Contacts of the helix formed by residues 82 - 87 (chain 6) in PDB entry 3EXG
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.
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 THR 82 (chain 6).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376 TYR* 3.5 19.5 - - - +
806 PHE* 3.7 10.3 - - - +
816 MET* 1.3 84.6 - - + +
836 PHE* 1.3 65.0 + - - +
846 ASN* 2.8 27.2 + - - +
856 PHE* 3.0 40.6 + - + +
1176 PRO* 3.4 18.8 - - + -
1186 ASN* 5.8 0.4 - - - -
1286 HIS* 5.1 7.9 - - + +
1736 GLU* 5.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806 PHE* 3.9 22.0 - + - -
826 THR* 1.3 69.8 - - - +
846 ASN* 1.3 65.9 + - - +
856 PHE 3.1 0.2 - - - -
866 SER* 2.5 45.7 + - - +
876 MET 3.5 2.4 + - - -
1146 PHE* 4.0 17.7 - - + -
1156 ARG 4.0 0.7 - - - -
1166 GLY* 3.3 26.0 - - - -
1176 PRO 2.9 25.8 + - - -
1186 ASN* 3.9 20.5 - - + +
1326 PHE* 3.7 14.7 - - + -
1366 TYR* 3.8 17.9 - + - -
1686 VAL* 3.8 22.7 - - + -
1696 VAL 3.7 6.7 - - - -
1706 LEU* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 84 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373 ILE* 4.8 8.4 - - + +
914 ASP* 4.8 1.2 - - - +
954 ASN* 4.6 2.9 + - - -
994 LYS* 5.5 0.2 + - - -
826 THR* 2.8 26.4 + - - +
836 PHE* 1.3 77.3 - - - +
856 PHE* 1.3 64.0 + - + +
876 MET* 3.3 29.6 + - + +
886 GLN* 5.7 0.5 - - - +
1196 GLY 5.4 2.2 + - - +
1276 GLN 3.5 21.5 - - - +
1286 HIS* 3.0 29.4 + - + +
1296 SER* 3.3 2.1 + - - +
1306 GLN* 3.1 39.2 + - - +
1326 PHE* 3.7 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613 PHE* 6.2 0.4 - + - -
1363 GLY 4.2 10.8 - - - -
1373 ILE* 4.1 31.0 - - + -
1383 VAL* 5.0 8.1 - - + -
596 GLU* 3.8 33.3 - - + +
806 PHE* 5.0 0.7 - - + -
816 MET* 3.6 30.3 - - + +
826 THR* 3.0 47.0 + - + +
846 ASN* 1.3 72.9 - - + +
866 SER* 1.3 61.2 + - - +
876 MET 3.0 7.0 + - - -
886 GLN* 3.2 25.7 + - + +
1286 HIS* 3.9 22.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806 PHE* 3.4 46.8 - - - -
826 THR 3.7 1.2 + - - -
836 PHE* 2.5 34.4 + - - -
856 PHE* 1.3 72.7 - - - +
876 MET* 1.3 66.9 + - - +
886 GLN 3.0 2.7 - - - -
896 ALA 2.9 3.5 + - - +
906 ILE* 2.9 23.0 + - - +
936 VAL* 5.8 0.6 - - - +
1326 PHE* 5.2 0.7 - - - -
1366 TYR* 3.0 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874 MET 4.2 3.1 - - - +
904 ILE* 3.8 19.6 + - + +
914 ASP* 4.2 18.1 + - + -
944 ILE* 4.0 20.6 - - + -
954 ASN* 2.8 34.5 - - - +
994 LYS* 5.0 0.2 - - - +
836 PHE 3.5 0.2 + - - -
846 ASN* 3.3 17.1 + - + +
856 PHE 3.0 1.6 - - - -
866 SER* 1.3 80.4 + - - +
886 GLN* 1.3 61.4 + - + +
896 ALA 3.4 0.2 + - - -
906 ILE* 3.4 23.3 + - + +
1306 GLN* 3.6 15.0 - - - +
1326 PHE* 3.5 40.6 - - + -
1356 TRP* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
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