Contacts of the helix formed by residues 265 - 280 (chain A) in PDB entry 2RIO
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 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A LEU* 4.6 0.9 - - - +
264A HIS* 1.3 76.3 + - - +
266A ARG* 1.3 63.3 + - - +
267A SER* 2.9 30.6 + - - -
268A LEU* 3.2 39.5 + - + +
269A ILE* 3.4 14.3 + - - +
302A LYS* 4.5 10.6 + - - -
400A TYR* 5.9 0.7 - - - -
401A ASP* 4.4 14.4 - - - +
404A THR* 4.1 8.7 - - - +
405A LYS* 5.9 0.9 - - - -
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Residues in contact with ARG 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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264A HIS 3.3 11.1 + - - +
265A ASP* 1.3 73.5 + - - +
267A SER* 1.4 56.8 + - - +
269A ILE* 3.1 22.0 + - + +
270A ALA* 3.1 25.8 + - - +
404A THR 5.7 0.2 - - - +
405A LYS 6.1 2.2 - - - +
408A PRO* 3.7 24.2 - - + +
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Residues in contact with SER 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 2.9 22.2 + - - -
266A ARG* 1.4 74.9 - - - +
268A LEU* 1.3 58.4 + - - +
270A ALA* 3.3 4.2 + - - +
271A GLU* 3.1 44.5 + - - +
305A LYS* 5.3 1.2 + - - -
400A TYR* 5.0 4.4 + - - -
404A THR* 2.9 30.7 + - - +
407A PHE 5.3 0.2 - - - -
408A PRO* 3.1 29.3 - - - +
411A LEU* 5.7 3.1 - - - -
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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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118A ILE* 4.0 26.7 - - + -
263A LEU* 3.9 18.4 - - + +
265A ASP* 3.2 36.8 + - + +
266A ARG 3.2 0.6 - - - -
267A SER* 1.3 76.7 + - - +
269A ILE* 1.3 60.7 + - - +
271A GLU* 3.5 8.5 - - - +
272A ALA* 2.8 31.9 + - - +
298A LEU* 3.6 14.2 - - + +
302A LYS* 6.0 5.8 - - - -
305A LYS* 3.4 29.4 - - - +
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Residues in contact with ILE 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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257A LEU 5.8 1.3 - - - +
258A ASP* 6.5 0.9 - - - -
260A MET* 4.0 27.1 - - + +
263A LEU* 3.5 44.0 - - + +
264A HIS 4.9 1.6 - - - +
265A ASP 3.4 13.9 + - - +
266A ARG* 3.1 24.8 + - + +
268A LEU* 1.3 78.6 - - - +
270A ALA* 1.3 54.5 + - - +
272A ALA* 4.0 0.7 - - - +
273A THR* 2.5 45.9 + - - +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ARG 3.1 8.8 + - - +
267A SER 3.4 9.6 - - - +
269A ILE* 1.3 79.2 - - - +
271A GLU* 1.3 57.0 + - - +
273A THR* 3.5 6.6 + - - -
274A ASP* 3.1 25.6 + - - +
337A PHE* 5.9 0.4 - - + -
408A PRO* 3.4 11.9 - - + +
409A ASN* 3.4 29.2 - - - +
412A ILE* 4.0 12.5 - - + +
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A SER* 3.1 28.9 + - - +
268A LEU* 3.5 13.7 - - - +
270A ALA* 1.3 73.6 - - - +
272A ALA* 1.3 58.7 + - - +
274A ASP 3.5 1.2 + - - -
275A LEU* 3.0 23.7 + - - +
296A HIS* 3.2 14.6 - - + -
297A PRO* 5.0 0.2 - - + -
298A LEU* 3.8 22.7 - - + +
305A LYS* 3.0 33.2 + - - -
400A TYR* 4.3 0.5 + - - -
408A PRO 5.2 0.3 - - - +
411A LEU* 3.8 26.4 - - + +
412A ILE* 3.9 30.0 + - + +
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Residues in contact with ALA 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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233A LEU* 3.5 32.8 - - + -
260A MET* 4.0 12.6 - - - -
263A LEU* 4.4 1.1 - - + -
268A LEU 2.8 22.1 + - - +
271A GLU* 1.3 71.1 - - - +
273A THR* 1.3 63.6 + - - +
275A LEU* 4.5 1.6 - - - +
276A ILE* 3.0 29.5 + - + +
298A LEU* 3.8 20.0 - - + +
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Residues in contact with THR 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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257A LEU* 3.8 23.2 + - + +
260A MET* 3.7 17.6 - - - +
