Contacts of the helix formed by residues 266 - 282 (chain A) in PDB entry 4II9
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 TYR 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LYS* 5.3 0.7 - - + -
175A ARG* 2.9 61.4 + - + -
176A PRO* 3.5 23.2 - - + +
179A ASP* 5.6 0.7 - - - -
264A THR* 3.1 5.5 + - - -
265A TYR* 1.3 81.1 - - - +
267A ALA* 1.3 64.6 + - - +
268A PRO* 3.2 8.7 - - - -
269A TYR* 2.9 56.4 + + + +
9C C 5.3 2.7 - - - -
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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
----------------------------------------------------------
181A VAL* 4.0 13.7 - - + -
233A ALA* 3.6 17.9 - - + +
240A LEU* 3.7 19.3 - - + -
241A SER* 3.4 17.6 + - - +
264A THR 2.9 17.9 + - - +
265A TYR 3.1 1.4 - - - -
266A TYR* 1.3 75.9 - - - +
268A PRO* 1.4 60.6 - - + +
270A ALA* 2.9 20.3 + - - +
271A VAL* 3.0 12.3 + - - +
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Residues in contact with PRO 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER* 3.7 20.9 - - - +
259A SER* 4.6 5.4 - - - -
264A THR* 3.6 15.3 - - - +
266A TYR* 3.3 6.3 - - - -
267A ALA* 1.4 91.2 - - + +
269A TYR* 1.3 59.8 + - + +
271A VAL* 3.4 6.3 + - + +
272A GLN* 3.1 31.4 + - - +
304A PHE* 3.8 16.5 - - + -
9C C 3.4 38.8 - - + +
10C A9Z 4.9 1.3 - - - +
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LYS* 3.6 48.6 + - + +
173A ILE* 4.7 6.0 - - + +
176A PRO* 4.3 3.8 - - + -
177A PHE* 5.4 0.2 - - - -
266A TYR* 2.9 44.5 + + - +
268A PRO* 1.3 77.0 - - + +
270A ALA* 1.4 59.4 + - - +
272A GLN* 3.4 2.9 + - - +
273A SER* 2.9 28.3 + - - -
304A PHE* 3.3 36.7 - + - -
307A VAL* 3.8 20.0 - - + +
308A PHE* 3.8 26.7 - + + -
9C C 6.4 0.2 - - - -
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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
----------------------------------------------------------
176A PRO* 3.9 12.9 - - + +
177A PHE* 3.4 34.2 - - + -
181A VAL* 3.9 14.1 - - + -
183A VAL* 3.8 15.0 - - + -
266A TYR 3.5 1.4 + - - -
267A ALA 2.9 9.7 + - - +
269A TYR* 1.4 74.6 - - - +
271A VAL* 1.4 65.0 + - - +
273A SER* 3.2 2.6 + - - -
274A GLU* 3.1 28.1 + - - +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL* 4.6 6.7 - - + -
231A PHE* 4.0 17.0 - - + +
233A ALA* 3.8 17.0 - - + +
241A SER* 3.6 28.5 - - - +
242A THR* 4.4 8.1 - - - +
243A GLY* 4.0 9.9 - - - +
254A TYR* 5.7 0.7 - - + -
267A ALA 3.0 8.9 + - - +
268A PRO* 3.6 9.2 - - + +
270A ALA* 1.4 73.0 - - - +
272A GLN* 1.3 71.6 + - - +
274A GLU* 3.1 5.6 + - - +
275A MET* 3.0 49.8 + - + +
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Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.6 38.6 - - - -
268A PRO 3.1 15.5 + - - +
269A TYR 3.4 2.4 + - - +
271A VAL* 1.3 79.9 - - - +
273A SER* 1.3 64.4 + - - +
275A MET* 3.2 5.0 + - - +
276A ILE* 2.9 30.1 + - + +
287A TYR* 2.7 33.4 + - - -
289A LEU* 3.5 17.3 - - - +
304A PHE* 3.8 12.4 - - + -
308A PHE* 3.5 40.6 - - + -
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 2.9 43.9 + - - -
162A LEU* 5.8 0.5 - - - +
173A ILE* 3.5 28.6 - - - +
177A PHE* 4.1 12.2 - - - -
269A TYR 2.9 17.8 + - - -
270A ALA 3.6 6.1 - - - -
271A VAL 3.2 0.4 - - - -
272A GLN* 1.3 77.4 - - - +
274A GLU* 1.4 59.7 + - - +
276A ILE* 3.5 0.6 + - - -
277A GLN* 2.9 15.1 + - - +
308A PHE* 4.6 1.3 - - - -
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 4.4 14.8 - - + -
183A VAL* 3.8 29.4 - - + +
231A PHE* 3.7 28.6 - - + -
270A ALA 3.1 14.5 + - - +
271A VAL 3.1 4.4 + - - +
273A SER* 1.4 77.9 + - - +
275A MET* 1.4 62.0 + - - +
277A GLN* 3.3 15.5 + - - +
278A TRP* 3.0 26.2 + - - +
