Contacts of the helix formed by residues 262 - 280 (chain C) in PDB entry 7PRC
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 262 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C THR* 1.3 84.1 - - - +
263C GLN* 1.3 78.6 + - - +
264C ARG 3.2 0.3 + - - -
265C ALA* 3.2 7.6 + - - +
266C ILE* 3.2 27.0 + - + +
309M LEU* 3.8 21.1 - - + -
310M PRO* 3.3 28.7 - - + +
312M THR* 3.1 20.6 - - + +
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Residues in contact with GLN 263 (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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246C PHE* 3.6 28.0 - - + +
247C CYS* 4.0 6.3 - - - -
261C THR* 3.0 22.5 + - - +
262C PRO* 1.3 88.7 - - - +
264C ARG* 1.3 57.6 + - - +
266C ILE* 3.7 10.4 - - - +
267C ALA* 2.8 28.9 + - - +
340C HEM 3.2 54.4 + - + +
309M LEU* 4.1 8.3 - - - +
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Residues in contact with ARG 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ARG* 5.0 1.0 - - - +
247C CYS* 3.6 24.4 - - + +
248C HIS* 3.1 24.4 + - - -
253C PHE 2.9 26.9 + - - -
254C GLU* 4.5 1.8 - - - +
255C SER 3.4 11.9 + - - -
256C TRP* 3.6 30.5 - - + +
259C LYS 5.0 0.2 + - - -
260C SER* 2.8 37.4 + - - -
261C THR* 3.0 14.2 + - - +
263C GLN* 1.3 77.0 - - - +
265C ALA* 1.3 59.3 + - - +
267C ALA* 3.3 4.7 + - - -
268C TRP* 2.8 25.3 + - - +
339C HEM 3.2 65.3 + - + +
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Residues in contact with ALA 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C TRP* 3.5 3.5 - - - -
261C THR 3.9 1.4 + - - -
262C PRO 3.2 6.5 + - - +
264C ARG* 1.3 78.0 - - - +
266C ILE* 1.3 64.8 + - + +
268C TRP* 2.9 12.0 + - - +
269C TRP* 3.0 24.1 + - + +
312M THR* 3.5 24.7 - - + -
313M PRO 4.4 1.8 - - - +
315M PRO* 3.6 25.6 - - + -
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Residues in contact with ILE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C GLN 3.9 9.4 - - - +
124C HIS* 2.9 50.6 + - - +
262C PRO* 3.2 19.4 + - + +
263C GLN* 3.6 11.9 - - - +
264C ARG 3.2 0.4 - - - -
265C ALA* 1.3 75.3 - - + +
267C ALA* 1.3 62.6 + - - +
269C TRP* 3.1 11.4 + - - +
270C GLY 3.0 6.1 + - - -
340C HEM 3.6 46.9 - - + +
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Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ILE* 5.7 0.9 - - + -
263C GLN 2.8 21.5 + - - +
264C ARG 3.5 5.6 - - - +
266C ILE* 1.3 73.8 - - - +
268C TRP* 1.3 62.0 + - - +
270C GLY* 3.1 10.3 + - - +
271C ILE* 3.1 18.6 + - - +
339C HEM 3.5 40.6 - - + -
340C HEM 4.1 24.6 - - + +
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Residues in contact with TRP 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ARG* 3.7 14.9 - - - +
256C TRP* 4.3 2.0 - + + -
264C ARG 2.8 14.0 + - - +
265C ALA 2.9 8.7 + - - +
267C ALA* 1.3 77.9 - - - +
269C TRP* 1.3 99.2 - + - +
271C ILE* 3.4 8.7 + - - +
272C ARG* 3.0 60.7 - - + +
339C HEM 2.9 49.3 + - + +
315M PRO* 3.4 30.1 - - + -
316M ALA* 3.6 27.0 - - + +
321M ALA* 4.4 0.9 - - + -
322M PRO* 3.7 29.6 - - + -
323M LYS 4.5 0.9 - - - -
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Residues in contact with TRP 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C TRP* 3.9 16.4 - + + -
123C GLN* 3.1 65.3 - - + +
124C HIS* 4.2 4.3 - - + +
265C ALA* 3.0 30.0 + - + +
266C ILE* 3.1 6.9 + - - +
268C TRP* 1.3 95.9 - + - +
270C GLY* 1.3 56.1 + - - +
272C ARG* 3.1 6.3 + - + +
273C MET* 2.8 29.8 + - - +
315M PRO* 3.8 16.3 - - + +
318M LEU* 4.8 16.3 - - + +
320M GLY 5.5 0.4 - - - -
321M ALA* 4.5 7.2 - - + -
322M PRO* 3.5 37.7 - - + -
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C HIS* 3.3 31.2 + - - -
266C ILE 3.0 10.7 + - - -
267C ALA 3.1 3.9 + - - -
269C TRP* 1.3 73.7 - - - +
271C ILE* 1.3 60.6 + - - +
273C MET* 3.6 3.1 - - - +
274C VAL* 2.9 34.7 + - - +
340C HEM 3.6 11.5 - - - +
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Residues in contact with ILE 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C PHE* 4.7 2.0 - - + +
194C LEU* 4.1 13.2 - - + -
201C VAL* 4.7 9.4 - - + -
232C LEU* 4.9 7.2 - - + -
233C MET* 5.1 0.2 - - + -
236C ILE* 4.5 18.6 - - + -
267C ALA 3.1 13.9 + - - +
