Contacts of the helix formed by residues 296 - 319 (chain C) in PDB entry 5COX
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 PRO 296 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C VAL* 1.3 83.2 - - - +
297C GLY* 1.3 56.7 + - - +
298C LEU 3.3 0.2 - - - -
299C MET* 4.1 10.4 - - + +
300C MET* 3.1 28.4 + - - +
407C PHE* 3.3 39.7 - - + +
410C ASN 2.9 33.4 - - - +
411C ASN* 4.4 4.7 - - - +
413C ILE* 4.6 2.9 - - + -
414C LEU* 4.4 9.5 - - + +
422C PHE* 3.9 27.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C PHE* 3.6 44.1 - - - +
295C VAL* 2.6 14.3 + - - +
296C PRO* 1.3 74.2 - - - +
298C LEU* 1.3 63.7 + - - +
300C MET* 3.5 22.1 - - - +
301C TYR* 3.8 6.6 - - - -
407C PHE* 4.3 2.0 - - - -
426C PHE* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C PHE 4.2 2.5 - - - +
203C GLN* 3.4 52.5 - - + +
204C HIS* 3.7 26.7 + - + +
207C HIS* 5.9 1.1 - - + -
291C VAL* 5.3 3.8 - - + +
292C PHE* 3.8 42.6 - - + +
294C LEU* 5.4 0.7 - - + -
295C VAL* 2.8 26.6 + - + +
297C GLY* 1.3 74.3 - - - +
299C MET* 1.3 60.4 + - - +
300C MET 2.8 8.8 + - - -
301C TYR* 2.9 8.1 + - - +
302C ALA* 2.8 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C PRO* 4.0 4.9 - - - -
275C TYR* 3.5 23.8 - - - +
285C PHE* 3.3 41.5 - - + +
287C VAL* 3.4 27.4 - - + -
292C PHE* 3.0 33.2 + - + +
293C GLY* 3.7 5.8 - - - -
295C VAL 3.5 7.8 + - - +
296C PRO* 4.4 8.7 - - + +
298C LEU* 1.3 78.8 - - - +
300C MET* 1.3 59.2 + - - +
302C ALA* 3.7 6.2 - - - -
303C THR* 2.7 32.8 + - - +
411C ASN* 6.1 2.9 - - + -
414C LEU* 3.9 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C MET* 3.5 34.3 - - + -
200C PHE* 4.7 1.8 - - + -
296C PRO 3.1 17.9 + - - +
297C GLY* 3.5 17.7 - - - +
298C LEU 2.8 2.8 + - - -
299C MET* 1.3 73.3 - - - +
301C TYR* 1.3 70.5 + - + +
303C THR* 3.1 6.4 + - - -
304C ILE* 3.0 45.9 + - + +
414C LEU* 4.4 10.1 - - + +
419C LEU* 3.7 17.4 - - + +
422C PHE* 4.1 23.8 - - + +
423C VAL* 4.1 9.9 - - - -
426C PHE* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C MET* 2.8 41.0 + - + +
200C PHE* 3.6 8.5 - - + -
201C PHE* 3.0 61.4 - + - +
204C HIS* 3.8 24.2 - + + -
297C GLY 3.8 14.3 + - - -
298C LEU 2.9 6.8 + - - +
300C MET* 1.3 82.7 - - + +
302C ALA* 1.3 56.9 + - - +
303C THR 2.9 4.9 - - - -
304C ILE* 2.8 40.7 + - + +
305C TRP* 2.9 25.5 + - + -
564C ILE* 3.9 11.2 - - + +
567C LEU* 5.1 1.6 - - + -
568C ILE* 4.5 5.6 - - + -
580C PHE* 3.6 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C HIS* 3.8 19.6 - - + -
232C HIS 6.0 0.7 - - - +
233C ILE* 5.7 3.1 - - - +
263C PRO* 4.6 4.1 - - - +
287C VAL* 4.0 27.7 - - + +
292C PHE* 4.3 7.9 - - + -
298C LEU 2.8 15.7 + - - +
299C MET* 3.8 12.3 - - - +
301C TYR* 1.3 76.6 - - - +
303C THR* 1.3 57.7 + - - +
305C TRP* 4.2 3.2 - - - +
306C LEU* 3.5 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C VAL* 3.4 26.9 - - + +
262C TYR* 3.9 10.6 - - + -
263C PRO* 3.2 32.2 - - + +
