Contacts of the helix formed by residues 91 - 97 (chain 1) 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 ALA 91 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871 THR* 3.7 17.5 - - + -
891 TYR 3.1 7.1 + - - +
901 ARG* 1.3 72.9 - - - +
921 HIS* 1.3 67.6 + - - +
931 GLY 3.5 2.0 - - - -
941 PHE* 4.0 6.1 - - - -
951 THR* 2.8 27.5 + - - +
1231 SER 5.1 3.4 - - - +
1241 MET 5.9 0.2 - - - -
1261 MET* 4.5 5.6 - - + +
1311 PHE* 4.0 6.7 - - + -
1341 GLY* 3.6 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451 MET* 5.0 5.2 - - - +
461 GLU* 3.2 36.9 + - - +
491 ALA* 5.0 0.2 - - - +
621 CYS* 3.8 24.2 - - - -
631 HIS 3.6 17.3 + - - -
641 LEU* 4.4 2.2 - - - +
651 CYS* 4.7 1.2 - - - -
891 TYR 5.0 1.0 + - - -
901 ARG 3.6 2.4 - - - -
911 ALA* 1.3 80.9 - - - +
931 GLY* 1.3 66.1 + - - +
951 THR* 3.0 13.3 + - - -
961 PHE* 3.2 10.6 + - - +
1051 ILE* 4.1 15.1 - - + +
1091 LEU* 3.9 18.4 - - + +
1231 SER* 2.8 34.8 + - - -
1261 MET* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421 VAL* 3.9 22.4 - - - +
651 CYS* 3.4 24.9 - - - -
721 CYS* 3.9 11.9 - - - -
901 ARG 5.0 0.2 + - - -
911 ALA 3.5 0.4 - - - -
921 HIS* 1.3 77.3 - - - +
941 PHE* 1.3 57.1 + - - +
961 PHE* 3.1 6.4 + - - +
971 THR* 3.1 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651 CYS* 6.1 1.8 - - + -
711 CYS* 4.6 2.2 - - + -
721 CYS* 3.6 36.6 - - + -
751 LEU* 3.9 14.8 - - + -
761 GLU* 5.8 0.9 - - - -
851 LEU* 3.3 28.5 - - + -
871 THR* 4.5 11.2 - - + -
901 ARG 4.2 17.3 - - - -
911 ALA* 3.6 3.7 + - - +
921 HIS 3.2 0.4 - - - -
931 GLY* 1.3 74.7 - - - +
951 THR* 1.3 66.1 + - - +
971 THR* 3.6 8.3 - - - -
981 ARG* 3.1 29.4 + - + +
1311 PHE* 4.0 21.7 - - + -
1641 LEU* 3.1 36.1 - - + -
1941 GLU* 3.8 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911 ALA* 2.8 21.9 + - - +
921 HIS 3.0 6.7 + - - -
941 PHE* 1.3 78.1 - - - +
961 PHE* 1.3 63.1 + - - +
981 ARG* 3.4 5.2 + - - +
991 GLY 3.8 0.3 + - - -
1001 LEU* 3.1 57.7 + - + +
1051 ILE* 3.5 16.4 - - + -
1261 MET* 3.4 23.3 - - + +
1281 ALA* 5.0 2.0 - - + +
1311 PHE* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 ARG* 6.4 0.4 - - + -
381 MET* 3.8 29.6 - - + -
411 THR* 3.4 34.1 - - + -
421 VAL* 3.7 26.2 - - + -
451 MET* 5.1 4.5 - - + -
921 HIS 3.2 7.5 + - - +
931 GLY 3.1 9.4 + - - +
951 THR* 1.3 72.9 - - - +
971 THR* 1.3 67.5 + - + +
981 ARG 2.8 10.3 + - - -
991 GLY* 3.2 11.1 + - - -
1001 LEU 3.6 19.0 - - - +
1011 SER* 4.8 1.3 - - - -
1021 VAL* 4.0 23.3 - - + -
1051 ILE* 3.8 8.0 - - + +
3161 GLU* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 MET* 4.8 12.3 - - - -
421 VAL* 4.8 1.6 - - + -
721 CYS* 3.6 37.9 + - - +
731 VAL* 4.3 13.9 - - + -
761 GLU* 3.2 36.5 + - - +
931 GLY 3.1 16.3 + - - +
941 PHE* 3.5 15.6 + - - -
961 PHE* 1.3 87.1 - - + +
981 ARG* 1.3 58.1 + - - +
991 GLY 3.5 1.4 + - - -
----------------------------------------------------------
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