLU*     3.4    40.7    -      -       +      +
    116H  ARG*     4.4     9.0    -      -       +      +
    119H  MET*     3.9    24.9    -      -       +      -
    132H  MET*     4.0    20.9    -      -       +      -
    133H  TYR*     1.3    85.9    +      -       -      +
    135H  ALA*     1.3    57.7    +      -       -      +
    370H  VAL*     3.8    23.8    -      -       +      -
    374H  CYS*     3.7    23.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104H  LEU*     4.4    15.2    -      -       +      +
    105H  LEU      3.4     5.1    +      -       -      -
    106H  THR*     3.2     6.2    -      -       -      -
    107H  GLU*     2.7    33.7    +      -       -      -
    133H  TYR*     3.9    19.2    -      -       +      -
    134H  VAL*     1.3    74.9    -      -       -      +
    136H  ILE*     1.3    57.6    +      -       -      +
    139H  VAL*     6.1     2.2    -      -       +      -
    140H  LEU*     3.4    26.2    -      -       +      -
    346H  LEU*     5.3     3.6    -      -       +      -
    375H  PHE*     6.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107H  GLU*     3.3    28.7    +      -       +      +
    108H  ALA      4.4     6.5    -      -       -      +
    109H  PRO*     3.8    27.6    -      -       +      -
    110H  LEU      5.3     0.2    -      -       -      +
    134H  VAL      4.3     0.2    +      -       -      -
    135H  ALA*     1.3    70.6    -      -       -      +
    137H  GLN*     1.3    65.0    +      -       -      +
    138H  ALA*     3.9    10.5    -      -       +      +
    139H  VAL*     3.5    23.1    +      -       +      +
    140H  LEU*     2.9    19.2    -      -       -      +
    161H  HIS*     4.2    24.2    -      -       +      +
    163H  VAL*     5.4     1.1    -      -       +      -
    175H  ILE*     5.6     3.1    -      -       +      -
    374H  CYS      6.1     0.7    -      -       -      +
    375H  PHE*     4.2    32.4    -      -       +      -
----------------------------------------------------------
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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