Contacts of the strand formed by residues 16 - 21 (chain I) 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 I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13I  GLY*     3.0    19.0    +      -       -      -
     14I  SER      3.7     0.4    -      -       -      -
     15I  GLY*     1.3    88.9    -      -       -      +
     17I  CYS*     1.3    57.7    +      -       -      +
     18I  LYS*     2.9    32.5    +      -       +      +
     30I  VAL*     3.5    28.5    -      -       +      +
     31I  PHE*     3.5    23.1    -      -       -      +
     32I  PRO*     4.1    11.9    -      -       +      -
     33I  SER*     3.7     5.4    -      -       -      -
    210I  ARG*     4.8    10.3    -      -       -      +
    336I  LYS*     4.3    12.8    -      -       -      +
    337I  TYR*     5.5     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 17 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10I  VAL*     5.9     3.4    -      -       +      -
     11I  ASP      3.3    12.8    -      -       -      +
     12I  ASN*     4.3    11.7    -      -       -      -
     16I  MET*     1.3    74.2    -      -       -      +
     18I  LYS*     1.3    63.3    +      -       -      +
     19I  ALA*     6.1     0.4    -      -       +      -
     29I  ALA      3.7     1.1    -      -       -      +
     30I  VAL*     3.3     3.6    -      -       -      +
     31I  PHE*     2.8    56.4    +      -       +      -
     33I  SER*     3.0    24.7    -      -       -      -
     71I  ILE*     4.4     8.1    -      -       -      -
     85I  ILE*     3.9    27.6    -      -       -      -
     89I  THR*     5.7     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 18 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10I  VAL*     5.0     0.3    -      -       -      +
     11I  ASP*     2.8    60.8    +      -       +      +
     13I  GLY*     4.4     6.3    -      -       -      -
     16I  MET*     2.9    31.3    +      -       +      +
     17I  CYS*     1.3    78.3    -      -       -      +
     19I  ALA*     1.3    59.1    +      -       -      +
     27I  PRO*     3.6    22.7    -      -       +      -
     29I  ALA      3.2     5.8    -      -       -      -
     30I  VAL*     4.0     8.7    -      -       +      +
    336I  LYS*     3.5    27.6    -      -       -      +
    337I  TYR*     3.9    21.8    -      -       +      -
    340I  TRP*     3.3    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 19 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9I  VAL      3.2     9.2    -      -       -      +
     10I  VAL*     4.4     5.2    -      -       +      -
     17I  CYS*     6.1     0.7    -      -       +      -
     18I  LYS*     1.3    75.4    -      -       -      +
     20I  GLY*     1.3    59.0    +      -       -      +
     27I  PRO*     4.3     0.6    -      -       -      +
     28I  ARG      3.1     4.7    +      -       -      -
     29I  ALA*     3.0    36.5    +      -       +      +
     31I  PHE*     4.9     4.7    -      -       +      -
     89I  THR*     3.7    20.4    -      -       +      -
     94I  LEU*     3.6    26.2    -      -       +      +
    340I  TRP*     3.7     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 20 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8I  LEU*     3.1    10.9    -      -       -      +
      9I  VAL      2.9    26.1    +      -       -      -
     19I  ALA*     1.3    76.4    -      -       -      +
     21I  PHE*     1.3    68.4    +      -       -      -
     28I  ARG*     4.2     9.2    -      -       -      -
     94I  LEU*     3.9    12.3    -      -       -      +
    340I  TRP*     3.4    17.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 21 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3I  ASP*     3.4    33.4    -      -       -      +
      4I  ASP*     5.9     1.1    -      -       -      -
      6I  ALA*     4.5     7.4    -      -       +      -
      7I  ALA      3.6     3.1    -      -       -      +
      8I  LEU*     3.2    34.8    -      -       +      -
     20I  GLY*     1.3    78.6    -      -       -      -
     22I  ALA*     1.3    69.7    +      -       -      +
     24I  ASP*     3.1    37.2    +      -       -      +
     28I  ARG*     3.3    41.3    -      -       -      +
     94I  LEU*     4.3    26.7    -      -       +      -
     96I  VAL*     3.8    21.8    -      -       +      -
    101I  HIS*     5.3     1.3    -      +       -      -
    340I  TRP*     3.8     9.0    -      -       -      -
----------------------------------------------------------
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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