Contacts of the strand formed by residues 103 - 107 (chain G) 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 VAL 103 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  LEU*     3.6    18.6    -      -       +      +
     10G  VAL*     5.5     1.1    -      -       +      -
     90G  PHE*     4.0    29.2    -      -       +      -
     98G  PRO*     5.6     2.2    -      -       +      +
    101G  HIS      4.2     2.5    -      -       -      +
    102G  PRO*     1.3    78.8    -      -       -      +
    104G  LEU*     1.3    62.1    +      -       -      +
    105G  LEU*     4.4    12.3    -      -       +      -
    123G  MET*     3.8    19.1    -      -       -      -
    129G  THR*     3.8    18.8    -      -       +      -
    131G  ALA      3.1     4.4    +      -       -      -
    132G  MET*     3.3    20.7    -      -       +      -
    133G  TYR      3.1    23.2    +      -       -      +
    356G  TRP*     3.3     4.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 104 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  ALA*     5.1     0.4    -      -       -      +
      8G  LEU      3.2     8.2    +      -       -      +
      9G  VAL*     3.7    27.4    -      -       +      -
     10G  VAL*     3.0    26.0    +      -       -      +
    102G  PRO      4.3     0.4    +      -       -      -
    103G  VAL*     1.3    73.6    -      -       -      +
    105G  LEU*     1.3    60.0    +      -       -      +
    106G  THR*     4.0     9.0    -      -       +      -
    133G  TYR*     3.4    14.8    -      -       +      +
    135G  ALA*     4.4     8.1    -      -       +      -
    140G  LEU*     3.9    24.0    -      -       +      -
    343G  GLY*     4.1     4.0    -      -       -      +
    346G  LEU*     3.5    31.4    -      -       +      -
    347G  ALA*     4.4    12.3    -      -       +      +
    352G  PHE*     3.5    22.0    -      -       +      -
    356G  TRP*     4.0     8.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10G  VAL*     3.4    28.9    -      -       +      -
     12G  ASN*     4.3     3.6    -      -       -      +
     86G  TRP*     4.4    12.8    -      -       +      -
     90G  PHE*     5.6     0.4    -      -       +      -
    103G  VAL*     4.4     9.9    -      -       +      -
    104G  LEU*     1.3    75.0    -      -       -      +
    106G  THR*     1.3    68.2    +      -       -      +
    119G  MET*     3.5    31.9    -      -       +      -
    123G  MET*     3.8    35.0    -      -       +      -
    132G  MET*     3.5    27.4    -      -       +      -
    133G  TYR      2.8     9.2    +      -       -      +
    134G  VAL*     3.4    19.7    -      -       +      -
    135G  ALA      3.4     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 106 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  VAL*     5.1     2.0    -      -       +      -
     10G  VAL      2.9    14.2    +      -       -      +
     11G  ASP*     2.7    33.7    +      -       +      +
     12G  ASN*     3.4    21.0    +      -       -      +
    104G  LEU*     4.0     8.3    -      -       +      -
    105G  LEU*     1.3    79.3    -      -       -      +
    107G  GLU*     1.3    62.1    -      -       -      +
    119G  MET*     4.7     4.0    -      -       -      +
    134G  VAL*     4.4     0.6    -      -       -      +
    135G  ALA      3.2     9.2    -      -       -      +
    137G  GLN*     3.8    12.6    +      -       -      +
    140G  LEU*     3.2    35.0    -      -       +      -
    339G  VAL*     4.0     9.2    -      -       +      +
    340G  TRP*     6.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 107 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106G  THR*     1.3    77.1    -      -       -      +
    108G  ALA*     1.3    68.8    +      -       -      +
    111G  ASN*     3.1    31.9    +      -       -      +
    116G  ARG*     3.0    38.3    +      -       -      +
    119G  MET*     4.4     3.6    -      -       +      -
    134G  VAL*     3.4    21.5    -      -       +      +
    135G  ALA      2.7    22.8    +      -       -      +
    136G  ILE*     3.3    24.5    +      -       -      +
    137G  GLN*     3.0    33.9    +      -       -      +
----------------------------------------------------------
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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