Contacts of the helix formed by residues 263 - 281 (chain A) in PDB entry 4BU2
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 SER 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ARG* 5.6 10.8 - - - +
236A ARG* 4.9 15.9 - - - +
262A ASN* 1.3 81.4 - - - +
264A TRP* 1.3 67.0 + - - +
265A GLY* 3.4 6.3 + - - -
266A ASP* 2.6 31.4 + - - +
267A PHE* 3.1 20.5 + - - +
330A MSE 4.4 1.0 - - - +
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Residues in contact with TRP 264 (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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263A SER* 1.3 71.7 - - - +
265A GLY* 1.3 62.2 + - - +
266A ASP 3.0 0.2 - - - -
267A PHE* 3.0 33.5 + + + +
268A LEU* 2.7 34.4 + - + +
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Residues in contact with GLY 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A SER* 3.3 6.7 + - - -
264A TRP* 1.3 80.0 - - - +
266A ASP* 1.3 59.5 - - - +
268A LEU* 3.9 8.1 - - - +
269A LEU* 3.3 31.3 + - - +
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Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASN* 3.1 40.7 - - - +
263A SER* 2.6 37.7 + - - +
264A TRP 3.0 0.6 - - - -
265A GLY* 1.3 74.5 - - - +
267A PHE* 1.3 61.8 + - - +
269A LEU* 3.6 6.9 + - - +
270A ASP* 2.9 29.5 + - - +
330A MSE 3.6 11.4 - - - +
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Residues in contact with PHE 267 (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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263A SER 3.1 12.5 + - - +
264A TRP* 3.0 39.7 + + + +
266A ASP* 1.3 75.8 - - - +
268A LEU* 1.3 66.6 + - - +
270A ASP* 3.0 12.3 + - - -
271A THR* 2.8 43.4 + - + +
325A LEU* 4.1 28.0 - - + -
327A SER* 6.1 2.7 - - - -
330A MSE 4.1 24.0 - - + -
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Residues in contact with LEU 268 (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 TRP* 2.7 21.6 + - + +
265A GLY* 3.9 9.2 - - - +
267A PHE* 1.3 75.1 - - - +
269A LEU* 1.3 64.7 + - + +
271A THR* 3.1 9.3 + - - +
272A ILE* 2.8 47.9 + - + +
275A LEU* 6.1 1.8 - - + -
319A LEU* 6.0 5.8 - - + -
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Residues in contact with LEU 269 (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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265A GLY 3.3 18.2 + - - +
266A ASP* 4.0 6.5 - - - +
267A PHE 3.3 0.4 - - - -
268A LEU* 1.3 85.3 - - + +
270A ASP* 1.3 60.8 + - - +
271A THR 3.2 1.2 + - - -
272A ILE* 3.4 23.8 - - + +
273A SER* 4.9 2.4 + - - -
328A SER* 4.9 2.4 + - - -
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Residues in contact with ASP 270 (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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266A ASP 2.9 19.8 + - - +
267A PHE* 3.0 8.8 + - - +
269A LEU* 1.3 76.2 - - - +
271A THR* 1.3 61.7 + - - +
326A LEU 3.0 2.6 - - - +
327A SER* 3.0 22.5 + - - -
328A SER* 2.9 26.4 + - - -
329A ASP* 2.8 15.1 + - - +
330A MSE 2.7 47.5 + - - +
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Residues in contact with THR 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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267A PHE* 2.8 46.5 + - + +
268A LEU* 3.1 12.0 + - - +
270A ASP* 1.3 93.0 - - - +
272A ILE* 1.3 65.3 + - - +
273A SER 3.1 4.0 + - - -
274A GLY* 3.3 6.0 + - - -
275A LEU* 3.3 18.3 + - - +
325A LEU* 4.0 29.3 - - + +
326A LEU 3.3 22.8 + - - +
327A SER* 4.6 1.3 - - - +
328A SER* 4.8 0.4 - - - -
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Residues in contact with ILE 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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268A LEU* 2.8 30.7 + - + +
