Contacts of the helix formed by residues 283 - 298 (chain A) in PDB entry 2Y4U
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 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A LEU* 2.9 37.7 + - + +
281A ASP* 3.9 27.4 + - + +
282A GLY* 1.3 75.1 - - - +
284A TYR* 1.3 53.2 + - - +
285A THR* 3.5 4.0 - - - -
286A ASP* 2.7 36.3 + - + +
287A ALA* 2.8 31.7 + - - +
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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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279A ILE* 4.1 19.2 + - + -
282A GLY* 3.0 42.1 + - - -
283A ARG* 1.3 71.5 - - - +
285A THR* 1.3 56.7 + - - +
287A ALA* 3.0 4.6 + - - +
288A THR* 2.6 39.5 + - - -
314A HIS* 4.8 6.1 - + - -
315A CYS* 3.3 44.9 - - - +
318A LYS* 3.4 44.2 + - + +
319A ASP* 3.6 26.9 - - + +
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 4.7 1.2 - - - -
284A TYR* 1.3 75.7 + - - +
286A ASP* 1.3 68.9 + - - +
288A THR* 3.4 10.1 + - - -
289A SER* 3.1 25.5 + - - -
316A PHE* 6.1 3.8 - - + -
319A ASP* 3.8 8.7 + - - +
321A LYS* 3.3 29.8 - - - +
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Residues in contact with ASP 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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278A LEU* 4.4 11.2 - - + -
283A ARG* 2.7 53.3 + - + +
285A THR* 1.3 85.4 + - - +
287A ALA* 1.3 65.0 + - - +
289A SER* 3.2 8.6 + - - -
290A LYS* 3.0 27.3 + - - +
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Residues in contact with ALA 287 (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 ALA* 3.9 10.3 - - + +
278A LEU* 4.1 9.1 - - + +
279A ILE* 3.3 34.5 - - + +
283A ARG 2.8 13.0 + - - +
284A TYR* 3.4 8.5 - - - +
286A ASP* 1.3 75.5 - - - +
288A THR* 1.3 62.4 + - - +
290A LYS* 3.1 9.0 + - - +
291A TYR* 2.9 28.3 + - + +
315A CYS* 3.6 8.1 - - - -
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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
----------------------------------------------------------
284A TYR 2.6 22.0 + - - -
285A THR* 3.5 11.4 - - - -
286A ASP 3.2 0.2 - - - -
287A ALA* 1.3 71.3 - - - +
289A SER* 1.3 65.1 + - - +
291A TYR* 3.3 4.2 + - - +
292A GLU* 3.2 33.1 + - - +
312A ILE* 4.0 32.9 - - + +
315A CYS* 3.5 18.6 - - - +
316A PHE* 4.3 20.4 - - + -
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A THR 3.1 11.1 + - - -
286A ASP* 3.2 11.0 + - - -
288A THR* 1.3 79.9 - - - +
290A LYS* 1.3 66.6 + - - +
292A GLU* 2.9 21.2 + - - +
293A SER* 3.3 14.2 + - - -
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Residues in contact with LYS 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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270A LYS 5.1 0.4 + - - -
271A LEU* 3.7 37.7 - - + +
274A SER* 3.3 28.8 + - - +
275A ALA* 3.8 13.7 - - + -
278A LEU* 3.7 17.5 - - + -
286A ASP* 3.0 16.1 + - + +
287A ALA 3.1 9.4 + - - +
289A SER* 1.3 75.5 - - - +
291A TYR* 1.3 58.0 + - - +
293A SER* 2.9 26.8 + - - -
294A VAL* 3.1 13.8 + - - +
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Residues in contact with TYR 291 (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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272A ILE* 3.3 34.5 - - + +
275A ALA* 3.4 26.0 - - + -
276A GLU* 2.3 34.4 + - - -
279A ILE* 5.0 5.2 - - + -
287A ALA* 2.9 20.1 + - + +
288A THR* 3.9 4.5 - - - +
289A SER 3.2 0.4 - - - -
290A LYS* 1.3 75.1 - - - +
