Contacts of the helix formed by residues 272 - 288 (chain A) in PDB entry 3A61
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 ARG 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A HIS* 3.4 45.5 - - + +
215A ILE* 4.0 8.2 - - + +
271A ASN* 1.3 72.3 - - + +
273A ALA* 1.3 69.3 + - - +
275A ASP* 2.8 20.9 + - - +
276A TRP* 3.5 7.7 - - - +
337A GLY 3.5 2.6 + - - -
338A ALA* 2.5 35.1 + - - +
339A GLY 3.0 16.2 + - - -
340A PRO* 4.4 7.1 - - - +
342A ASP* 2.7 31.4 + - - +
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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
----------------------------------------------------------
263A GLU* 3.8 1.6 - - - +
271A ASN* 2.7 26.3 + - - +
272A ARG* 1.3 72.9 - - - +
274A VAL* 1.3 55.0 + - - +
276A TRP* 2.5 40.3 + - - +
277A TRP 3.3 6.1 + - - -
332A ALA* 3.5 33.9 - - + +
335A ARG* 3.6 12.5 + - - +
338A ALA* 4.8 12.2 - - + +
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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
----------------------------------------------------------
215A ILE* 6.1 4.0 - - + -
217A ARG* 3.8 23.8 - - + +
261A ALA* 3.8 19.1 - - + +
263A GLU* 4.0 17.5 - - + +
264A ILE* 3.2 43.1 - - + -
270A HIS* 4.1 15.5 - - + +
271A ASN* 3.6 13.0 - - - +
272A ARG 3.0 0.2 + - - -
273A ALA* 1.3 78.2 - - - +
275A ASP* 1.3 66.5 + - - +
276A TRP 3.0 1.2 + - - -
277A TRP* 3.1 4.9 + - - +
278A SER* 3.0 22.2 + - - +
335A ARG* 3.7 0.9 - - - +
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Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.6 28.0 - - + +
209A LEU* 5.8 0.9 - - - +
210A HIS* 2.5 32.4 + - + -
214A ILE 4.6 0.3 - - - +
215A ILE* 3.6 3.8 - - - -
216A TYR* 2.9 26.8 + - - +
217A ARG* 2.9 30.0 + - - -
219A LEU* 4.3 2.9 - - - +
272A ARG 2.8 11.2 + - - +
273A ALA 2.7 3.4 + - - -
274A VAL* 1.3 77.7 - - - +
276A TRP* 1.3 57.4 + - + +
278A SER* 3.1 26.7 + - - -
279A LEU* 3.1 7.4 + - - +
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Residues in contact with TRP 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER* 4.0 16.6 - - - -
206A LEU* 4.0 20.4 - - + -
210A HIS* 3.8 17.5 - + - -
272A ARG* 3.5 23.4 - - - +
273A ALA* 2.5 16.3 + - - +
275A ASP* 1.3 68.7 - - - +
277A TRP* 1.3 66.7 + - - +
278A SER 3.1 1.1 - - - -
279A LEU* 2.7 42.2 + - + +
280A GLY 3.2 4.7 + - - -
327A LEU* 4.1 10.3 - - + +
335A ARG* 4.3 6.3 - - + -
336A LEU 4.0 15.9 - - - +
337A GLY* 3.3 28.7 + - - -
338A ALA 4.4 0.4 - - - -
342A ASP* 3.6 29.4 + - - -
343A ALA* 3.5 30.7 - - + -
346A VAL* 3.8 25.4 - - + -
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Residues in contact with TRP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLU 6.1 0.4 - - - -
259A TYR* 4.2 2.2 - - - +
260A MET* 3.0 20.3 + - - +
261A ALA* 3.1 24.2 - - + -
262A PRO* 3.5 28.9 - - + -
273A ALA 3.3 2.8 + - - -
274A VAL 3.1 8.2 + - - +
276A TRP* 1.3 77.1 - - - +
278A SER* 1.3 71.4 + - - +
279A LEU 2.7 1.9 + - - -
280A GLY 2.8 11.4 + - - -
281A ALA* 3.4 10.6 + - - +
292A PRO* 6.4 0.4 - - + -
293A PHE* 3.5 34.8 - + - -
305A ILE* 4.0 12.7 - - + +
308A CYS* 4.1 9.6 - - + -
327A LEU 3.8 11.9 - - - -
328A LEU* 2.8 58.3 - - + +
329A LYS 4.0 12.1 - - - -
330A ARG* 4.4 2.2 - - - -
335A ARG* 3.3 20.9 - - - +
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG 3.6 11.1 + - - -
218A ASP 3.5 16.8 + - - -
219A LEU* 3.9 13.5 - - - -
259A TYR* 3.0 28.6 + - - +
260A MET* 3.9 5.0 - - - -
274A VAL* 3.0 13.3 + - - +
275A ASP* 3.1 12.3 + - - -
277A TRP* 1.3 80.2 - - - +
279A LEU* 1.3 60.7 + - - +
281A ALA* 3.1 14.1 + - - +
282A LEU* 3.1 15.1 + - - +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 4.1 30.1 - - + +
202A ILE* 4.2 16.8 - - + -
203A SER* 4.9 4.9 - - - +
206A LEU* 5.1 3.1 - - + -
219A LEU* 3.9 21.3 - - + -
275A ASP 3.1 6.2 + - - +
276A TRP* 2.7 47.8 + - + +
278A SER* 1.3 74.4 - - - +
280A GLY* 1.3 66.8 + - - +
282A LEU* 3.3 8.0 + - + +
283A MET* 3.1 17.3 + - - +
323A LEU* 6.2 0.7 - - + -
327A LEU* 3.9 14.4 - - + -
