Contacts of the helix formed by residues 299 - 317 (chain C) in PDB entry 6Q3W
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 299 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C ALA* 2.7 21.5 + - - +
297C ARG* 3.1 38.2 + - + +
298C GLY* 1.3 72.4 - - - +
300C TYR* 1.3 64.5 + - - +
301C ARG* 4.1 7.4 + - - +
302C ALA* 3.2 23.2 + - - +
303C PHE* 3.2 15.4 + - - +
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Residues in contact with TYR 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C LEU* 5.7 3.1 - - + +
215C ASP* 3.1 33.8 + - - +
217C LYS* 6.3 1.3 - - + -
218C LEU* 4.3 19.8 - - + +
295C LEU* 4.3 25.0 + - + -
298C GLY* 2.8 39.9 + - - -
299C ASP* 1.3 72.1 - - - +
301C ARG* 1.3 62.0 + - - +
303C PHE* 3.1 9.8 + - + +
304C GLY 3.0 21.0 + - - -
339C TYR* 3.4 50.1 - + + +
355C LEU* 6.4 0.2 - - + -
357C GLU* 4.6 2.9 - - - -
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Residues in contact with ARG 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ASP* 3.3 7.1 - - - +
300C TYR* 1.3 79.6 - - - +
302C ALA* 1.3 60.9 + - - +
304C GLY* 3.7 0.7 + - - -
305C ARG* 3.2 22.2 + - - +
339C TYR* 3.5 22.8 - - + +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ALA* 4.6 6.3 - - + -
297C ARG* 5.0 2.5 - - - +
299C ASP* 3.2 30.2 + - + +
300C TYR 3.3 0.4 - - - -
301C ARG* 1.3 76.0 - - - +
303C PHE* 1.3 66.1 + - - +
305C ARG* 3.3 7.7 + - - +
306C LEU* 3.0 34.0 + - + +
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Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ALA* 4.8 10.8 - - + +
294C ALA* 4.3 13.2 - - + +
295C LEU* 5.3 7.6 - - + +
299C ASP 3.2 13.1 + - - +
300C TYR* 3.1 18.1 + - + +
302C ALA* 1.3 76.4 - - - +
304C GLY* 1.3 63.5 + - - +
306C LEU* 3.1 13.0 + - - +
307C MET* 3.0 27.8 + - + +
339C TYR* 5.8 0.2 - - + -
355C LEU* 6.3 2.2 - - + -
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Residues in contact with GLY 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C TYR 3.0 10.5 + - - -
301C ARG 4.1 0.2 - - - -
303C PHE* 1.3 75.6 - - - +
305C ARG* 1.3 57.3 + - - +
307C MET* 3.0 14.7 + - - +
308C VAL* 2.9 32.3 + - - +
339C TYR* 3.3 33.3 - - - +
340C GLY* 3.4 4.8 - - - -
355C LEU* 6.0 0.4 - - - +
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Residues in contact with ARG 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ARG 3.2 18.2 + - - +
302C ALA* 3.6 8.3 - - - +
303C PHE 3.2 0.8 - - - -
304C GLY* 1.3 75.8 - - - +
306C LEU* 1.3 59.2 + - + +
308C VAL* 3.4 8.0 + - - +
309C GLU* 2.9 27.5 + - - +
339C TYR 3.8 2.8 + - - +
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C ARG* 3.6 36.8 - - + +
290C GLN* 3.7 29.4 - - + +
291C ALA* 3.6 36.6 - - + +
294C ALA* 5.0 1.1 - - + -
302C ALA* 3.0 26.2 + - + +
303C PHE* 3.3 6.5 - - - +
305C ARG* 1.3 76.5 - - + +
307C MET* 1.3 53.3 + - + +
309C GLU* 3.4 7.9 + - + +
310C SER* 2.7 34.2 + - - -
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Residues in contact with MET 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.3 31.6 - - + +
41C ILE* 4.8 8.3 - - + -
291C ALA* 6.4 0.2 - - + -
303C PHE* 3.0 19.7 + - - +
304C GLY* 3.0 20.2 + - - +
306C LEU* 1.3 74.3 - - + +
308C VAL* 1.3 60.5 + - - +
310C SER* 3.1 6.5 + - - -
311C HIS 2.8 23.7 + - - -
340C GLY 4.3 11.7 - - - +
341C SER* 4.0 7.2 - - - +
342C ARG* 3.6 32.1 - - + +
353C VAL* 3.9 25.8 - - + +
355C LEU* 4.4 19.3 - - + +
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Residues in contact with VAL 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C GLY 2.9 14.9 + - - +
305C ARG* 3.4 8.3 + - - +
307C MET* 1.3 71.5 - - - +
309C GLU* 1.3 61.7 + - - +
