Contacts of the strand formed by residues 16 - 21 (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 MET 16 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13G  GLY*     3.0    19.0    +      -       -      -
     14G  SER      3.7     0.2    -      -       -      -
     15G  GLY*     1.3    86.5    -      -       -      +
     17G  CYS*     1.3    58.4    +      -       -      +
     18G  LYS*     2.9    33.3    +      -       +      +
     30G  VAL*     3.5    28.3    -      -       +      +
     31G  PHE*     3.5    24.5    -      -       -      +
     32G  PRO*     4.1    12.3    -      -       +      -
     33G  SER*     3.7     5.6    -      -       -      -
    210G  ARG*     4.8    10.3    -      -       -      +
    336G  LYS*     4.3    13.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 17 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10G  VAL*     5.9     3.4    -      -       +      -
     11G  ASP      3.3    12.6    -      -       -      +
     12G  ASN*     4.3    13.2    -      -       -      -
     16G  MET*     1.3    74.0    -      -       -      +
     18G  LYS*     1.3    62.5    +      -       -      +
     19G  ALA*     6.1     0.4    -      -       +      -
     29G  ALA      3.7     1.0    -      -       -      +
     30G  VAL*     3.3     3.1    -      -       -      +
     31G  PHE*     2.8    57.1    +      -       +      -
     33G  SER*     3.0    24.0    -      -       -      -
     71G  ILE*     4.4     7.4    -      -       -      -
     85G  ILE*     3.9    27.4    -      -       -      -
     89G  THR*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 18 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10G  VAL*     5.0     0.3    -      -       -      +
     11G  ASP*     2.8    62.4    +      -       +      +
     13G  GLY*     4.4     6.1    -      -       -      -
     16G  MET*     2.9    32.4    +      -       +      +
     17G  CYS*     1.3    79.0    -      -       -      +
     19G  ALA*     1.3    59.1    +      -       -      +
     27G  PRO*     3.6    22.9    -      -       +      -
     29G  ALA      3.2     6.1    -      -       -      -
     30G  VAL*     4.0     7.9    -      -       +      -
    336G  LYS*     3.5    28.9    -      -       -      +
    337G  TYR*     3.9    20.9    -      -       +      -
    340G  TRP*     3.3    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 19 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  VAL      3.2     9.4    -      -       -      +
     10G  VAL*     4.4     5.2    -      -       +      -
     17G  CYS*     6.1     0.7    -      -       +      -
     18G  LYS*     1.3    75.0    -      -       -      +
     20G  GLY*     1.3    59.0    +      -       -      +
     27G  PRO*     4.3     0.6    -      -       -      +
     28G  ARG      3.1     4.5    +      -       -      -
     29G  ALA*     3.0    36.9    +      -       +      +
     31G  PHE*     4.9     4.3    -      -       +      -
     89G  THR*     3.7    20.0    -      -       +      -
     94G  LEU*     3.6    27.4    -      -       +      +
    340G  TRP*     3.7     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 20 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  LEU*     3.1    10.6    -      -       -      +
      9G  VAL      2.9    27.1    +      -       -      -
     19G  ALA*     1.3    75.8    -      -       -      +
     21G  PHE*     1.3    69.3    +      -       -      -
     28G  ARG*     4.2     9.9    -      -       -      -
     94G  LEU*     3.9    11.5    -      -       -      +
    340G  TRP*     3.4    17.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 21 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3G  ASP*     3.4    33.0    -      -       -      -
      4G  ASP*     5.9     0.9    -      -       -      -
      6G  ALA*     4.5     7.2    -      -       +      -
      7G  ALA      3.6     3.8    -      -       -      +
      8G  LEU*     3.2    34.5    -      -       +      -
      9G  VAL*     4.7     0.2    -      -       -      -
     20G  GLY*     1.3    77.6    -      -       -      -
     22G  ALA*     1.3    68.9    +      -       -      +
     24G  ASP*     3.1    38.1    +      -       -      +
     28G  ARG*     3.3    41.7    -      -       -      +
     94G  LEU*     4.3    28.0    -      -       +      -
     96G  VAL*     3.8    21.5    -      -       +      -
    101G  HIS*     5.3     1.6    -      +       -      -
    340G  TRP*     3.8     8.6    -      -       -      -
----------------------------------------------------------
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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