268C TRP 3.6 5.6 - - - +
269C TRP 3.3 0.2 - - - -
270C GLY* 1.3 75.6 - - - +
272C ARG* 1.3 79.1 + - - +
274C VAL* 3.4 5.0 + - - +
275C ARG* 3.1 44.9 + - - +
339C HEM 4.2 33.0 - - + +
340C HEM 3.5 20.6 - - + +
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Residues in contact with ARG 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C TRP* 4.0 18.0 - - + -
200C GLN* 5.2 6.9 + - - +
268C TRP* 3.0 68.1 + - + +
269C TRP* 3.1 11.5 + - + +
271C ILE* 1.3 96.2 - - - +
273C MET* 1.3 63.5 + - - +
275C ARG* 3.1 32.2 + - - +
276C ASP* 3.1 13.5 + - - +
339C HEM 2.8 27.9 + - - -
316M ALA* 5.4 1.0 - - - +
322M PRO* 4.4 10.8 - - + -
323M LYS* 3.0 40.9 + - - +
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Residues in contact with MET 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 4.3 6.5 - - - -
121C TRP* 3.5 54.0 - - + -
124C HIS* 3.5 27.1 - - + -
125C VAL* 4.1 8.1 - - + -
269C TRP 2.8 19.9 + - - +
270C GLY* 3.6 4.5 - - - +
272C ARG* 1.3 73.4 - - - +
274C VAL* 1.3 62.3 + - - +
276C ASP* 3.3 3.5 + - - +
277C LEU* 3.1 34.6 + - + +
340C HEM 3.4 56.5 - - + -
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 3.6 26.5 - - + +
270C GLY 2.9 20.1 + - - +
271C ILE 3.6 2.9 - - - +
272C ARG 3.3 0.2 - - - -
273C MET* 1.3 76.3 - - + +
275C ARG* 1.3 59.0 + - - +
277C LEU* 3.5 9.1 + - + +
278C ASN* 2.9 52.3 + - - +
303C ALA* 3.7 10.1 - - + +
304C ASP* 4.2 8.3 - - - +
340C HEM 3.6 47.8 - - + -
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Residues in contact with ARG 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C PHE* 2.7 33.8 + - - +
194C LEU* 3.6 18.2 - - - +
196C ASN 2.9 24.5 + - - +
197C ASP* 3.8 18.4 + - + +
199C ARG 2.9 29.3 + - - +
201C VAL* 4.5 7.9 - - - +
271C ILE* 3.1 31.0 + - - +
272C ARG* 3.1 31.4 + - - +
274C VAL* 1.3 73.9 - - - +
276C ASP* 1.3 59.8 + - - +
278C ASN* 3.2 0.3 + - - -
279C MET* 2.8 51.9 + - + +
323M LYS* 4.9 6.1 + - - -
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Residues in contact with ASP 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ALA* 5.6 1.4 - - - +
121C TRP* 3.0 36.3 + - + +
272C ARG 3.1 11.2 + - - +
273C MET 3.3 10.1 - - - +
275C ARG* 1.3 75.9 - - - +
277C LEU* 1.3 58.8 + - - +
279C MET* 4.4 4.8 - - - +
280C ASN* 2.8 60.2 + - - +
281C TYR* 4.2 15.5 + - - -
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Residues in contact with LEU 277 (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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113C MET* 4.1 15.0 - - + +
116C ALA* 5.9 0.9 - - + -
117C ILE* 3.6 40.4 - - + +
121C TRP* 5.1 2.0 - - + -
273C MET* 3.1 30.4 + - + +
274C VAL* 3.8 11.4 - - + +
276C ASP* 1.3 84.0 - - - +
278C ASN* 1.3 60.2 + - - +
281C TYR* 3.1 14.2 + - + +
282C LEU* 2.7 42.4 + - + +
303C ALA* 5.2 4.0 - - + -
338C HEM 4.5 15.9 - - + -
340C HEM 4.6 11.0 - - + -
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Residues in contact with ASN 278 (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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190C PHE* 4.2 1.8 - - - -
194C LEU 2.9 26.0 + - - +
195C ALA* 3.8 13.1 - - - +
274C VAL* 2.9 21.2 + - - +
275C ARG 3.8 2.2 - - - +
277C LEU* 1.3 77.1 - - - +
279C MET* 1.3 62.9 + - - +
282C LEU* 3.7 8.8 + - - +
283C ALA* 2.9 33.9 + - - +
302C GLN* 3.2 25.0 - - - +
303C ALA* 3.1 44.9 + - - +
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Residues in contact with MET 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ALA 3.7 17.5 - - - +
196C ASN* 3.9 11.9 - - + -
197C ASP* 3.7 39.9 - - + +
275C ARG* 2.8 37.2 + - + +
276C ASP* 4.2 4.0 - - - +
278C ASN* 1.3 73.7 - - - +
280C ASN* 1.3 70.1 + - - +
283C ALA* 4.4 4.1 - - - +
284C PRO* 3.4 18.0 - - - +
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Residues in contact with ASN 280 (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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109C ARG* 2.5 33.2 + - - +
276C ASP* 2.8 38.8 + - - +
279C MET* 1.3 91.9 - - - +
281C TYR* 1.3 60.6 + - + +
284C PRO* 4.2 8.5 - - - +
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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