Contacts of the helix formed by residues 292 - 302 (chain C) in PDB entry 6XHU
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 292 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY 3.7 23.3 - - - +
110C GLN* 4.2 4.9 - - + -
111C THR* 3.7 25.8 - - + +
203C ASN* 3.5 5.6 - - - +
206C ALA* 3.9 1.6 - - - -
291C PHE* 1.3 76.4 - - - +
293C PRO* 1.3 75.7 - - - +
294C PHE* 3.3 14.8 + - + +
295C ASP* 2.9 30.9 + - - -
296C VAL* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C VAL* 4.0 16.4 - - + +
203C ASN* 3.8 10.5 - - - +
206C ALA* 3.7 14.8 - - + -
249C ILE* 3.8 35.4 - - + +
250C LEU* 3.8 28.7 - - + -
253C LEU* 4.6 5.6 - - + +
292C THR* 1.3 86.5 - - - +
294C PHE* 1.3 64.4 + - + +
296C VAL* 3.3 3.5 + - - +
297C VAL* 3.1 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C GLN* 6.3 0.9 - - - -
249C ILE* 4.0 33.2 - - + -
292C THR* 3.2 14.6 + - + +
293C PRO* 1.3 75.2 - - + +
295C ASP* 1.3 63.9 + - - +
297C VAL* 3.4 7.2 + - + +
298C ARG* 2.9 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE* 5.3 0.5 - - - -
111C THR* 2.7 32.0 + - - +
127C GLN* 4.1 4.6 + - - -
151C ASN* 5.7 1.0 + - - -
290C GLU 4.1 1.2 - - - +
291C PHE* 3.8 19.7 - - + -
292C THR* 2.9 37.2 + - - +
294C PHE* 1.3 76.9 - - - +
296C VAL* 1.3 62.7 + - - +
298C ARG* 2.8 36.3 + - - +
299C GLN* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 4.0 21.8 - - + -
206C ALA* 3.6 31.4 - - + +
207C TRP* 4.4 0.7 - - - +
210C ALA* 3.8 25.6 - - + +
213C ILE* 5.0 0.4 - - + -
253C LEU* 4.1 22.0 - - + -
291C PHE* 4.2 9.2 - - + -
292C THR 3.1 14.2 + - - +
293C PRO 3.7 6.3 - - - +
294C PHE 3.3 0.4 - - - -
295C ASP* 1.3 75.7 - - - +
297C VAL* 1.3 58.6 + - - +
299C GLN* 3.8 0.3 - - - +
300C CYS* 2.9 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C PRO* 5.0 14.4 - - + -
253C LEU* 4.1 24.5 - - + -
256C GLN* 5.8 1.8 - - - +
293C PRO* 3.1 18.0 + - + +
294C PHE* 3.8 7.0 - - + +
296C VAL* 1.3 75.0 - - - +
298C ARG* 1.3 57.4 + - + +
300C CYS* 4.8 3.4 - - - -
301C SER* 2.8 44.7 + - - +
303C VAL* 5.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER* 4.7 10.9 + - - -
6C MET* 5.0 14.6 + - - +
7C ALA 6.2 1.2 - - - -
8C PHE* 3.4 40.4 - - - -
127C GLN* 4.1 7.5 - - - +
152C ILE 5.8 0.2 - - - -
294C PHE* 2.9 22.8 + - + +
295C ASP* 2.8 37.1 + - - +
297C VAL* 1.3 76.9 - - + +
299C GLN* 1.3 59.5 + - - +
302C GLY* 2.8 26.7 + - - -
303C VAL* 3.3 36.0 + - + +
305C PHE* 4.2 22.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 5.5 0.3 + - - -
139A SER* 2.5 30.7 + - - +
141A LEU* 3.4 20.1 - - - +
2C GLY 5.1 0.7 - - - +
3C PHE* 3.3 33.2 - - + -
4C ARG* 2.8 41.5 + - - +
6C MET* 4.3 25.2 - - + +
291C PHE* 4.2 5.1 - - - -
295C ASP* 3.0 16.4 + - - +
298C ARG* 1.3 78.9 - - - +
300C CYS* 1.3 59.6 + - - +
302C GLY* 4.0 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.5 20.3 - - - +
3C PHE* 4.3 14.8 - - - -
210C ALA* 4.9 1.6 - - - -
213C ILE* 4.2 34.1 - - + -
214C ASN* 4.5 10.1 - - - -
253C LEU* 6.2 0.4 - - + -
256C GLN* 5.0 8.7 + - - +
296C VAL* 2.9 34.2 + - - +
297C VAL* 4.3 2.9 - - - +
299C GLN* 1.3 78.5 - - - +
301C SER* 1.3 57.7 + - - +
302C GLY 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.8 5.8 - - - +
297C VAL* 2.8 29.0 + - - +
300C CYS* 1.3 77.5 - - - +
302C GLY* 1.3 59.9 + - - +
303C VAL* 3.4 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 3.7 26.4 - - - +
123A SER* 4.9 0.9 - - - -
141A LEU* 3.4 18.3 - - - +
298C ARG 2.8 11.7 + - - -
299C GLN* 4.6 1.1 - - - -
301C SER* 1.3 78.2 - - - +
303C VAL* 1.3 65.7 + - - +
304C THR* 3.5 12.5 + - - +
----------------------------------------------------------
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