Contacts of the strand formed by residues 286 - 290 (chain C) in PDB entry 3ELP


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 286 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304B  LYS*     5.1     0.9    +      -       -      -
    280C  LEU*     2.9    49.6    -      -       +      +
    281C  GLU*     4.8     4.4    -      -       -      +
    283C  ASN*     3.3    21.3    +      -       +      +
    284C  PRO      3.4     0.7    -      -       -      +
    285C  TRP*     1.3    85.2    -      -       -      +
    287C  GLU*     1.3    65.3    +      -       -      +
    288C  LYS*     3.6    23.6    -      -       -      +
    289C  VAL*     3.8    14.1    -      -       +      -
    316C  PHE*     4.2    11.7    -      -       +      -
    317C  TYR      3.7     7.4    -      -       -      +
    319C  LYS*     3.9    11.1    +      -       -      +
    394C  LEU*     4.4     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 287 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  GLU*     3.2    23.2    -      -       -      +
    304B  LYS*     3.4    18.7    +      -       -      -
    286C  VAL*     1.3    74.9    -      -       -      +
    288C  LYS*     1.3    66.2    +      -       +      +
    317C  TYR*     2.8    27.8    +      -       +      +
    318C  ILE      4.7     1.1    -      -       -      +
    319C  LYS*     3.3    38.9    +      -       +      +
    320C  GLY      5.6     0.9    -      -       -      +
    372C  THR*     5.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 288 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  GLU*     4.7    22.4    -      -       +      +
    281C  GLU*     6.2     0.9    -      -       -      +
    286C  VAL*     3.4     6.0    -      -       -      +
    287C  GLU*     1.3    84.7    -      -       +      +
    289C  VAL*     1.3    66.1    +      -       -      +
    290C  ILE*     4.1    17.5    -      -       +      +
    316C  PHE*     3.5     1.4    -      -       -      -
    317C  TYR*     2.9    60.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 289 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277C  ALA*     3.9     6.5    -      -       -      +
    280C  LEU*     3.9     6.1    -      -       +      -
    281C  GLU*     3.5    56.9    +      -       +      +
    286C  VAL*     3.8    11.7    -      -       +      -
    288C  LYS*     1.3    79.8    -      -       -      +
    290C  ILE*     1.3    81.7    +      -       -      +
    291C  TYR*     3.9     2.3    +      -       +      -
    294C  LEU*     3.9    18.4    -      -       +      -
    296C  SER*     4.6     9.5    +      -       -      +
    297C  HIS*     5.7     1.0    -      -       -      -
    314C  VAL*     4.1    17.3    -      -       +      -
    315C  THR      3.5    11.0    -      -       -      +
    316C  PHE*     4.2     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 290 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163C  THR*     3.3    26.7    -      -       +      +
    164C  GLN*     3.4    11.3    +      -       +      -
    288C  LYS*     4.1    24.2    -      -       +      +
    289C  VAL*     1.3    84.2    -      -       -      +
    291C  TYR*     1.3    59.9    +      -       -      +
    296C  SER      6.1     0.4    -      -       -      +
    297C  HIS*     3.9    22.2    -      -       +      +
    298C  PRO*     5.0    14.6    -      -       +      -
    315C  THR*     2.6    43.8    +      -       +      +
    317C  TYR*     3.8    24.0    -      -       +      +
----------------------------------------------------------
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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