299C MET* 2.7 25.6 + - - +
300C MET 3.6 4.7 - - - -
301C TYR 2.9 0.6 - - - -
302C ALA* 1.3 76.1 - - - +
304C ILE* 1.3 60.0 + - - +
305C TRP 3.3 0.4 - - - -
306C LEU* 3.6 4.4 - - + +
307C ARG* 2.9 50.0 + - + +
414C LEU* 4.7 1.7 - - - +
419C LEU* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C MET* 3.0 33.1 + - + +
301C TYR* 2.8 29.4 + - + +
303C THR* 1.3 78.4 - - - +
305C TRP* 1.3 56.1 + - - +
307C ARG* 3.4 10.9 - - - +
308C GLU* 2.9 25.1 + - - +
419C LEU* 4.0 12.8 - - + -
423C VAL* 4.4 2.7 - - + -
567C LEU* 3.9 41.1 - - + +
568C ILE* 3.9 23.6 - - + -
571C ASN* 3.7 7.2 - - + -
572C VAL* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C PHE* 4.8 17.0 - + - -
204C HIS* 3.4 34.6 + + - +
232C HIS* 5.7 1.5 + - - -
233C ILE* 3.5 32.9 - - + +
301C TYR* 2.9 21.7 + + + +
302C ALA* 4.8 2.7 - - - +
304C ILE* 1.3 72.1 - - - +
306C LEU* 1.3 68.0 + - - +
307C ARG 3.1 1.1 - - - -
308C GLU* 2.8 13.8 + - + +
309C HIS* 2.8 23.9 + - - +
336C LEU* 4.1 30.8 - - + +
339C GLU* 4.2 9.4 - - + -
340C THR* 3.3 40.8 - - + -
343C ILE* 4.6 6.5 - - + -
567C LEU* 3.5 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ILE* 4.9 8.8 - - + +
252C LEU* 4.8 9.2 - - + -
253C LYS 3.9 16.8 - - - +
254C TYR* 4.0 9.9 - - + -
261C VAL* 3.7 26.9 - - + -
263C PRO* 3.5 41.7 - - + -
264C PRO* 4.3 1.6 - - + -
287C VAL* 6.0 2.7 - - - -
302C ALA 3.5 17.0 + - - +
303C THR* 3.4 5.7 + - + +
305C TRP* 1.3 77.7 - - - +
307C ARG* 1.3 68.6 + - + +
309C HIS* 3.1 19.3 + - - +
310C GLN* 3.6 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C GLU* 3.3 32.7 + - - +
261C VAL* 2.4 59.7 + - + +
303C THR* 2.9 39.1 + - + +
304C ILE* 3.4 10.1 - - - +
306C LEU* 1.3 81.4 - - + +
308C GLU* 1.3 60.6 + - - +
310C GLN* 3.9 5.8 + - - +
311C ARG* 3.4 17.3 + - - +
419C LEU* 4.3 23.3 - - - +
571C ASN* 3.1 41.7 + - + +
572C VAL* 5.2 0.6 - - - +
573C LYS 5.0 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C ILE 2.9 15.0 + - - +
305C TRP* 2.8 29.2 + - + +
307C ARG* 1.3 74.8 - - - +
309C HIS* 1.3 68.8 + - - +
311C ARG* 2.6 49.1 + - - +
312C VAL* 3.2 15.9 + - - +
336C LEU* 4.1 4.9 - - + +
339C GLU* 2.7 34.8 - - - +
567C LEU* 4.1 9.1 - - + -
570C ASN* 5.3 1.0 + - - -
571C ASN* 3.3 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ILE* 5.7 1.1 - - + -
234C TYR* 2.5 45.5 + + - +
250C GLY 3.1 25.9 + - - -
252C LEU* 3.3 20.8 - - + +
305C TRP 2.8 14.0 + - - +
306C LEU* 3.1 11.4 + - - +
308C GLU* 1.3 71.0 - - - +
310C GLN* 1.3 71.6 + - - +
311C ARG 2.7 0.9 + - - -
312C VAL* 2.7 31.4 + - - +
313C CYS* 3.0 18.4 + - - +
329C PHE* 3.9 9.8 - + - -
332C SER* 3.5 19.3 + - - -
333C LYS 4.0 2.9 - - - -
336C LEU* 3.7 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LYS* 3.3 31.6 - - + +
252C LEU* 2.4 54.4 + - - +
254C TYR* 3.2 24.3 - - + -
306C LEU* 3.6 14.5 + - - +
307C ARG* 4.1 7.4 - - - +
309C HIS* 1.3 81.3 - - - +
311C ARG* 1.3 56.6 + - - +
313C CYS* 3.2 10.1 - - - +
