Contacts of the helix formed by residues 304 - 322 (chain C) in PDB entry 6RRC
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 304 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ASP* 3.7 8.3 - - - +
162C TYR* 5.6 1.1 - - - +
216C ARG* 3.4 51.8 - - - +
219C ARG* 3.5 15.5 - - - +
220C HIS* 6.0 1.3 - - - +
302C ASP* 2.7 21.0 + - - +
303C ALA* 1.3 82.4 - - + +
305C ALA* 1.3 69.6 + - - +
306C GLU* 4.2 10.8 - - + +
307C ILE* 3.3 20.0 + - + +
308C ARG* 3.3 24.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
303C ALA 4.0 1.0 + - - -
304C ILE* 1.3 75.8 - - - +
306C GLU* 1.3 58.3 + - - +
308C ARG* 3.1 16.1 + - - +
309C ALA* 2.9 23.6 + - - +
343C GLN* 3.7 31.4 - - + +
345C GLU* 3.8 20.0 - - - +
346C VAL* 3.4 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LEU* 4.4 9.1 - - - +
165C THR* 4.7 5.7 - - - +
175C ARG* 4.5 13.2 + - - -
220C HIS* 3.2 35.7 + - + +
304C ILE* 3.4 7.7 - - + +
305C ALA* 1.3 78.9 - - - +
307C ILE* 1.3 58.6 + - - +
309C ALA* 3.6 6.2 - - + +
310C ILE* 2.8 39.2 + - + +
345C GLU* 3.6 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ARG* 4.6 2.9 - - + -
219C ARG* 4.0 13.5 - - - +
220C HIS* 4.1 39.0 - - + +
223C THR* 4.0 26.5 - - + +
299C ARG* 3.8 7.2 - - + +
302C ASP* 3.4 41.1 - - + +
304C ILE* 3.3 25.1 + - + +
305C ALA 3.2 0.8 - - - -
306C GLU* 1.3 75.5 - - - +
308C ARG* 1.3 64.1 + - - +
310C ILE* 3.4 7.2 + - - +
311C CYS* 3.2 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 3.6 19.4 - - - +
299C ARG 3.9 5.4 - - - -
300C TYR* 3.3 24.9 - - - +
301C ARG* 4.1 4.3 - - - +
302C ASP 2.8 49.0 + - - +
303C ALA 3.5 18.8 + - - -
304C ILE 3.5 6.5 + - - +
305C ALA* 3.1 15.3 + - - +
307C ILE* 1.3 77.9 - - - +
309C ALA* 1.3 57.1 + - - +
311C CYS* 3.2 2.4 + - - +
312C ILE* 3.0 35.5 + - + +
338C THR* 5.3 2.5 - - + -
341C ASP* 2.7 42.3 + - - -
342C ARG* 5.1 1.6 - - - +
343C GLN* 3.4 22.8 - - - +
346C VAL* 4.1 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ALA 2.9 15.9 + - - +
306C GLU* 3.7 13.2 - - + +
307C ILE 3.3 0.2 - - - -
308C ARG* 1.3 76.0 - - - +
310C ILE* 1.3 62.2 + - + +
312C ILE* 4.6 1.3 - - - +
313C GLU* 3.0 28.5 + - - +
345C GLU* 4.4 9.9 - - + +
346C VAL* 4.3 12.1 - - + +
349C LYS* 3.8 31.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
175C ARG* 3.9 18.6 - - - +
220C HIS* 3.3 39.5 - - + +
223C THR* 4.3 5.6 - - + -
224C LEU* 3.9 35.4 - - + +
227C MET* 3.7 21.1 - - + -
306C GLU* 2.8 28.6 + - + +
307C ILE* 3.7 5.8 - - - +
308C ARG 3.2 0.2 - - - -
309C ALA* 1.3 77.4 - - - +
311C CYS* 1.3 61.6 - - - +
313C GLU* 4.0 7.5 - - - +
314C GLU* 3.3 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C THR* 3.6 14.4 - - - -
227C MET* 4.1 11.0 - - - -
296C PHE* 3.2 37.5 - - + -
299C ARG* 3.6 35.4 - - - -
300C TYR* 3.7 11.4 - - + -
307C ILE 3.2 15.1 + - - -
308C ARG 3.2 6.3 + - - +
310C ILE* 1.3 78.9 - - - +
312C ILE* 1.3 65.4 + - - +
314C GLU* 3.3 2.1 + - - +
315C ILE 3.1 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C PHE* 5.0 2.0 - - + -
300C TYR* 4.9 12.8 - - + +
308C ARG* 3.0 22.6 + - + +
309C ALA 4.1 2.7 - - - +
311C CYS* 1.3 77.7 - - + +
313C GLU* 1.3 63.9 + - - +
315C ILE* 3.1 19.5 - - + +
316C GLY* 3.3 6.9 + - - -
334C TYR 3.9 10.8 - - - +
335C VAL* 4.3 14.1 - - + -
338C THR* 3.4 40.8 - - + +
346C VAL* 4.6 2.0 - - + -
349C LYS* 3.7 12.3 - - + +
350C CYS* 3.6 37.0 - - - +
353C ALA* 4.2 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ARG* 5.4 5.7 + - - -
228C LYS* 5.4 5.6 + - - -
309C ALA 3.0 19.8 + - - +
