Contacts of the helix formed by residues 184 - 193 (chain D) in PDB entry 6GR2
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 ILE 184 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ASP* 3.5 3.9 + - + +
167D ALA* 4.9 2.6 - - + +
168D GLN* 4.5 20.9 - - + +
171D GLN* 3.0 30.0 - - + +
183D GLY* 1.3 72.7 - - - -
185D MET* 1.3 72.6 + - - +
186D ASP 3.4 1.1 + - - -
187D GLN* 3.5 8.0 + - - +
188D PHE* 2.9 37.7 + - + +
201D ILE* 4.4 11.2 - - + -
203D CYS* 3.3 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ARG* 4.3 6.3 - - - -
39D ASN* 3.0 48.9 - - + +
42D GLY 5.1 0.2 - - - +
43D GLU* 4.7 4.9 - - - +
46D ASP* 3.5 24.4 + - + +
52D VAL* 3.9 22.7 - - + -
54D PRO* 3.0 37.2 - - + -
183D GLY 3.3 2.0 - - - -
184D ILE* 1.3 85.9 - - - +
186D ASP* 1.3 70.5 + - - +
188D PHE* 3.0 4.6 + - - +
189D ILE* 2.9 33.2 + - + +
201D ILE* 4.5 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ARG* 2.5 47.4 + - - +
46D ASP* 6.1 0.2 - - - -
140D SER* 3.8 11.6 - - - -
142D SER* 5.5 1.3 + - - +
143D ALA* 3.6 20.5 - - + +
182D CYS* 5.4 7.2 - - - +
183D GLY 4.5 2.4 + - - +
184D ILE 3.4 0.8 - - - -
185D MET* 1.3 82.6 - - - +
187D GLN* 1.3 69.8 + - - +
189D ILE* 3.1 21.0 - - - +
190D SER* 3.1 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ALA* 4.1 10.6 - - + +
146D GLU* 3.2 19.5 + - - +
147D VAL* 3.9 11.1 - - + +
167D ALA* 3.7 25.4 - - + +
170D CYS* 3.5 26.9 - - + -
171D GLN* 3.9 11.7 - - - +
174D GLU* 3.2 17.2 + - - -
182D CYS* 3.6 12.7 - - - -
183D GLY 3.0 23.2 - - - +
184D ILE* 3.7 6.7 - - - +
186D ASP* 1.3 76.1 + - - +
188D PHE* 1.3 62.9 + - - +
190D SER* 3.4 2.8 + - - -
191D LEU* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D ILE 5.4 0.7 - - - -
164D ALA* 4.0 30.3 - - + -
167D ALA* 4.0 18.8 - - + +
184D ILE* 2.9 34.1 + - + +
185D MET* 3.0 4.5 + - - +
187D GLN* 1.3 77.2 - - - +
189D ILE* 1.3 56.9 + - - +
191D LEU* 3.2 2.3 + - - -
192D MET* 2.8 79.3 + - + +
199D LEU* 4.7 1.3 - - + -
201D ILE* 4.1 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ARG* 3.4 33.2 - - + -
54D PRO* 3.9 23.3 - - + +
55D MET* 3.9 6.3 - - - -
56D ALA* 3.7 32.8 - - - +
185D MET 2.9 17.6 + - - +
186D ASP* 3.1 16.6 - - - +
188D PHE* 1.3 74.8 - - - +
190D SER* 1.3 63.3 + - - +
192D MET 4.3 0.2 - - - +
193D GLY* 3.0 29.6 + - - -
197D HIS 6.0 0.4 - - - +
199D LEU* 3.8 35.0 - - + -
201D ILE* 4.5 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ALA* 3.7 12.1 - - - +
35D PRO* 2.9 53.8 + - - +
36D GLY 5.6 0.9 - - - -
37D ARG* 6.1 0.2 - - - -
56D ALA* 5.5 0.2 - - - -
143D ALA* 4.6 4.9 - - - -
144D SER* 4.0 2.8 - - - -
147D VAL* 3.7 18.9 - - - +
186D ASP 3.1 19.0 + - - -
187D GLN 3.7 4.5 - - - -
189D ILE* 1.3 81.1 - - - +
191D LEU* 1.3 59.2 + - - +
193D GLY 4.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D VAL* 3.5 28.3 - - + -
150D TYR* 5.6 3.6 - - + -
151D THR* 4.9 5.8 - - - +
154D GLN* 5.5 2.0 - - - +
163D ILE* 3.7 24.6 - - + +
166D ARG* 3.7 27.1 - - + +
167D ALA* 3.2 45.5 - - + +
170D CYS* 5.3 0.9 - - - -
187D GLN 3.0 14.1 + - - +
188D PHE* 3.7 4.0 - - - +
190D SER* 1.3 77.9 - - - +
192D MET* 1.3 61.8 + - + +
193D GLY 3.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D ILE* 3.4 43.7 - - + -
188D PHE* 2.8 51.3 + - + +
191D LEU* 1.3 75.6 - - + +
193D GLY* 1.3 67.3 + - - +
194D GLN* 3.5 14.1 + - - +
199D LEU* 3.2 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PRO* 6.1 0.7 - - - -
56D ALA* 4.3 14.1 - - - -
189D ILE* 3.0 29.4 + - - -
190D SER 4.6 1.2 + - - -
191D LEU 3.6 3.2 - - - +
192D MET* 1.3 81.5 - - - +
194D GLN* 1.3 68.3 + - - +
197D HIS 6.0 0.2 - - - -
199D LEU* 4.5 2.2 - - - -
----------------------------------------------------------
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