Contacts of the helix formed by residues 276 - 290 (chain A) in PDB entry 3U86
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 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU* 3.8 10.5 - - + +
228A MET* 3.7 30.5 - - + -
234A MET* 4.1 17.7 - - + -
237A ALA* 3.7 31.6 - - + -
238A PHE* 3.7 36.7 - - + -
241A CYS* 4.2 10.5 - - - +
272A HIS 4.6 3.1 - - - +
273A LEU* 2.9 22.4 + - - +
274A GLU 3.4 1.2 + - - -
275A ARG* 1.3 78.6 - - - +
277A PRO* 1.3 67.8 - - - +
278A MET* 3.9 14.3 - - + +
279A ALA* 3.1 40.8 + - + +
280A LEU* 3.2 10.7 + - - +
33B PRO 4.5 6.6 + - - -
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Residues in contact with PRO 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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228A MET* 4.0 9.0 - - + -
275A ARG 3.3 9.6 - - - +
276A TYR* 1.3 88.2 - - - +
278A MET* 1.3 65.5 + - + +
280A LEU* 3.2 7.8 + - + +
281A GLY* 3.1 18.5 + - - -
305A GLY* 3.6 26.3 - - - +
308A SER* 3.7 12.1 - - - +
309A ALA* 4.0 15.0 - - - +
313A TYR* 3.8 8.1 - - + -
317A HIS* 4.0 20.0 - - - +
320A PRO* 4.0 21.4 - - + +
323A TYR* 5.2 1.4 - - - -
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Residues in contact with MET 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 5.2 2.2 - - + -
178A SER 3.9 19.1 - - - +
179A GLU* 4.3 17.3 - - + +
228A MET* 3.7 25.8 - - + -
276A TYR* 3.2 16.2 - - + +
277A PRO* 1.3 78.9 - - + +
279A ALA* 1.3 61.6 + - - +
281A GLY* 3.4 0.9 + - - -
282A ASN* 2.8 30.8 + - - +
317A HIS* 6.2 0.7 - - - +
319A TYR* 3.7 40.2 - - + -
320A PRO* 5.8 1.6 - - + -
323A TYR* 3.7 9.7 + - - -
32B PHE* 4.2 12.1 - - + -
33B PRO 4.6 4.9 - - - +
34B GLY* 3.7 25.7 - - - +
35B ALA 4.6 1.3 - - - -
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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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237A ALA* 5.1 0.7 - - + -
241A CYS* 3.7 22.2 - - - -
264A LEU* 4.4 7.3 - - + +
273A LEU* 3.9 23.3 - - + +
276A TYR* 3.1 38.1 + - + +
278A MET* 1.3 77.9 - - - +
280A LEU* 1.3 57.4 + - - +
282A ASN* 3.5 2.1 + - - +
283A LEU* 2.9 29.3 + - - +
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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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268A TYR* 4.4 15.9 - - + -
273A LEU* 3.6 52.0 - - + +
274A GLU* 4.8 1.6 - - - +
276A TYR 3.2 8.0 + - - +
277A PRO 3.2 8.2 + - - +
279A ALA* 1.3 78.5 - - - +
281A GLY* 1.3 57.4 + - - +
283A LEU* 3.2 6.8 + - + +
284A ALA* 2.8 27.0 + - - +
301A LEU* 4.3 19.3 - - + +
304A LYS* 3.9 16.8 - - + +
305A GLY* 3.7 31.9 - - - +
308A SER* 4.3 9.6 - - - -
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Residues in contact with GLY 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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277A PRO 3.1 7.9 + - - -
278A MET 3.8 1.8 - - - -
280A LEU* 1.3 76.8 - - - +
282A ASN* 1.3 64.4 + - - +
284A ALA* 3.0 9.4 + - - +
285A ASP 2.9 20.8 + - - -
301A LEU 5.0 0.6 + - - -
302A TYR* 4.4 7.6 - - - -
305A GLY* 5.2 1.2 - - - -
323A TYR* 3.3 36.2 - - - -
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Residues in contact with ASN 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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241A CYS* 3.8 11.8 - - - +
260A GLN* 3.7 22.5 + - - +
264A LEU* 4.4 3.4 - - + -
278A MET 2.8 22.9 + - - +
279A ALA* 3.5 10.1 - - - +
281A GLY* 1.3 71.6 - - - +
283A LEU* 1.3 63.3 + - - +
285A ASP* 3.2 6.2 + - - +
286A LEU* 3.1 39.1 + - - +
323A TYR* 3.4 15.0 + - - +