310C ILE* 4.0 7.3 - - - +
312C ILE* 1.3 78.3 - - - +
314C GLU* 1.3 69.1 + - - +
316C GLY* 3.5 1.9 + - - -
317C VAL* 3.3 25.1 + - + +
349C LYS* 3.2 43.7 + - + +
353C ALA* 5.3 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C MET* 3.3 37.2 - - + +
228C LYS* 3.0 36.2 + - - +
231C THR* 2.4 31.8 + - - +
310C ILE* 3.3 14.5 + - - +
311C CYS 3.3 4.1 + - - +
312C ILE 3.3 0.4 - - - -
313C GLU* 1.3 84.5 - - - +
315C ILE* 1.3 62.4 + - - +
316C GLY 3.2 0.4 - - - -
317C VAL* 3.0 23.7 + - - +
318C TRP* 3.1 32.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
292C PHE* 4.2 11.2 - - + -
296C PHE* 3.5 34.1 - - + -
311C CYS 3.1 14.5 + - - +
312C ILE* 3.1 23.6 - - + +
314C GLU* 1.3 76.5 - - - +
316C GLY* 1.3 61.6 + - - +
318C TRP* 3.4 21.7 + - + +
319C MET* 3.1 33.3 + - + +
326C PHE* 6.0 0.2 - - + -
331C TYR* 3.4 33.4 - - + +
334C TYR* 4.3 4.5 - - + -
335C VAL* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C ILE 3.3 4.8 + - - -
313C GLU 3.9 2.5 - - - -
314C GLU 3.2 1.2 - - - -
315C ILE* 1.3 81.5 - - - +
317C VAL* 1.3 63.5 + - - +
319C MET* 3.6 16.4 + - - +
320C LYS* 3.1 23.7 + - - +
353C ALA* 3.8 25.6 - - - -
356C SER* 4.7 4.0 + - - -
357C LEU* 4.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LYS* 6.0 0.4 - - - +
231C THR* 4.1 9.2 - - + +
313C GLU* 3.3 21.9 + - + +
314C GLU* 3.0 31.7 + - - +
316C GLY* 1.3 76.9 - - - +
318C TRP* 1.3 57.3 + - - +
320C LYS* 3.3 5.3 + - - +
321C MET* 2.9 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C MET* 3.7 24.9 - - + -
230C MET* 3.4 35.2 - - + -
231C THR* 2.9 41.3 + - - +
234C VAL* 4.3 9.0 - - + -
291C ILE* 5.9 0.7 - - + -
292C PHE* 3.9 25.6 - + - -
296C PHE* 4.0 8.7 - + + -
314C GLU* 3.1 27.8 + - + +
315C ILE* 3.5 30.5 - - + +
316C GLY 3.3 0.2 - - - -
317C VAL* 1.3 78.3 - - + +
319C MET* 1.3 57.1 + - - +
321C MET* 3.5 9.8 - - - +
322C TYR* 2.9 34.8 + - - +
326C PHE* 3.8 33.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C ILE* 3.1 28.1 + - + +
316C GLY* 3.7 15.3 - - - +
318C TRP* 1.3 76.7 - - - +
320C LYS* 1.3 61.1 + - - +
323C SER* 3.3 26.2 - - - -
326C PHE* 3.3 34.5 - - + +
327C LEU* 4.1 8.7 - - + +
331C TYR* 4.3 11.7 - - + -
332C LEU* 3.6 30.5 - - + -
335C VAL* 4.0 22.9 - - + -
353C ALA* 5.2 2.0 - - + -
354C LEU* 5.6 1.1 - - + -
357C LEU* 3.8 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU* 4.9 6.3 + - - -
316C GLY 3.1 18.9 + - - +
317C VAL* 3.7 4.9 - - - +
318C TRP 3.2 0.2 - - - -
319C MET* 1.3 80.6 - - - +
321C MET* 1.3 60.9 + - - +
322C TYR 3.7 0.2 + - - -
323C SER* 4.4 5.2 + - - -
356C SER* 2.6 46.5 + - - +
357C LEU* 3.8 11.1 - - + +
359C THR* 4.0 6.9 + - - -
360C ASN* 4.5 17.2 - - - +
363C LEU* 5.3 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C THR* 3.8 25.1 - - + +
234C VAL* 3.7 28.7 - - + -
235C ASN* 3.3 40.4 - - - +
238C LEU* 3.7 21.7 - - + +
317C VAL* 2.9 28.5 + - + +
318C TRP* 3.5 11.4 - - - +
320C LYS* 1.3 78.5 - - + +
322C TYR* 1.3 60.2 + - - +
323C SER 3.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C VAL* 3.8 26.9 - - + -
237C ALA* 4.2 23.9 + - + +
238C LEU* 3.6 28.9 - - + -
241C SER* 5.0 9.1 - - - -
281C GLN* 5.7 2.6 + - - -
285C GLU* 5.3 6.1 + - - -
288C MET* 5.7 3.1 - - + -
318C TRP 2.9 12.9 + - - +
321C MET* 1.3 78.5 - - - +
323C SER* 1.3 58.6 + - - +
324C ASP* 3.2 17.9 - - + -
325C ALA* 3.1 33.8 + - + +
326C PHE* 2.9 35.8 + + + +
----------------------------------------------------------
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