292A GLU* 1.3 57.5 - - - +
293A SER 3.3 0.2 - - - -
294A VAL* 3.3 14.7 + - + +
295A MSE 3.1 21.5 + - - +
307A ARG 5.3 0.9 - - - -
308A SER* 3.4 42.6 + - - +
311A ARG* 3.6 30.3 - - + +
312A ILE* 4.1 19.7 - - + -
315A CYS* 5.6 0.9 - - - -
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Residues in contact with GLU 292 (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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288A THR* 3.2 25.4 + - - +
289A SER* 2.9 14.5 + - - +
291A TYR* 1.3 75.8 - - - +
293A SER* 1.3 60.7 + - - +
294A VAL 3.1 0.4 - - - -
295A MSE 3.5 15.4 + - + +
296A LYS* 3.1 30.5 + - - +
312A ILE* 4.5 14.1 - - + +
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Residues in contact with SER 293 (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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271A LEU* 4.4 15.7 - - - -
289A SER* 3.4 13.5 + - - -
290A LYS* 2.9 9.3 + - - -
292A GLU* 1.3 75.6 - - - +
294A VAL* 1.3 66.5 + - - +
296A LYS* 3.4 8.6 - - - +
297A THR* 2.8 32.6 + - - +
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Residues in contact with VAL 294 (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 LEU* 4.5 11.9 - - + -
271A LEU* 3.7 29.8 - - + +
272A ILE* 3.8 34.8 - - + +
290A LYS 3.1 14.0 + - - +
291A TYR* 3.3 20.4 - - + +
292A GLU 3.1 0.2 - - - -
293A SER* 1.3 77.5 - - - +
295A MSE 1.3 63.7 + - - +
297A THR* 3.0 18.4 + - - -
298A GLU* 3.1 12.0 + - - +
304A TYR* 5.0 9.4 - - + +
308A SER* 3.7 15.3 - - - +
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Residues in contact with MSE 295 (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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291A TYR 3.1 9.8 + - - +
292A GLU* 3.5 16.1 + - + +
293A SER 3.3 0.2 - - - -
294A VAL* 1.3 77.2 - - - +
296A LYS* 1.3 63.2 + - + +
298A GLU 3.4 5.2 - - - +
299A PRO* 3.3 28.4 - - - +
304A TYR* 4.1 1.8 - - - +
305A THR* 3.5 43.5 - - + +
308A SER* 3.7 24.5 - - - +
309A LYS* 3.7 32.1 - - - -
312A ILE* 4.5 9.2 - - - -
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Residues in contact with LYS 296 (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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292A GLU 3.1 20.5 + - - +
293A SER* 3.4 11.7 - - - +
295A MSE 1.3 80.0 - - + +
297A THR* 1.3 63.9 + - + +
299A PRO* 3.5 15.7 - - - +
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Residues in contact with THR 297 (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 GLN* 3.8 14.6 + - - +
267A LYS* 3.4 35.9 - - - +
268A LEU* 3.5 24.4 - - - +
271A LEU* 3.9 15.9 - - + +
293A SER* 2.8 23.8 + - - +
294A VAL* 3.0 8.2 + - - -
296A LYS* 1.3 79.6 - - + +
298A GLU* 1.3 60.4 + - - +
299A PRO* 3.3 8.1 - - - +
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Residues in contact with GLU 298 (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 TYR* 3.0 27.3 + - + +
264A GLN* 3.4 8.1 + - - +
268A LEU* 3.1 24.5 - - + -
294A VAL 3.1 9.1 + - - +
295A MSE 3.4 7.8 - - - +
297A THR* 1.3 76.8 + - - +
299A PRO* 1.3 62.8 - - - +
300A SER* 3.0 19.1 + - - -
301A ILE* 2.8 38.3 + - - +
304A TYR* 3.6 39.5 - - + +
305A THR* 4.8 2.1 - - - +
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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
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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