Contacts of the helix formed by residues 295 - 313 (chain C) in PDB entry 6R7H
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 VAL 295 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C LEU* 4.0 23.5 - - + +
263C LEU* 4.3 13.2 - - + -
279C VAL* 4.8 22.4 - - + +
286C PHE* 3.7 46.4 - - + -
291C ASN 4.2 7.8 + - - +
292C MET* 6.0 3.6 - - - -
293C GLY 5.2 2.0 - - - +
294C LEU* 1.3 76.1 - - - +
296C LYS* 1.3 74.2 + - + +
297C GLN 3.3 0.4 - - - -
298C CYS* 3.4 15.8 + - + +
299C LEU* 3.8 6.1 + - - +
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Residues in contact with LYS 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C MET* 5.4 14.2 - - - +
293C GLY* 3.8 31.8 - - - +
294C LEU 3.2 1.2 - - - -
295C VAL* 1.3 84.4 - - + +
297C GLN* 1.3 63.1 + - + +
299C LEU* 3.4 19.5 + - - +
300C SER* 3.9 8.7 + - - -
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Residues in contact with GLN 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C THR* 3.5 37.2 + - - +
194C GLY* 5.4 2.4 - - - -
198C PHE* 4.8 8.4 - - + -
233C ILE* 3.8 25.0 - - + +
293C GLY 3.7 14.4 - - - +
294C LEU* 3.7 20.4 + - - +
295C VAL 3.3 0.4 - - - -
296C LYS* 1.3 79.6 - - + +
298C CYS* 1.3 60.4 + - - +
300C SER* 3.7 6.2 + - - +
301C SER* 3.2 21.8 + - - -
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Residues in contact with CYS 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LEU* 3.7 49.8 - - - -
232C LEU* 4.8 18.6 - - + -
233C ILE* 4.2 7.9 - - + -
263C LEU* 5.0 6.3 - - + -
267C TYR* 3.9 12.3 - - + -
275C LEU* 4.0 9.6 - - + +
294C LEU 4.0 9.9 - - - -
295C VAL* 3.4 8.5 + - + +
296C LYS 3.2 0.6 - - - -
297C GLN* 1.3 78.0 - - - +
299C LEU* 1.3 64.0 + - - +
300C SER 3.4 0.2 - - - -
301C SER* 3.5 14.5 + - - -
302C LEU 3.5 8.0 + - - -
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C PRO* 5.6 4.3 - - + +
275C LEU* 3.8 32.1 - - + +
276C ARG* 5.1 10.5 - - + +
279C VAL* 5.3 11.2 - - + -
295C VAL 3.8 5.8 + - - +
296C LYS* 3.4 13.8 + - - +
297C GLN 3.3 1.0 - - - -
298C CYS* 1.3 80.6 - - - +
300C SER* 1.3 63.5 + - - +
301C SER 3.5 0.3 + - - -
302C LEU* 3.6 10.3 + - + +
303C TYR* 3.6 33.0 - - + +
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Residues in contact with SER 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C LYS 3.9 8.0 + - - -
297C GLN* 3.7 7.2 + - - -
298C CYS 3.4 0.2 - - - -
299C LEU* 1.3 80.3 - - - +
301C SER* 1.3 62.5 + - - +
302C LEU 3.3 0.2 - - - -
303C TYR* 3.5 6.9 + - - -
304C LYS* 3.4 22.4 + - - +
337C TYR* 2.8 33.5 + - - -
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Residues in contact with SER 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ILE* 3.4 38.2 + - - +
267C TYR* 3.2 18.9 + - - -
297C GLN 3.2 18.1 + - - -
298C CYS* 3.8 9.6 - - - -
299C LEU 3.3 1.0 - - - -
300C SER* 1.3 76.3 - - - +
302C LEU* 1.3 59.4 + - - +
304C LYS* 3.4 9.8 + - - +
305C LYS* 3.0 26.3 + - - +
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Residues in contact with LEU 302 (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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266C VAL 5.9 0.4 - - - +
267C TYR* 3.3 32.9 + - + +
270C ASN* 3.4 36.3 - - - +
271C ASN 3.6 34.3 - - - +
272C PRO* 3.8 11.0 - - + -
275C LEU* 3.7 23.1 - - + -
298C CYS 3.5 5.4 + - - +
299C LEU* 4.0 9.9 - - + +
300C SER 3.3 0.6 - - - -
301C SER* 1.3 77.8 - - - +
303C TYR* 1.3 64.7 + - + +
305C LYS* 3.4 1.2 + - + -
306C ASN* 3.1 39.4 + - - +
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Residues in contact with TYR 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C PRO* 3.6 30.5 + - + +
299C LEU* 3.6 41.3 - - + +
300C SER* 3.5 3.9 + - - -
301C SER 3.3 0.4 - - - -
302C LEU* 1.3 79.4 - - + +
304C LYS* 1.3 60.4 + - - +
306C ASN* 3.6 5.1 + - - +
307C ILE* 3.3 27.0 + - - +
326C VAL* 3.3 40.5 - - + +
327C GLN 3.9 11.3 + - - -
328C LEU* 4.3 10.8 - - + -
337C TYR* 3.4 35.9 - + + +
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C SER* 3.4 20.7 + - - +
301C SER* 3.9 7.6 - - - +
302C LEU 3.3 0.4 - - - -
303C TYR* 1.3 76.9 - - - +
305C LYS* 1.3 62.6 + - - +
307C ILE 3.5 1.1 + - - +
308C GLN* 3.3 32.3 + - - +
337C TYR* 3.0 38.4 + - + +
340C HIS* 5.0 12.0 - - - +
341C MET* 3.7 30.0 - - + +
344C ASP* 5.6 4.3 - - - -
346C GLU* 3.4 32.5 - - - +