311C HIS* 3.1 4.9 + - + +
312C ARG* 2.8 33.5 + - + +
333C LEU* 3.6 46.7 - - + -
339C TYR 4.8 1.3 - - - +
340C GLY* 3.8 5.4 - - - -
341C SER 3.9 9.4 - - - +
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Residues in contact with GLU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ARG* 4.0 17.2 + - - +
305C ARG 2.9 17.9 + - - +
306C LEU* 3.5 10.8 - - + +
308C VAL* 1.3 76.8 - - - +
310C SER* 1.3 55.7 + - - +
312C ARG* 3.8 5.9 - - - +
313C SER* 3.0 30.8 + - - -
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Residues in contact with SER 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ILE* 5.4 3.6 - - - -
280C HIS* 4.2 0.2 - - - -
284C GLU* 2.6 40.7 + - - -
287C ARG* 3.9 4.0 - - - +
306C LEU 2.7 17.4 + - - -
307C MET* 3.1 12.3 + - - -
309C GLU* 1.3 73.7 - - - +
311C HIS* 1.3 50.9 + - - +
313C SER* 3.2 4.2 + - - -
314C LEU* 2.8 37.7 + - - +
342C ARG* 3.1 24.1 + - - -
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Residues in contact with HIS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C MET 2.8 10.7 + - - +
308C VAL* 3.1 9.4 + - + +
310C SER* 1.3 73.2 + - - +
312C ARG* 1.3 54.9 + - - +
314C LEU* 2.9 11.2 + - - +
315C ARG* 2.6 55.4 + - + +
321C SER* 3.9 9.8 + - - -
325C LEU 3.9 8.7 - - - -
326C ASP* 3.1 27.4 + - - -
329C VAL* 3.6 25.4 - - + +
341C SER 4.0 3.6 - - - +
342C ARG* 3.4 19.6 - - + +
343C MET* 3.0 36.0 + - + +
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Residues in contact with ARG 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C VAL* 2.8 22.2 + - + +
309C GLU* 3.8 6.7 - - - +
311C HIS* 1.3 75.6 - - - +
313C SER* 1.3 55.3 + - - +
315C ARG* 4.3 18.8 - - - +
316C ASP* 2.7 46.5 + - - +
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Residues in contact with SER 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C HIS* 2.6 34.1 + - - +
287C ARG* 3.0 27.9 + - - -
309C GLU 3.0 16.1 + - - -
310C SER 3.5 2.2 - - - -
312C ARG* 1.3 75.9 - - - +
314C LEU* 1.3 51.5 + - - +
317C ASP* 3.0 19.5 + - - +
318C TYR* 2.6 34.0 + - - +
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLU* 3.7 15.5 - - + -
44C HIS* 3.9 7.4 - - + -
280C HIS* 3.4 25.6 - - + +
310C SER* 2.8 23.2 + - - +
311C HIS* 2.9 8.5 + - - +
313C SER* 1.3 77.9 - - - +
315C ARG* 1.3 53.8 + - - +
318C TYR* 3.5 5.1 - - + -
319C GLU 2.7 26.5 + - - -
320C VAL* 3.0 32.5 + - + -
321C SER 4.5 1.6 - - - -
342C ARG* 3.3 30.7 - - - +
343C MET* 3.7 31.4 - - + -
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Residues in contact with ARG 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C HIS* 2.6 33.2 + - + +
312C ARG* 3.9 12.5 - - - +
314C LEU* 1.3 75.6 - - - +
316C ASP* 1.3 88.3 + - - +
319C GLU* 3.6 16.6 - - - +
321C SER* 3.8 13.5 - - - -
326C ASP* 3.2 48.2 + - - +
330C GLU* 5.8 4.8 - - - +
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Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C ARG* 2.7 25.2 + - - +
315C ARG* 1.3 112.8 + - - +
317C ASP* 1.3 61.2 + - + +
319C GLU* 3.8 12.9 - - - +
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Residues in contact with ASP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ARG* 2.6 52.6 - - - +
277C ARG* 4.3 1.9 + - - -
279C ARG* 3.6 18.2 - - - +
280C HIS* 4.1 9.0 + - + +
312C ARG 3.8 0.4 + - - +
313C SER* 3.0 25.9 + - - +
316C ASP* 1.3 82.5 - - + +
318C TYR* 1.3 60.4 + - - +
319C GLU* 3.4 5.1 - - - +
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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) + - + + + + + -
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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