269A LEU* 3.4 32.5 - - + +
271A THR* 1.3 77.8 - - - +
273A SER* 1.3 68.5 + - - +
275A LEU* 3.1 16.5 + - + +
276A VAL* 2.9 30.1 + - + +
312A LEU* 5.3 7.6 - - + -
315A LEU* 4.0 27.1 - - + -
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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
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269A LEU 4.9 2.0 + - - -
271A THR 3.1 0.8 - - - +
272A ILE* 1.3 85.5 - - - +
274A GLY* 1.3 64.8 + - - +
275A LEU 3.0 0.3 + - - -
276A VAL* 3.2 3.5 + - - +
277A PHE* 2.9 27.6 + - - +
328A SER* 4.0 18.5 + - - -
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Residues in contact with GLY 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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271A THR* 3.3 7.8 + - - +
273A SER* 1.3 79.0 - - - +
275A LEU* 1.3 60.6 + - - +
277A PHE* 4.0 6.8 - - - +
278A ASP* 3.1 25.8 + - - +
326A LEU* 4.5 28.7 + - - +
328A SER* 5.1 1.6 + - - -
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Residues in contact with LEU 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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268A LEU* 6.1 2.5 - - + -
271A THR 3.3 11.4 + - - +
272A ILE* 3.1 20.8 + - + +
273A SER 3.0 1.0 - - - -
274A GLY* 1.3 75.6 - - - +
276A VAL* 1.3 60.0 + - - +
278A ASP* 3.3 6.1 + - + +
279A THR* 2.8 39.9 + - - +
315A LEU* 4.0 32.3 - - + +
318A ARG* 5.1 4.0 - - - +
319A LEU* 3.5 44.6 - - + +
322A THR* 4.6 15.9 - - + +
324A GLU 5.7 1.8 - - - +
325A LEU* 5.7 6.5 - - + -
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 2.9 28.5 + - + +
273A SER* 3.8 3.8 - - - +
275A LEU* 1.3 75.7 - - - +
277A PHE* 1.3 57.2 + - - +
279A THR* 3.1 0.3 + - - -
280A ALA* 2.7 42.3 + - + +
286A LEU* 4.0 19.6 - - + +
315A LEU* 3.8 34.3 - - + -
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Residues in contact with PHE 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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273A SER 2.9 18.3 + - - +
274A GLY* 4.1 7.4 - - - +
276A VAL* 1.3 81.8 - - - +
278A ASP* 1.3 66.2 + - + +
280A ALA* 4.1 4.6 - - - +
281A LYS* 3.4 26.6 + - + +
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Residues in contact with ASP 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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274A GLY 3.1 20.2 + - - +
275A LEU* 3.8 5.8 - - + +
277A PHE* 1.3 82.9 - - + +
279A THR* 1.3 62.0 + - - +
281A LYS* 3.5 22.2 - - - +
282A GLU* 3.9 4.7 - - - +
318A ARG* 2.6 44.7 + - - -
322A THR* 5.7 1.9 + - - +
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Residues in contact with THR 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 LEU* 2.8 26.6 + - - +
276A VAL 3.7 2.7 - - - -
278A ASP* 1.3 73.8 - - - +
280A ALA* 1.3 56.8 + - - +
281A LYS 3.0 4.5 - - - -
282A GLU* 2.9 21.5 + - - +
283A ASP* 3.1 14.1 + - + +
286A LEU* 3.8 14.6 - - + -
314A THR* 4.4 18.2 - - + -
315A LEU* 3.7 20.6 - - + +
318A ARG* 2.7 36.9 + - + +
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Residues in contact with ALA 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 VAL* 2.7 26.9 + - + +
277A PHE* 4.1 5.8 - - - +
279A THR* 1.3 66.8 - - - +
281A LYS* 1.3 56.3 + - - +
282A GLU 3.0 5.8 - - - -
283A ASP 3.3 6.9 - - - +
286A LEU* 3.5 29.5 - - + +
287A ARG* 2.9 40.9 + - + +
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Residues in contact with LYS 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 PHE* 3.4 20.3 + - + +
278A ASP* 3.5 21.8 - - - +
279A THR 3.0 0.6 - - - -
280A ALA* 1.3 79.2 - - - +
282A GLU* 1.3 67.5 + - + +
287A ARG* 3.7 10.8 + - - +
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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