314C ASP* 2.8 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C ARG 3.4 12.0 + - - +
308C GLU* 2.6 51.7 + - - +
309C HIS 2.7 4.9 + - - -
310C GLN* 1.3 74.0 - - - +
312C VAL* 1.3 69.5 + - - +
313C CYS 3.3 0.2 + - - -
314C ASP* 3.3 6.8 + - - +
315C ILE* 3.0 50.6 + - + +
339C GLU* 4.8 2.2 + - - -
558C ILE* 4.8 11.3 - - - +
570C ASN* 3.7 45.3 + - - +
571C ASN* 4.1 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C GLU* 3.2 12.7 + - - +
309C HIS 2.7 12.8 + - - +
311C ARG* 1.3 74.3 - - - +
313C CYS* 1.3 64.6 + - - +
315C ILE* 2.9 9.3 + - - +
316C LEU* 2.8 35.3 + - + +
332C SER* 3.3 24.2 - - - +
335C ILE* 3.8 17.7 - - + -
336C LEU* 3.8 22.0 - - + -
558C ILE* 3.8 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ASP 3.3 26.5 - - - +
250C GLY* 3.5 24.7 - - - -
251C LYS* 3.7 6.1 - - + -
309C HIS* 3.0 22.4 + - - -
310C GLN* 3.2 11.7 - - - +
312C VAL* 1.3 74.8 - - - +
314C ASP* 1.3 59.1 + - - +
316C LEU* 2.7 24.8 + - - +
317C LYS* 2.7 17.7 + - - +
328C LEU* 4.4 6.0 - - - +
332C SER* 3.4 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ASP* 4.9 0.2 - - - +
251C LYS* 2.9 42.4 + - - -
310C GLN* 2.8 16.0 + - - +
311C ARG* 3.8 6.9 - - - +
313C CYS* 1.3 73.9 - - - +
315C ILE* 1.3 60.1 + - + +
317C LYS* 4.1 19.4 + - - +
318C GLN* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ARG* 3.0 50.5 - - + +
312C VAL* 2.9 8.7 + - - +
313C CYS 2.8 2.0 + - - -
314C ASP* 1.3 74.9 - - + +
316C LEU* 1.3 68.8 + - + +
318C GLN* 3.2 7.1 + - - +
319C GLU* 3.1 23.9 + - + +
554C VAL* 3.8 29.8 - - + -
558C ILE* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C VAL* 2.8 29.5 + - + +
313C CYS* 2.7 12.6 + - - +
315C ILE* 1.3 77.3 - - + +
317C LYS* 1.3 50.7 + - - +
319C GLU* 2.9 11.9 + - + +
320C HIS* 2.6 37.9 + - - +
323C TRP* 4.0 13.9 - - + -
328C LEU* 3.5 17.5 - - + +
331C THR* 3.7 31.4 - - + -
332C SER* 3.9 9.0 - - - +
335C ILE* 4.0 11.2 - - + -
550C PHE 4.2 13.2 - - - +
551C GLY* 4.8 8.5 - - - +
554C VAL* 5.0 2.7 - - + -
555C GLY* 4.6 11.2 - - - +
558C ILE* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ASP* 2.8 39.1 + - + +
251C LYS* 6.0 0.2 - - - +
313C CYS 2.7 21.3 + - - +
314C ASP* 4.3 15.1 + - - +
316C LEU* 1.3 69.2 - - - +
318C GLN* 1.3 66.7 + - - +
320C HIS 3.6 16.5 - - - +
321C PRO* 3.7 6.9 - - + +
328C LEU* 3.4 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ASP 3.3 13.5 + - - +
315C ILE* 3.2 11.4 + - - +
316C LEU 3.0 0.6 - - - -
317C LYS* 1.3 81.3 - - - +
319C GLU* 1.3 85.3 + - + +
320C HIS 3.0 2.1 + - - -
321C PRO* 3.5 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C ILE* 3.1 11.6 + - + +
316C LEU* 2.9 13.2 + - + +
318C GLN* 1.3 98.1 + - + +
320C HIS* 1.3 78.6 + - + +
321C PRO* 3.4 7.7 - - - +
551C GLY 5.4 1.6 - - - +
554C VAL* 4.0 36.0 - - + +
50D THR* 5.1 4.9 - - - +
----------------------------------------------------------
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