Contacts of the helix formed by residues 292 - 311 (chain C) in PDB entry 6UZA
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 ASP 292 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C SER* 4.0 2.9 - - - -
291C GLU* 1.3 79.5 - - + +
293C PRO* 1.3 62.2 - - - +
294C VAL* 3.4 5.0 + - - +
295C MET* 3.7 16.7 - - + +
296C THR* 3.1 24.8 + - - -
365C ARG* 3.1 25.7 + - - -
855C TYR* 2.9 31.0 + - + -
859C MET* 3.9 12.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
286C LEU* 3.3 25.5 - - + +
287C SER* 4.5 0.9 - - - +
290C SER* 3.6 9.9 - - - +
291C GLU 3.5 11.0 - - - +
292C ASP* 1.3 82.8 - - - +
294C VAL* 1.3 60.1 + - - +
296C THR* 3.9 3.7 - - - -
297C ALA* 2.9 31.7 + - - +
328C PHE* 3.7 23.6 - - + -
332C LEU* 4.5 3.8 - - + -
859C MET* 3.8 19.7 - - + -
863C ILE* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ASP* 3.3 3.0 + - - +
293C PRO* 1.3 75.0 - - - +
295C MET* 1.3 60.9 + - - +
297C ALA* 3.4 4.8 + - - +
298C LEU* 3.0 34.8 + - + +
328C PHE* 5.0 0.7 - - - -
329C VAL* 3.7 27.8 - - + +
332C LEU* 3.8 27.1 - - + -
345C ILE* 4.2 22.7 - - + +
365C ARG* 3.8 35.9 - - - +
377C PHE* 5.2 1.6 - - + -
859C MET* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ASP* 3.7 26.6 + - + +
294C VAL* 1.3 78.9 - - - +
296C THR* 1.3 58.4 + - - +
298C LEU* 3.4 8.7 + - + +
299C GLU* 3.0 72.9 + - + +
365C ARG* 4.5 18.5 - - - +
368C LEU* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ARG* 5.1 12.8 - - - +
286C LEU* 4.0 20.2 - - + -
289C SER* 6.1 0.4 - - - +
290C SER* 4.0 21.0 + - - +
292C ASP 3.1 17.3 + - - -
293C PRO* 3.9 3.8 - - - -
294C VAL 3.3 0.2 - - - -
295C MET* 1.3 79.7 - - - +
297C ALA* 1.3 57.0 + - - +
299C GLU* 3.5 4.3 + - - +
300C LEU* 2.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C LEU* 4.1 13.9 - - + -
293C PRO 2.9 20.3 + - - +
294C VAL 3.9 0.2 - - - +
296C THR* 1.3 76.7 - - - +
298C LEU* 1.3 57.4 + - - +
300C LEU* 3.8 5.6 - - - +
301C SER* 2.9 30.1 + - - -
325C CYS* 3.9 12.6 - - - +
328C PHE* 3.7 15.3 - - + -
329C VAL* 3.7 24.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
294C VAL* 3.0 29.7 + - + +
295C MET* 3.8 8.1 - - + +
297C ALA* 1.3 75.8 - - - +
299C GLU* 1.3 61.5 + - + +
301C SER* 2.7 19.5 + - - +
302C ASN 3.0 6.9 + - - -
326C LYS* 6.2 0.9 - - + -
329C VAL* 4.7 15.7 - - + -
365C ARG* 4.0 33.0 - - + +
368C LEU* 4.8 14.1 - - + -
369C ALA* 4.8 12.8 - - + +
372C TYR* 3.5 23.3 - - + -
374C VAL* 3.8 32.1 - - + -
377C PHE* 5.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C MET* 3.0 47.3 + - + +
296C THR* 4.0 4.9 - - - +
298C LEU* 1.3 74.8 - - - +
300C LEU* 1.3 57.6 + - - +
302C ASN* 3.4 8.3 + - - +
303C GLU* 2.9 29.5 + - - +
368C LEU* 4.0 2.4 - - - +
372C TYR* 3.0 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ARG* 3.5 35.4 - - - +
277C TYR* 4.3 17.9 - - + -
280C LEU* 3.4 31.6 - - + +
281C ALA* 3.8 5.8 - - + -
286C LEU* 4.2 11.4 - - + -
296C THR* 2.9 20.9 + - + +
297C ALA* 3.9 3.8 - - - +
299C GLU* 1.3 73.2 - - - +
301C SER* 1.3 62.2 + - - +
303C GLU* 3.3 6.9 + - - +
304C LEU* 2.9 41.7 + - + +
325C CYS* 3.8 21.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
297C ALA 2.9 15.8 + - - -
298C LEU* 2.7 28.1 + - - +
300C LEU* 1.3 76.4 - - - +