346A VAL* 4.6 10.3 - - + -
352A PHE* 5.4 5.6 - - + -
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TRP 3.2 6.5 + - - -
277A TRP 2.8 9.1 + - - -
279A LEU* 1.3 74.4 - - - +
281A ALA* 1.3 65.0 + - - -
283A MET* 2.6 17.9 + - - -
284A TYR* 2.7 14.9 + - - -
324A LEU* 4.1 10.5 - - - -
327A LEU* 3.4 19.0 - - - +
328A LEU* 3.8 13.2 - - - -
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLU 4.1 1.6 - - - +
259A TYR* 3.3 39.0 - - + +
277A TRP* 3.4 10.0 + - - +
278A SER* 3.1 10.6 + - - +
280A GLY* 1.3 69.8 - - - +
282A LEU* 1.3 66.5 + - - +
284A TYR* 3.7 0.5 - - - +
285A ASP* 2.7 26.7 + - - +
292A PRO* 3.9 27.4 - - + +
328A LEU* 3.7 6.4 - - + +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PHE* 3.1 29.6 - - + -
199A LEU* 4.5 2.0 - - + -
202A ILE* 4.2 19.1 - - + -
219A LEU* 3.2 50.0 - - + +
220A LYS 4.5 0.2 - - - +
221A PRO* 3.4 32.1 - - + -
224A ILE* 5.1 0.9 - - + -
259A TYR* 3.9 4.4 - - + -
278A SER 3.1 6.1 + - - +
279A LEU* 3.5 12.1 - - + +
280A GLY 2.8 3.4 + - - -
281A ALA* 1.3 74.5 - - - +
283A MET* 1.3 50.9 + - - +
285A ASP* 2.7 7.0 + - - +
286A MET* 2.5 47.2 + - + +
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Residues in contact with MET 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 3.1 28.0 - - + +
279A LEU 3.1 7.5 + - - +
280A GLY 2.6 9.6 + - - +
282A LEU* 1.3 76.2 - - - +
284A TYR* 1.3 58.0 + - - +
286A MET* 2.6 26.1 + - - +
287A LEU* 2.8 31.1 + - + +
320A ALA* 4.3 8.7 - - - +
323A LEU* 3.3 36.6 - - + -
324A LEU* 4.2 21.8 - - + -
327A LEU* 4.7 6.1 - - + -
351A PHE* 3.3 38.8 - - + -
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Residues in contact with TYR 284 (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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280A GLY 2.7 17.6 + - - +
281A ALA 3.7 2.9 - - - +
283A MET* 1.3 76.3 - - - +
285A ASP* 1.3 56.4 + - - +
287A LEU* 3.3 3.1 + - - +
288A THR* 2.8 49.8 + - + +
290A ALA 3.4 18.6 - - - -
291A PRO 3.8 2.2 - - - -
292A PRO* 3.5 42.9 + - + +
310A LEU* 4.4 9.4 - - + -
311A ASN* 2.7 34.3 + - - +
312A LEU* 4.7 1.3 - - + -
313A PRO* 4.0 22.1 - - + +
316A LEU* 5.3 0.7 - - + -
324A LEU* 3.4 37.9 - - + +
328A LEU* 4.6 2.0 - - + -
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Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PHE* 3.6 9.5 - - - -
184A LEU* 3.0 32.9 - - - +
259A TYR* 3.0 27.7 + - + +
281A ALA 2.7 20.2 + - - +
282A LEU 3.1 3.4 - - - +
284A TYR* 1.3 72.6 - - - +
286A MET* 1.3 62.4 + - - +
288A THR 2.7 18.1 - - - +
289A GLY* 3.1 6.9 - - - +
290A ALA* 2.7 40.7 + - - -
291A PRO* 3.7 3.0 - - + +
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Residues in contact with MET 286 (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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180A LEU* 4.1 11.9 - - + -
181A PHE* 3.8 31.4 - - + -
184A LEU* 3.9 6.1 - - + +
189A ILE* 3.5 5.5 - - - -
190A PHE* 2.9 42.0 + - + -
195A ALA* 3.8 28.0 - - + +
198A TYR* 4.5 7.9 - - + -
199A LEU* 3.5 41.3 - - + -
202A ILE* 4.5 9.9 - - + -
282A LEU* 2.5 22.2 + - + +
283A MET* 2.6 10.4 + - - +
285A ASP* 1.3 78.7 - - - +
287A LEU* 1.3 59.9 + - - +
288A THR 3.2 1.4 + - - -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 2.9 24.3 - - - +
190A PHE 3.8 16.2 - - - +
192A GLU* 4.1 19.7 - - + +
195A ALA* 3.1 35.9 - - + -
283A MET* 2.8 40.6 + - + +
284A TYR* 4.2 3.4 - - - +
286A MET* 1.3 72.3 - - - +
288A THR* 1.3 60.7 + - - +
315A TYR* 3.8 9.9 - - - -
316A LEU* 4.0 29.2 - - + -
320A ALA* 4.3 16.8 - - + -
324A LEU* 5.6 2.0 - - + -
351A PHE* 4.9 2.7 - - + -
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 4.4 4.7 - - - -
284A TYR* 2.8 29.2 + - + +
285A ASP* 2.7 25.8 - - - +
287A LEU* 1.3 81.2 + - - +
289A GLY* 1.3 54.6 + - - +
290A ALA* 2.5 31.9 + - + +
313A PRO* 3.5 26.3 - - + +
315A TYR* 3.7 11.7 + - - +
316A LEU* 5.1 1.2 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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