Contacts of the helix formed by residues 263 - 276 (chain A) in PDB entry 7CR3
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 THR 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A TYR* 3.4 20.9 - - - -
261A PHE 4.5 0.3 - - - -
262A ASP* 1.3 89.1 + - + +
264A TYR* 1.3 63.1 + - - +
265A ALA* 3.3 17.6 + - - +
266A ASP* 3.4 19.2 + - - +
267A ALA* 3.5 13.5 + - - +
114B THR* 4.2 27.4 - - - +
115B ILE* 4.2 14.6 - - + +
116B LYS 5.2 2.2 - - - +
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Residues in contact with TYR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 3.5 33.8 + - + +
247A SER* 4.5 2.7 - - - -
248A PHE* 3.5 40.9 - + + +
251A TYR* 3.7 24.2 + + + -
263A THR* 1.3 74.2 - - - +
265A ALA* 1.3 60.3 + - - +
267A ALA* 3.5 2.8 + - + +
268A LEU* 3.0 59.1 + - + +
107B LEU* 6.4 0.2 - - + -
111B VAL* 4.2 17.0 - - + -
114B THR* 4.1 16.8 + - + +
201B ARG* 4.2 29.2 - - - +
205B ILE* 5.0 4.3 - - + +
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A THR* 3.2 10.1 + - - +
264A TYR* 1.3 76.1 - - - +
266A ASP* 1.3 61.8 + - - +
268A LEU* 3.1 7.0 + - - +
269A TRP* 2.9 26.0 + - - +
111B VAL* 4.2 24.4 - - + +
114B THR* 4.5 2.2 - - - +
115B ILE* 4.0 26.2 - - + -
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Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A HIS 4.0 11.4 - - - +
261A PHE* 4.7 2.2 - - - -
262A ASP* 4.5 8.7 - - - +
263A THR* 3.4 27.2 + - - +
264A TYR 3.5 0.4 - - - -
265A ALA* 1.3 78.7 - - - +
267A ALA* 1.3 57.0 + - - +
269A TRP* 3.2 7.6 + - - +
270A TRP* 2.9 26.7 + - - +
283A LYS* 3.6 29.1 - - - +
291G ARG* 3.3 24.5 + - - +
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A SER* 2.5 26.0 + - - +
251A TYR* 3.8 24.9 - - + -
261A PHE* 3.5 29.0 - - + -
263A THR 3.5 9.6 + - - +
264A TYR* 3.6 11.4 - - + +
265A ALA 3.2 0.4 - - - -
266A ASP* 1.3 79.2 - - - +
268A LEU* 1.3 54.4 + - - +
270A TRP* 3.2 5.0 + - - +
271A GLY 3.0 19.8 + - - -
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU* 4.2 20.8 - - + +
244A ILE* 4.8 9.0 - - + -
247A SER* 3.5 20.9 - - - +
264A TYR* 3.0 49.4 + - + +
265A ALA* 3.1 8.7 + - - +
267A ALA* 1.3 73.4 - - - +
269A TRP* 1.3 66.5 + - - +
271A GLY* 3.3 1.0 + - - -
272A LEU* 3.0 25.5 + - - +
107B LEU* 5.7 4.0 - - + -
111B VAL* 4.0 23.6 - - + -
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Residues in contact with TRP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ALA 2.9 13.1 + - - +
266A ASP* 3.2 11.0 + - - +
268A LEU* 1.3 76.4 - - - +
270A TRP* 1.3 64.3 + - - +
272A LEU* 3.4 26.2 + - + +
273A ILE* 3.0 59.2 + - + +
280A TYR* 3.8 17.1 - + - -
282A ASP* 3.7 22.7 + - - -
283A LYS* 4.3 12.1 - - + -
270G TRP* 6.3 0.2 - + - -
284G TYR* 5.2 0.6 - - + +
285G PRO* 4.0 26.9 + - + -
291G ARG* 3.8 57.8 - - + +
294G ALA* 4.6 8.5 - - + -
295G ALA* 4.8 4.3 - - + -
