Contacts of the strand formed by residues 312 - 314 (chain K) in PDB entry 1LWU


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 TYR 312 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259K  VAL*     3.9     0.3    -      -       -      +
    260K  PHE*     3.1    27.9    +      +       +      +
    272K  VAL*     2.6    49.2    +      -       +      +
    273K  VAL      4.0     4.9    -      -       -      -
    274K  GLN*     3.2     5.0    -      -       -      +
    275K  ASN*     3.1    32.4    +      -       +      -
    283K  PHE*     3.9    11.5    -      -       -      -
    293K  GLU*     5.0     0.4    -      -       +      -
    294K  PHE*     3.1    14.6    -      -       -      +
    295K  GLY*     3.8     2.2    -      -       -      -
    296K  ASN      3.2    27.1    -      -       -      +
    297K  ILE*     3.4    40.2    -      -       +      -
    310K  GLY      3.7     8.5    -      -       -      -
    311K  GLU*     1.3    75.6    -      -       -      +
    313K  TRP*     1.3    59.9    +      -       -      +
    314K  LEU*     3.3    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 313 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273K  VAL*     3.5    11.7    -      -       +      -
    274K  GLN*     3.3    37.7    -      -       +      -
    283K  PHE*     4.4     2.2    -      -       +      -
    290K  TYR*     3.0    48.6    +      +       -      -
    293K  GLU*     2.9    19.4    -      -       -      +
    294K  PHE*     2.8    37.7    +      +       +      -
    312K  TYR*     1.3    74.6    -      -       -      +
    314K  LEU*     1.3    88.8    +      -       -      +
    316K  THR*     3.0    21.6    +      -       -      +
    319K  VAL*     5.3     2.0    -      -       +      -
    395K  PHE*     3.8    13.7    -      +       -      -
    422K  TRP*     4.5     2.5    -      +       -      -
    423K  TRP*     3.8    30.3    -      +       -      -
    433K  ASN*     3.3    24.9    -      -       -      -
    472K  MET*     4.4    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 314 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257K  TYR*     3.9    23.6    -      -       +      +
    258K  LYS      4.1     8.1    -      -       -      +
    259K  VAL*     3.7    31.4    -      -       +      -
    271K  THR*     4.8     4.9    -      -       +      -
    273K  VAL*     2.8    38.3    +      -       +      +
    293K  GLU*     3.3    18.2    -      -       -      +
    297K  ILE*     5.3     0.4    -      -       +      -
    312K  TYR*     3.3    16.0    -      -       +      -
    313K  TRP*     1.3    82.5    +      -       -      +
    315K  GLY*     1.3    69.7    +      -       -      +
    318K  THR*     3.8    28.0    -      -       +      +
    319K  VAL*     3.7     8.8    -      -       +      +
    322K  LEU*     5.3     4.0    -      -       +      -
----------------------------------------------------------
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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