34B GLY* 3.6 21.5 + - - -
35B ALA 6.0 0.2 - - - -
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Residues in contact with LEU 283 (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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261A GLN* 4.3 9.6 - - + +
264A LEU* 3.9 31.8 - - + +
265A TRP* 3.9 54.7 - - + +
268A TYR* 4.5 1.6 - - + -
273A LEU* 4.0 22.9 - - + -
279A ALA 2.9 15.1 + - - +
280A LEU* 3.4 9.6 - - + +
282A ASN* 1.3 76.2 - - - +
284A ALA* 1.3 63.0 + - - +
286A LEU* 3.2 4.5 + - + +
287A GLU* 3.0 24.4 + - + +
301A LEU* 4.3 15.9 - - + -
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Residues in contact with ALA 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 LEU 2.8 13.9 + - - +
281A GLY* 3.3 9.4 - - - +
283A LEU* 1.3 75.4 - - - +
285A ASP* 1.3 63.2 + - - +
287A GLU* 3.0 13.6 + - - +
288A GLU* 3.1 10.2 + - - +
298A PRO* 3.9 9.1 - - + +
301A LEU* 3.7 28.0 - - + +
302A TYR* 3.3 36.2 + - + -
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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
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281A GLY 2.9 5.5 + - - -
282A ASN* 3.5 10.8 - - - +
284A ALA* 1.3 75.3 - - - +
286A LEU* 1.3 63.9 - - + +
288A GLU* 3.3 15.3 + - - +
289A LEU* 3.5 18.7 + - - +
302A TYR* 2.5 30.0 + - - -
323A TYR* 3.2 27.6 - - + +
330A ARG* 3.1 18.8 + - - -
37B PRO* 3.3 24.7 - - - +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.5 35.7 - - + +
260A GLN* 3.8 19.7 - - + +
261A GLN* 4.0 36.3 - - + +
264A LEU* 3.7 29.6 - - + -
282A ASN* 3.1 24.6 + - - +
283A LEU* 3.5 9.2 - - + +
284A ALA 3.2 0.2 - - - -
285A ASP* 1.3 77.6 - - + +
287A GLU* 1.3 61.9 + - - +
289A LEU* 3.4 15.1 + - + +
290A GLU* 3.3 16.8 + - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLN* 3.1 10.2 + - - +
265A TRP* 2.6 46.9 + - + -
283A LEU* 3.0 17.5 + - + +
284A ALA* 3.0 10.1 + - - +
286A LEU* 1.3 75.9 - - - +
288A GLU* 1.3 63.1 + - - +
291A PRO* 3.0 42.0 - - + +
292A THR* 2.8 36.2 + - - +
295A ARG* 4.9 3.1 - - - -
296A PRO 4.9 5.8 - - - +
298A PRO* 4.2 17.0 - - + +
301A LEU* 4.2 7.9 - - + -
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Residues in contact with GLU 288 (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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284A ALA 3.1 10.5 + - - +
285A ASP* 3.6 10.5 - - - +
286A LEU 3.3 0.2 - - - -
287A GLU* 1.3 78.3 - - - +
289A LEU* 1.3 66.7 + - + +
291A PRO* 4.2 6.8 - - - +
298A PRO* 3.8 14.9 - - + +
302A TYR* 3.9 2.9 + - - -
327A TYR* 3.3 22.8 - - + -
330A ARG* 3.2 40.7 + - - +
331A ASN* 3.5 18.5 + - - +
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Residues in contact with LEU 289 (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* 4.5 22.9 - - + -
285A ASP 3.7 14.4 - - - +
286A LEU* 3.4 18.5 + - + +
287A GLU 3.2 0.8 - - - -
288A GLU* 1.3 85.2 - - + +
290A GLU* 1.3 73.0 + - + +
291A PRO* 3.8 3.7 - - - +
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Residues in contact with GLU 290 (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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70A ASP* 5.1 9.2 - - - +
254A LEU* 5.3 15.2 - - + +
261A GLN* 3.0 29.2 + - - +
286A LEU 3.3 4.2 + - - +
287A GLU 3.5 2.0 - - - -
289A LEU* 1.3 88.3 - - + +
291A PRO* 1.3 74.0 - - - +
292A THR* 4.4 0.2 - - - -
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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
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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