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Residues in contact with TRP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ALA* 4.5 7.0 - - + -
247A SER* 4.2 12.8 - - - -
250A VAL* 3.7 32.5 - - + -
261A PHE* 3.5 33.4 - + + -
266A ASP 2.9 10.5 + - - +
267A ALA 3.2 11.4 + - - +
269A TRP* 1.3 78.8 - - - +
271A GLY* 1.3 85.8 + - - +
273A ILE* 3.1 5.7 + - + +
274A THR* 3.0 49.9 + - + +
275A LEU* 6.2 2.2 - - + -
283A LYS* 2.9 35.8 + - + +
285A PRO* 3.7 14.8 - - + +
294A ALA* 4.0 23.8 - - + -
280B TYR* 3.0 22.7 + - - -
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Residues in contact with GLY 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU* 3.5 20.6 - - - -
247A SER* 4.4 2.9 - - - -
267A ALA 3.0 13.3 + - - -
268A LEU 3.3 0.6 + - - -
270A TRP* 1.3 93.9 - - - +
272A LEU* 1.3 62.4 + - - +
274A THR* 4.1 2.0 - - - -
275A LEU* 3.0 33.5 + - - +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU* 3.6 16.4 - - + +
268A LEU 3.0 16.8 + - - +
269A TRP* 3.9 21.8 - - + +
271A GLY* 1.3 76.9 - - - +
273A ILE* 1.3 54.2 + - + +
275A LEU* 5.1 2.0 - - - -
276A THR* 2.5 44.5 + - + +
278A ILE* 6.5 0.2 - - + -
305A PHE* 5.0 7.0 - - + -
295G ALA* 3.6 40.6 - - + +
298G THR* 3.8 22.9 - - + -
299G LEU* 4.5 11.4 - - + -
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A TRP* 3.0 65.7 + - + +
270A TRP* 3.1 6.2 + - + +
272A LEU* 1.3 81.9 - - + +
274A THR* 1.3 62.7 + - + +
276A THR* 3.3 3.9 + - - -
278A ILE* 3.1 42.8 + - + +
279A GLY* 3.3 6.2 + - - +
280A TYR* 3.6 48.5 - - + +
282A ASP* 5.3 3.6 - - - +
280B TYR* 5.9 1.1 - - + -
298G THR* 6.5 0.4 - - + -
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Residues in contact with THR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A TRP* 3.0 38.8 + - + +
271A GLY* 3.4 9.0 + - - -
273A ILE* 1.3 78.8 - - + +
275A LEU* 1.3 71.5 + - - +
276A THR 3.1 1.8 - - - -
277A THR* 2.7 26.9 + - - +
279A GLY 4.9 3.8 - - - +
302A VAL* 3.9 9.0 - - - +
278B ILE* 4.2 17.8 - - - +
280B TYR* 3.1 35.2 - - + +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLY 4.6 0.4 - - - +
242A CYS* 4.5 4.0 - - + +
243A LEU* 3.7 30.1 - - + +
246A ALA* 5.5 7.6 - - + -
270A TRP* 6.2 2.7 - - + -
271A GLY* 3.0 19.8 + - - +
272A LEU* 4.8 1.3 - - - +
274A THR* 1.3 90.4 + - - +
276A THR* 1.3 59.9 + - - +
277A THR* 3.2 1.3 - - - +
297A PHE 4.4 9.0 - - - +
298A THR* 4.9 7.4 - - - +
301A GLY* 3.6 26.0 - - - -
302A VAL* 3.5 21.5 - - + +
305A PHE* 3.3 51.6 - - + +
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Residues in contact with THR 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 2.5 37.9 + - + +
273A ILE 3.3 8.3 + - - -
275A LEU* 1.3 76.1 - - - +
277A THR* 1.3 74.8 + - - +
278A ILE* 3.2 19.6 + - - +
305A PHE* 4.1 26.2 - - + +
277G THR* 3.9 13.0 - - - +
298G THR* 4.5 8.9 + - - +
299G LEU* 4.3 8.7 - - + -
302G VAL* 4.7 15.6 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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