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Residues in contact with LYS 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ILE 3.9 10.5 + - - -
234C LEU 3.6 16.1 + - - -
235C LEU 3.2 30.3 + - - -
236C GLY* 4.3 2.0 - - - +
267C TYR* 4.0 18.5 + - + +
270C ASN* 4.2 15.7 - - - +
301C SER* 3.0 17.1 + - - +
302C LEU* 3.8 6.3 - - - +
303C TYR 3.3 0.4 - - - -
304C LYS* 1.3 76.3 - - - +
306C ASN* 1.3 61.2 - - - +
308C GLN* 3.4 18.8 + - + +
309C ARG* 2.9 29.4 + - + +
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Residues in contact with ASN 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ASN* 3.3 30.8 + - - +
272C PRO* 4.6 12.9 - - - +
302C LEU* 3.1 27.3 + - - +
303C TYR* 4.0 6.3 - - - +
304C LYS 3.4 0.4 - - - -
305C LYS* 1.3 74.8 - - - +
307C ILE* 1.3 65.5 + - - +
309C ARG* 3.7 26.6 + - - +
310C LEU* 3.2 30.4 + - + +
325C ARG 4.3 3.8 + - - -
326C VAL* 4.1 34.2 + - + +
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Residues in contact with ILE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C TYR 3.3 15.6 + - - +
304C LYS 3.9 6.1 - - - +
305C LYS 3.3 0.6 - - - -
306C ASN* 1.3 76.6 - - - +
308C GLN* 1.3 60.1 + - - +
310C LEU* 3.4 16.0 + - - +
311C THR* 3.0 18.2 + - - +
322C MET* 4.4 17.0 - - + -
326C VAL* 4.7 9.4 - - + -
337C TYR* 3.8 20.6 - - + -
338C VAL* 4.0 18.8 - - + -
341C MET* 3.7 33.4 - - + -
347C ILE* 5.1 5.8 - - + -
360C PHE* 4.0 28.9 - - + -
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Residues in contact with GLN 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LYS* 3.3 22.5 + - - +
305C LYS* 4.0 21.2 - - + +
306C ASN 3.4 0.2 - - - -
307C ILE* 1.3 75.1 - - - +
309C ARG* 1.3 64.0 + - - +
311C THR* 3.4 20.7 + - - -
312C LYS* 3.8 5.5 + - - +
341C MET* 4.2 14.6 - - + -
346C GLU* 3.4 32.1 + - - +
347C ILE* 4.5 17.4 - - + +
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Residues in contact with ARG 309 (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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409A LEU* 3.9 39.8 - - + +
269C THR 4.8 2.0 + - - -
270C ASN* 3.6 39.7 + - - +
305C LYS* 2.9 20.3 + - + +
306C ASN* 3.7 32.4 + - - +
307C ILE 3.2 0.2 - - - -
308C GLN* 1.3 78.6 - - - +
310C LEU* 1.3 69.6 + - + +
311C THR 3.3 0.7 + - - -
312C LYS* 3.4 14.0 + - - +
313C THR* 3.6 12.2 + - - +
325C ARG* 4.9 17.2 + - - +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A THR* 6.0 1.6 - - + -
306C ASN* 3.2 19.0 + - + +
307C ILE* 3.4 8.0 + - - +
308C GLN 3.3 0.2 - - - -
309C ARG* 1.3 84.0 - - + +
311C THR* 1.3 59.9 + - - +
313C THR* 4.5 2.7 - - - +
314C PHE* 2.8 63.3 + - + +
317C LEU* 4.2 21.1 - - + -
322C MET* 4.3 7.9 - - + -
325C ARG* 3.8 28.0 - - + +
326C VAL* 4.2 21.5 - - + -
360C PHE* 5.2 11.6 - - + -
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Residues in contact with THR 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ARG* 3.1 18.5 + - - +
307C ILE* 3.0 16.1 + - - +
308C GLN* 3.5 13.4 + - - -
309C ARG 3.2 1.0 - - - -
310C LEU* 1.3 79.0 - - - +
312C LYS* 1.3 57.3 + - - +
314C PHE 2.9 15.7 - - - +
347C ILE* 4.6 18.0 - - + +
360C PHE* 3.7 43.2 - - + +
361C HIS 4.6 8.3 - - - +
362C ASP* 4.8 11.2 - - - +
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Residues in contact with LYS 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ILE* 3.7 16.6 - - + +
409A LEU* 5.9 3.1 - - + -
413A ILE 4.8 2.9 - - - -
414A SER* 3.3 37.2 + - - +
415A ALA 2.9 8.1 - - - +
416A ARG* 2.5 54.7 + - - +
428A ASP* 3.9 7.1 + - - +
308C GLN 3.8 4.9 + - - +
309C ARG* 3.4 10.7 + - - +
310C LEU 3.3 0.2 - - - -
311C THR* 1.3 80.1 - - - +
313C THR* 1.3 58.1 + - - +
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Residues in contact with THR 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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404A LEU 4.0 2.0 - - - +
405A THR* 3.9 28.2 - - + +
408A ILE* 3.5 35.1 - - + +
409A LEU* 3.9 15.8 - - - +
415A ALA 3.2 11.4 - - - +
416A ARG* 3.3 0.7 - - - -
417A VAL* 3.0 28.6 + - + +
309C ARG* 3.6 13.0 + - - +
310C LEU* 3.6 2.8 + - - -
311C THR 3.4 0.2 - - - -
312C LYS* 1.3 77.3 - - - +
314C PHE* 1.3 80.5 + - + +
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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