269A ILE* 2.5 34.0 + - - +
270A ALA* 3.6 7.4 - - - -
272A ALA* 1.3 71.5 - - - +
274A ASP* 1.3 58.0 + - - +
277A SER* 3.0 37.5 + - - +
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Residues in contact with ASP 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 ALA 3.1 14.2 + - - +
271A GLU 3.6 7.6 - - - +
273A THR* 1.3 74.3 - - - +
275A LEU* 1.3 66.2 + - - +
277A SER* 3.6 5.4 + - - -
278A GLN* 3.1 45.4 + - - +
296A HIS* 2.6 26.7 + - - -
412A ILE* 3.5 23.7 - - + +
415A TYR* 4.8 4.9 - - - -
416A MET* 3.6 22.6 - - - +
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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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229A PHE* 4.2 17.5 - - + -
271A GLU 3.0 17.9 + - - +
272A ALA* 3.9 4.5 - - - +
274A ASP* 1.3 79.1 + - - +
276A ILE* 1.3 61.7 + - + +
278A GLN* 3.3 6.3 + - - +
279A MET* 2.9 48.1 + - + +
288A PRO* 4.4 9.4 - - + -
292A LYS 5.1 0.7 - - - +
293A VAL* 4.2 15.3 - - + -
296A HIS* 3.7 35.9 - - + -
298A LEU* 4.1 15.7 - - + -
299A PHE* 4.0 26.9 - - + -
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Residues in contact with ILE 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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121A LEU* 5.4 0.7 - - + -
226A GLY 3.7 15.5 - - - +
229A PHE* 3.9 11.4 - - + -
230A TYR* 3.8 24.0 - - + +
233A LEU* 3.9 22.2 - - + -
257A LEU* 3.6 28.0 - - + -
260A MET* 4.0 12.8 - - + -
272A ALA* 3.0 19.6 + - + +
273A THR 4.2 1.3 - - - +
275A LEU* 1.3 83.0 - - + +
277A SER* 1.3 61.6 + - - +
279A MET* 3.0 35.6 + - + +
280A ILE* 3.1 19.8 + - + +
298A LEU* 6.1 0.2 - - + -
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 3.7 34.3 - - - -
257A LEU* 3.9 7.8 - - - +
273A THR* 3.0 22.5 + - - +
274A ASP* 3.6 8.1 + - - -
276A ILE* 1.3 75.3 - - - +
278A GLN* 1.3 63.8 + - - +
280A ILE* 3.8 5.3 - - - +
281A ASP* 3.4 21.0 + - - +
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Residues in contact with GLN 278 (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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274A ASP* 3.1 44.8 + - - +
275A LEU* 3.3 8.8 + - - +
276A ILE 3.1 0.6 - - - -
277A SER* 1.3 77.3 + - - +
279A MET* 1.3 67.2 + - - +
280A ILE 3.1 2.5 + - - -
281A ASP* 3.1 17.3 + - - +
286A LYS 4.2 9.3 - - - +
287A ARG* 3.5 15.2 - - - -
288A PRO* 3.7 19.9 - - + +
296A HIS* 4.6 4.6 + - - -
419A LYS* 5.9 5.1 - - - +
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Residues in contact with MET 279 (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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222A ILE* 3.5 16.5 - - + +
223A PHE* 3.3 9.9 + - - -
225A MET* 4.9 2.7 - - - +
226A GLY* 3.4 19.1 - - - -
229A PHE* 3.4 33.7 - - + -
275A LEU* 2.9 31.9 + - + +
276A ILE* 3.0 44.8 + - + +
278A GLN* 1.3 75.5 - - - +
280A ILE* 1.3 58.5 + - - +
287A ARG* 3.0 23.4 - - - -
288A PRO* 3.8 16.4 - - + -
293A VAL* 4.1 13.9 - - + -
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Residues in contact with ILE 280 (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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223A PHE* 3.5 37.3 - - + +
226A GLY 3.6 31.0 - - - +
227A CYS* 3.7 8.1 - - - +
239A PRO* 3.7 30.3 - - + -
240A PHE* 3.9 10.0 - - + -
255A PHE* 3.7 34.1 - - + -
257A LEU* 4.2 7.0 - - + -
276A ILE* 3.3 16.2 - - + +
277A SER* 3.8 7.6 - - - +
279A MET* 1.3 78.0 - - - +
281A ASP* 1.3 67.8 + - - +
282A HIS* 3.3 1.6 + - - -
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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
------------------------------------------------------------
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