Contacts of the strand formed by residues 131 - 136 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102E  PRO*     3.3    13.5    -      -       +      +
    103E  VAL      3.1    20.4    +      -       -      -
    124E  PHE*     4.0     4.5    -      -       -      -
    129E  THR*     3.1     9.8    -      -       -      +
    130E  PRO*     1.4    82.3    -      -       +      +
    132E  MET*     1.3    67.9    +      -       -      +
    353E  GLN*     4.9     4.0    -      -       -      +
    356E  TRP*     3.8    24.7    -      -       +      -
    357E  ILE      3.2    15.5    -      -       -      +
    358E  SER*     4.2     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 132 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103E  VAL*     3.3    19.3    -      -       +      +
    105E  LEU*     3.5    35.9    -      -       +      -
    119E  MET      3.9     5.8    -      -       -      +
    120E  THR*     4.1    21.3    -      -       -      -
    123E  MET*     3.8    20.6    -      -       +      -
    124E  PHE*     3.6    26.0    -      -       +      -
    129E  THR*     4.8     1.8    -      -       +      -
    131E  ALA*     1.3    80.0    -      -       -      +
    133E  TYR*     1.3    62.2    +      -       -      +
    134E  VAL*     4.0    24.2    -      -       +      -
    356E  TRP*     3.4     5.2    -      -       -      -
    357E  ILE*     2.9    44.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 133 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103E  VAL      3.1     5.1    +      -       -      +
    104E  LEU*     3.4    10.6    -      -       +      -
    105E  LEU*     2.8    32.2    +      -       -      +
    132E  MET*     1.3    78.7    -      -       -      +
    134E  VAL*     1.3    84.5    +      -       -      +
    135E  ALA*     3.9    13.0    -      -       +      -
    346E  LEU*     5.1     2.0    -      -       +      -
    352E  PHE*     3.5    23.1    -      +       +      -
    355E  MET*     3.1    45.1    -      -       +      +
    356E  TRP*     3.4    21.1    -      -       +      -
    357E  ILE*     5.1     0.2    -      -       +      -
    373E  LYS      3.7    17.2    +      -       -      -
    374E  CYS*     3.7    31.8    -      -       -      -
    375E  PHE*     4.5    12.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105E  LEU*     3.4    11.9    -      -       +      +
    107E  GLU*     3.4    40.5    -      -       +      +
    116E  ARG*     4.4     8.5    -      -       +      +
    119E  MET*     3.9    24.7    -      -       +      -
    132E  MET*     4.0    20.0    -      -       +      -
    133E  TYR*     1.3    85.7    +      -       -      +
    135E  ALA*     1.3    57.9    +      -       -      +
    136E  ILE      4.3     0.3    +      -       -      -
    370E  VAL*     3.8    24.2    -      -       +      -
    374E  CYS*     3.7    21.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104E  LEU*     4.4    15.7    -      -       +      +
    105E  LEU      3.4     4.9    +      -       -      -
    106E  THR*     3.2     6.8    -      -       -      -
    107E  GLU*     2.7    33.5    +      -       -      -
    133E  TYR*     3.9    19.8    -      -       +      -
    134E  VAL*     1.3    74.2    -      -       -      +
    136E  ILE*     1.3    57.7    +      -       -      +
    139E  VAL*     6.1     1.8    -      -       +      -
    140E  LEU*     3.4    25.6    -      -       +      -
    346E  LEU*     5.3     3.4    -      -       +      -
    375E  PHE*     6.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107E  GLU*     3.3    27.5    +      -       +      +
    108E  ALA      4.4     6.5    -      -       -      +
    109E  PRO*     3.8    28.3    -      -       +      -
    135E  ALA*     1.3    71.9    -      -       -      +
    137E  GLN*     1.3    64.4    +      -       -      +
    138E  ALA*     3.9    10.1    -      -       +      +
    139E  VAL*     3.5    24.2    +      -       +      +
    140E  LEU*     2.9    19.4    -      -       -      +
    161E  HIS*     4.2    23.6    -      -       +      +
    163E  VAL*     5.4     0.7    -      -       +      -
    175E  ILE*     5.6     2.7    -      -       +      -
    374E  CYS      6.1     0.7    -      -       -      +
    375E  PHE*     4.2    31.7    -      -       +      -
----------------------------------------------------------
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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