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Residues in contact with MET 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.7 28.9 - - + -
243A GLY* 3.3 43.5 - - - +
244A ILE 3.6 14.8 - - - +
245A ALA* 3.9 11.7 - - + -
252A ILE* 4.5 3.7 - - + +
254A TYR* 3.8 17.5 - - + -
271A VAL* 3.0 22.5 + - + +
272A GLN* 3.7 9.9 - - - +
274A GLU* 1.4 73.5 - - - +
276A ILE* 1.3 67.3 + - - +
278A TRP* 3.1 7.3 + - - +
279A ALA* 3.1 20.6 + - - +
287A TYR* 3.2 36.2 - - + +
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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
----------------------------------------------------------
150A LEU* 4.4 4.9 - - + -
152A LEU* 4.6 5.4 - - + -
161A THR* 3.7 19.3 - - + +
164A LEU* 3.6 29.6 - - + -
165A TYR* 3.6 22.2 - - - +
272A GLN* 2.9 23.0 + - + +
273A SER 3.7 3.8 - - - +
275A MET* 1.3 75.3 - - - +
277A GLN* 1.3 59.3 + - - +
279A ALA* 3.0 8.9 + - - +
280A LEU* 2.9 29.0 + - + +
287A TYR* 3.5 34.8 - - + -
308A PHE* 3.7 20.6 - - + -
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Residues in contact with GLN 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS 3.0 22.2 + - - -
160A THR* 3.2 11.5 - - - +
161A THR* 3.1 27.7 + - - +
273A SER 2.9 18.4 + - - +
274A GLU* 3.5 19.1 - - - +
275A MET 3.2 0.2 - - - -
276A ILE* 1.3 77.7 - - - +
278A TRP* 1.3 56.6 + - - +
280A LEU* 3.3 6.9 + - - +
281A ASP* 2.8 67.1 + - - +
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Residues in contact with TRP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASP* 3.5 23.7 + - - +
227A THR 3.5 23.6 - - - -
229A ARG* 3.4 57.8 - - + +
231A PHE* 3.9 21.3 - + + -
245A ALA* 3.6 26.7 - - + -
247A LYS* 3.6 12.7 - - + +
252A ILE* 3.6 25.4 - - + -
274A GLU 3.0 13.6 + - - +
275A MET* 3.2 10.3 - - - +
277A GLN* 1.3 74.3 - - - +
279A ALA* 1.3 59.8 + - - +
281A ASP* 3.4 7.6 + - + +
282A THR* 2.8 48.4 + - + +
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Residues in contact with ALA 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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152A LEU* 3.6 23.6 - - + -
252A ILE* 3.5 30.0 - - + +
275A MET 3.1 9.3 + - - +
276A ILE* 3.0 13.1 + - - +
278A TRP* 1.3 74.5 - - - +
280A LEU* 1.3 64.4 + - - +
282A THR* 3.3 2.5 + - - -
283A ASN 3.2 2.9 + - - -
284A THR* 2.9 31.1 + - - -
286A LEU 4.7 0.7 - - - +
287A TYR* 4.6 7.2 - - + -
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Residues in contact with LEU 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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152A LEU* 4.1 26.7 - - + +
155A PHE 5.2 2.9 - - - +
158A ALA* 4.0 28.6 - - + +
159A LYS 4.1 3.8 - - - +
160A THR* 3.4 43.3 - - - +
161A THR* 3.6 8.7 - - - +
164A LEU* 4.5 6.5 - - + -
276A ILE* 2.9 19.4 + - + +
277A GLN* 3.7 13.9 - - - +
279A ALA* 1.3 77.9 - - - +
281A ASP* 1.3 60.5 + - - +
283A ASN* 3.1 21.7 + - - +
284A THR 5.6 0.2 - - - -
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Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS 4.6 1.6 - - - +
277A GLN* 2.8 54.3 + - - +
278A TRP* 3.4 9.1 + - + +
280A LEU* 1.3 72.1 - - - +
282A THR* 1.3 61.5 + - + +
283A ASN* 3.5 6.8 + - - -
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Residues in contact with THR 282 (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 LYS* 3.5 23.1 + - - -
252A ILE* 4.0 1.6 - - - +
278A TRP* 2.8 44.5 + - + +
279A ALA* 3.3 3.5 + - - -
281A ASP* 1.3 78.2 - - + +
283A ASN* 1.3 72.5 + - - +
284A THR* 2.8 23.9 + - - -
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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