Contacts of the helix formed by residues 264 - 282 (chain A) in PDB entry 1BZH
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 ALA 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TRP* 3.6 41.4 - - + +
17A ALA* 3.8 10.1 - - + +
20A TYR* 3.6 22.9 - - + -
263A THR* 1.3 75.4 - - - +
265A GLU* 1.3 56.3 + - - +
267A LEU* 3.4 3.6 + - - +
268A ARG* 2.9 27.4 + - - +
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLY* 3.4 31.4 - - - -
184A VAL* 3.4 24.6 + - + +
263A THR* 3.1 12.0 + - - +
264A ALA* 1.3 76.1 - - - +
266A GLN* 1.3 53.6 + - - +
268A ARG* 3.2 12.7 + - + +
269A PHE* 2.6 36.4 + - - +
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Residues in contact with GLN 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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179A TRP* 4.4 7.0 - - + +
183A GLY 5.9 0.2 + - - -
184A VAL* 3.8 20.6 - - + -
220A GLY* 3.2 17.6 - - - +
221A ARG* 3.8 13.3 - - - +
224A THR* 4.1 10.5 + - - +
261A ILE* 3.8 8.3 - - + -
262A GLN* 2.8 27.9 + - - +
263A THR* 2.7 29.9 + - - +
265A GLU* 1.3 70.5 - - - +
267A LEU* 1.3 56.2 + - - +
269A PHE* 3.7 3.1 - - - +
270A SER* 2.7 37.6 + - - -
405I FLT 3.5 27.0 + - - -
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 4.3 4.9 - - + -
19A ILE* 3.4 33.7 - - + -
20A TYR* 3.8 25.8 - - + -
23A ILE* 4.0 12.1 - - + -
227A LEU* 4.9 0.4 - - + -
246A ILE* 4.0 13.7 - - + +
247A LYS* 5.2 1.3 - - + -
250A LEU* 4.0 22.7 - - + -
261A ILE* 3.4 14.7 - - + +
263A THR 3.1 9.6 + - - +
264A ALA 3.6 6.1 - - - +
265A GLU 3.3 0.4 - - - -
266A GLN* 1.3 74.8 - - - +
268A ARG* 1.3 63.1 + - - +
270A SER* 3.2 5.4 + - - -
271A TYR* 3.0 48.9 + - + -
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.2 29.0 - - + -
11A ASP* 2.9 37.0 + - - -
16A TRP* 3.1 39.9 - - + +
184A VAL* 6.2 1.8 - - - +
186A GLU 5.8 0.6 + - - -
264A ALA 2.9 17.7 + - - +
265A GLU* 3.2 12.1 + - + +
267A LEU* 1.3 77.8 - - - +
269A PHE* 1.3 57.3 + - - +
271A TYR 3.2 1.2 + - - -
272A LEU* 2.9 42.8 + - - +
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Residues in contact with PHE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TRP* 3.9 9.2 - + - -
184A VAL* 3.8 22.0 - - + +
185A PRO* 3.2 47.3 - - + -
187A SER 3.6 13.2 - - - -
188A PRO* 3.4 27.8 - - + -
191A PHE* 3.7 33.2 - + + -
224A THR* 3.8 17.7 - - + -
265A GLU 2.6 21.7 + - - +
266A GLN* 3.7 5.2 - - - +
267A LEU 3.3 0.2 - - - -
268A ARG* 1.3 73.6 - - - +
270A SER* 1.3 55.7 + - - +
272A LEU* 3.2 16.5 + - + +
273A ALA* 2.8 29.0 + - + +
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A THR* 3.7 27.7 + - - +
227A LEU* 4.0 14.1 - - - -
228A ALA* 5.1 2.5 - - - -
246A ILE* 3.8 18.2 - - - -
261A ILE* 4.1 6.8 - - - +
266A GLN 2.7 23.2 + - - -
267A LEU 3.6 5.2 - - - -
269A PHE* 1.3 73.3 - - - +
271A TYR* 1.3 65.3 + - - +
273A ALA* 3.6 6.8 - - - +
274A VAL* 2.9 30.9 + - - +
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Residues in contact with TYR 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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3A MET* 4.4 21.1 - - + -
6A GLU* 2.9 49.4 + - + -
7A PHE* 3.5 23.3 - + + -
10A ILE* 4.2 2.5 - - + +
16A TRP* 3.6 29.8 - + - -
19A ILE* 4.9 0.8 - - + +
246A ILE* 3.2 32.7 - - + +
247A LYS* 3.3 20.6 - - + +
267A LEU* 3.0 42.1 + - + -
268A ARG 3.6 3.6 - - - +
270A SER* 1.3 75.5 - - - +
272A LEU* 1.3 58.4 + - - +
274A VAL* 3.9 0.5 - - - +
275A ILE* 2.8 39.5 + - + +
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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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7A PHE* 3.4 31.1 - - + -
184A VAL* 6.3 0.2 - - + -
185A PRO 4.9 0.4 - - - +
186A GLU 3.9 17.0 - - - +
188A PRO* 3.8 28.7 - - + -
268A ARG* 2.9 30.5 + - - +
269A PHE* 3.2 22.9 - - + +
271A TYR* 1.3 76.0 - - - +
273A ALA* 1.3 53.9 + - - +
275A ILE* 3.6 7.0 - - + +
276A GLU* 2.7 39.0 + - + +
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Residues in contact with ALA 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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188A PRO* 3.5 20.0 - - + -
191A PHE* 4.2 17.9 - - + -
192A LEU* 3.3 17.3 - - + +
228A ALA* 4.2 15.5 - - + -
232A LEU* 5.0 0.4 - - - -
269A PHE* 2.8 21.5 + - + +
270A SER* 3.6 9.6 - - - +
272A LEU* 1.3 75.6 - - - +
274A VAL* 1.3 57.3 + - - +
277A GLY* 2.8 24.3 + - - -