302C ASN* 1.3 55.3 + - - +
304C LEU 3.5 0.2 + - - -
305C ALA* 3.0 26.3 + - - +
322C SER* 3.0 27.9 + - - +
325C CYS* 3.8 19.4 - - - +
326C LYS* 4.2 18.2 - - - +
372C TYR* 4.8 4.1 + - - +
374C VAL* 4.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LEU 3.0 8.8 + - - +
299C GLU* 3.7 11.7 + - - +
300C LEU 3.3 0.2 - - - -
301C SER* 1.3 82.4 + - - +
303C GLU* 1.3 58.0 + - - +
305C ALA* 3.3 6.6 + - - +
306C VAL* 2.9 40.1 + - - +
372C TYR* 3.4 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ARG* 2.7 37.0 + - - +
248C PRO 5.4 0.5 - - - +
277C TYR* 2.6 34.2 + - + +
299C GLU 2.9 17.7 + - - +
300C LEU* 3.3 8.6 + - + +
302C ASN* 1.3 78.0 - - - +
304C LEU* 1.3 59.3 + - - +
306C VAL* 3.3 6.3 + - - +
307C LEU* 3.0 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C TYR* 3.8 33.0 - - + -
281C ALA* 4.0 14.8 - - + -
300C LEU* 2.9 30.2 + - + +
303C GLU* 1.3 76.2 - - - +
305C ALA* 1.3 58.4 + - - +
307C LEU* 3.4 4.2 + - + +
308C ALA* 2.9 27.5 + - - +
318C TYR* 3.6 36.1 - - + +
321C LEU* 3.7 34.3 - - + +
322C SER* 3.9 14.8 - - - +
325C CYS* 4.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C SER 3.0 18.9 + - - +
302C ASN* 3.8 7.4 - - - +
304C LEU* 1.3 76.7 - - - +
306C VAL* 1.3 60.3 + - + +
308C ALA* 3.7 11.6 + - - +
309C ASN* 3.0 23.2 - - - +
318C TYR 5.5 0.2 - - - -
319C LYS* 4.9 10.8 + - + +
322C SER* 4.1 11.6 + - - +
326C LYS* 5.6 4.7 - - - +
372C TYR 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ASN* 2.9 35.4 + - - +
303C GLU* 3.6 7.0 - - - +
304C LEU 3.2 0.2 - - - -
305C ALA* 1.3 78.8 - - + +
307C LEU* 1.3 65.9 + - + +
309C ASN* 3.1 8.7 + - - +
310C ILE* 3.0 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C TYR* 5.4 10.5 - - + +
273C ARG* 3.7 17.3 - - - +
277C TYR* 3.7 33.9 - - + +
303C GLU* 3.0 37.3 + - + +
304C LEU* 4.0 7.2 - - + +
306C VAL* 1.3 83.4 - - + +
308C ALA* 1.3 59.8 + - - +
309C ASN 3.2 0.2 - - - -
310C ILE* 3.9 13.2 - - + +
311C GLU* 3.1 35.4 + - + +
318C TYR* 3.7 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LEU 2.9 17.4 + - - +
305C ALA* 3.8 8.7 - - - +
306C VAL 3.2 0.4 - - - -
307C LEU* 1.3 77.9 - - - +
309C ASN* 1.3 57.9 + - - +
311C GLU 3.5 10.0 - - - +
312C LYS* 4.8 1.0 - - - -
315C LYS* 3.4 31.8 - - - +
318C TYR* 3.7 21.1 - - + +
319C LYS* 4.0 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ALA 3.0 18.0 - - - +
306C VAL* 3.1 7.7 + - - +
308C ALA* 1.3 82.0 + - - +
310C ILE* 1.3 67.1 + - + +
311C GLU 3.4 2.2 - - - -
312C LYS* 4.6 4.7 + - - +
315C LYS* 5.2 5.4 - - - +
319C LYS* 4.4 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C TYR* 3.6 27.1 - - + -
252C PHE* 3.6 37.3 - - + -
306C VAL* 3.0 37.2 + - + +
307C LEU* 4.3 12.1 - - + -
309C ASN* 1.3 80.6 - - + +
311C GLU* 1.3 59.2 + - + +
312C LYS* 3.6 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C TYR* 3.3 45.6 + - + +
270C SER* 4.1 15.9 + - - +
273C ARG* 3.7 17.0 + - - -
307C LEU* 3.1 19.9 + - + +
308C ALA* 3.5 15.8 - - - +
310C ILE* 1.3 75.7 - - + +
312C LYS* 1.3 59.9 + - - +
313C GLU* 2.9 30.4 - - + +
314C PHE* 3.8 17.7 - - + -
315C LYS* 4.4 1.9 + - - +
318C TYR* 3.9 19.3 + - + -
----------------------------------------------------------
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