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Residues in contact with VAL 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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3A MET* 3.4 31.6 - - + -
228A ALA* 3.7 28.9 - - - +
231A CYS* 3.7 25.1 - - + -
232A LEU* 3.7 11.2 - - + +
235A MET* 3.6 17.7 - - - -
246A ILE* 5.0 4.5 - - + -
270A SER 2.9 25.5 + - - +
271A TYR* 3.9 2.5 - - - +
273A ALA* 1.3 69.8 - - - +
275A ILE* 1.3 61.5 + - - +
278A ALA* 2.8 34.5 + - - +
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Residues in contact with ILE 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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3A MET* 3.4 34.8 - - + +
4A GLU* 3.6 31.4 - - + +
7A PHE* 3.5 43.5 - - + -
235A MET* 5.5 1.1 - - - -
271A TYR* 2.8 26.8 + - + +
272A LEU* 3.6 7.4 - - + +
274A VAL* 1.3 80.8 - - - +
276A GLU* 1.3 70.5 + - - +
278A ALA* 3.9 4.1 - - - +
279A LYS* 3.3 19.9 + - - +
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Residues in contact with GLU 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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188A PRO* 3.7 23.6 - - + -
189A ALA* 5.8 0.9 - - - +
192A LEU* 4.0 4.9 - - + -
272A LEU* 2.7 20.4 + - + +
275A ILE* 1.3 83.2 - - - +
277A GLY* 1.3 62.1 + - - +
279A LYS* 3.2 25.6 + - - +
280A PHE* 3.0 47.9 - - + -
291A TRP* 5.0 1.8 - - + +
294A LEU* 5.5 6.2 - - + +
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Residues in contact with GLY 277 (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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192A LEU* 3.5 19.6 - - - +
196A PHE* 4.7 2.8 - - - -
232A LEU* 3.7 11.8 - - - +
273A ALA 2.8 23.2 + - - -
274A VAL 3.8 0.4 - - - -
276A GLU* 1.3 72.9 - - - +
278A ALA* 1.3 61.6 + - - +
280A PHE* 3.6 2.5 + - - +
281A ILE* 3.4 27.7 + - - +
291A TRP* 4.5 7.2 - - - -
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Residues in contact with ALA 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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232A LEU* 3.4 7.0 - - + +
235A MET* 3.6 36.3 - - + -
236A ASP* 4.9 2.5 - - - +
274A VAL 2.8 18.8 + - - +
275A ILE 3.9 3.4 - - - +
277A GLY* 1.3 75.2 - - - +
279A LYS* 1.3 58.0 + - - +
281A ILE* 3.2 2.3 + - - -
282A MET* 2.6 46.0 + - + +
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Residues in contact with LYS 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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275A ILE 3.3 10.6 + - - +
276A GLU* 3.2 31.5 + - - +
278A ALA* 1.3 80.6 - - - +
280A PHE* 1.3 84.0 + - + +
281A ILE 3.3 0.2 + - - -
282A MET* 3.7 7.9 + - - +
283A GLY 3.8 5.5 + - - -
284A ASP* 3.0 38.7 - - - +
290A GLN* 5.0 4.0 - - - -
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Residues in contact with PHE 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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276A GLU* 3.0 54.0 + - + -
277A GLY 4.1 2.5 - - - +
278A ALA 3.3 0.6 - - - -
279A LYS* 1.3 94.9 - - + +
281A ILE* 1.3 58.6 + - - +
284A ASP* 4.0 17.1 + - - +
287A VAL* 4.0 8.7 - - + +
288A GLN* 3.5 33.7 + - - +
290A GLN* 3.2 54.3 - - + -
291A TRP* 3.0 43.5 - + + -
294A LEU* 5.1 5.4 - - + -
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Residues in contact with ILE 281 (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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196A PHE* 4.1 29.6 - - + -
199A ARG* 5.7 3.8 - - - +
232A LEU* 6.1 0.4 - - + -
236A ASP* 3.1 35.0 - - + +
277A GLY 3.4 15.6 + - - +
278A ALA 3.2 2.0 + - - +
280A PHE* 1.3 74.6 - - + +
282A MET* 1.3 67.5 + - - +
283A GLY* 3.2 4.5 + - - -
284A ASP 4.9 0.2 + - - -
288A GLN* 3.9 37.0 - - + +
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Residues in contact with MET 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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235A MET* 4.8 2.5 - - - +
236A ASP* 3.0 32.7 + - - +
241A PRO* 3.3 43.3 - - + -
278A ALA* 2.6 30.8 + - + +
279A LYS* 4.2 4.0 - - - +
281A ILE* 1.3 73.2 - - - +
283A GLY* 1.3 57.5 + - - +
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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
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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