Contacts of the helix formed by residues 261 - 281 (chain A) in PDB entry 4J00
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 LYS 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A ILE* 5.2 1.1 - - - -
258A LEU* 3.3 45.9 + - + +
259A PRO 3.5 0.2 - - - -
260A GLU* 1.3 82.6 + - + +
262A MET* 1.3 52.0 + - - +
263A GLN 3.3 2.5 - - - -
264A GLN* 3.0 38.8 + - + +
265A ALA* 2.6 36.6 + - - +
280B TYR* 4.6 12.3 - - + -
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Residues in contact with MET 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.6 17.0 - - + +
258A LEU 3.5 8.8 + - - +
259A PRO* 3.2 37.2 + - + +
260A GLU 3.1 1.6 - - - -
261A LYS* 1.3 75.7 - - - +
263A GLN* 1.3 60.6 + - - +
265A ALA* 3.9 6.0 - - + +
266A LYS* 3.0 43.2 + - + +
294A PHE* 4.4 16.8 - - + -
296A LYS* 4.2 18.6 - - - +
247B ASN* 3.3 33.4 - - + +
286B VAL* 5.2 3.8 - - + +
288B VAL* 4.0 25.1 - - + -
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Residues in contact with GLN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PRO 4.5 1.0 + - - -
260A GLU 4.2 7.2 + - - +
261A LYS 3.3 0.2 - - - -
262A MET* 1.3 77.6 - - - +
264A GLN* 1.3 57.2 + - - +
266A LYS* 3.7 26.3 - - - +
267A ASP* 2.9 57.8 + - - +
246B PRO 5.9 0.6 + - - -
247B ASN* 4.9 2.7 + - - +
249B MET* 6.0 0.2 - - - +
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Residues in contact with GLN 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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260A GLU 4.8 0.4 + - - +
261A LYS* 3.0 48.9 + - - +
263A GLN* 1.3 78.9 - - - +
265A ALA* 1.3 60.9 + - - +
267A ASP* 4.6 3.1 - - - -
268A GLU* 2.8 46.4 + - - +
279B LYS* 5.1 6.7 - - - +
280B TYR* 4.0 15.0 + - - +
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.7 10.1 - - + -
261A LYS 2.6 19.0 + - - +
262A MET* 3.5 8.9 + - + +
264A GLN* 1.3 73.5 - - - +
266A LYS* 1.3 61.8 + - - +
268A GLU* 4.1 0.4 - - - -
269A LEU 3.3 6.1 + - - -
294A PHE* 6.0 2.0 - - + -
276B TRP* 3.1 37.1 + - + +
280B TYR* 3.5 40.2 - - + -
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Residues in contact with LYS 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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262A MET* 3.0 24.0 + - + +
263A GLN* 3.7 30.4 + - - +
265A ALA* 1.3 75.1 - - - +
267A ASP* 1.3 60.4 + - - +
269A LEU* 2.8 24.2 + - - +
270A ASP 2.8 11.8 + - - -
294A PHE* 3.5 41.7 - - + -
246B PRO 4.1 5.1 + - - -
247B ASN* 2.3 49.6 + - - +
248B THR 4.5 2.9 - - - +
249B MET* 3.3 30.2 - - + +
276B TRP* 5.1 0.2 - - - -
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Residues in contact with ASP 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 GLN* 2.9 41.3 + - - +
264A GLN* 3.6 3.7 + - - +
266A LYS* 1.3 79.0 - - - +
268A GLU* 1.3 70.9 + - - +
270A ASP* 3.2 9.1 + - - +
271A GLU* 3.0 29.9 + - - +
249B MET* 4.8 3.2 - - - +
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Residues in contact with GLU 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 GLN* 2.8 40.6 + - - +
265A ALA 4.4 3.1 - - - +
266A LYS 3.2 0.8 - - - -
267A ASP* 1.3 88.2 - - - +
269A LEU* 1.3 60.3 + - - +
271A GLU* 3.6 30.1 - - - +
272A ILE* 3.2 28.1 + - - +
276B TRP* 4.3 12.0 - - + +
279B LYS* 5.5 6.7 - - - +
280B TYR* 4.7 8.0 + - - +
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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 ALA 3.3 14.6 + - - +
266A LYS* 2.8 12.2 + - - +
268A GLU* 1.3 78.2 - - - +
270A ASP* 1.3 60.3 + - - +
272A ILE* 3.5 14.8 - - + +
273A ILE* 3.3 23.9 - - + +
292A MET* 4.0 24.4 - - + +
294A PHE* 4.3 11.0 - - + -
249B MET* 4.1 13.5 - - - -
273B ILE* 5.5 9.6 - - + -
276B TRP* 3.7 37.9 - - + +
290B LEU* 3.7 29.4 - - + -
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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 LYS 2.8 4.4 + - - +
267A ASP* 3.5 10.7 - - - +
269A LEU* 1.3 78.2 - - - +
271A GLU* 1.3 62.0 + - - +
273A ILE* 3.7 6.4 + - - +
274A ARG* 3.6 26.3 + - - +
249B MET* 3.7 27.9 - - + +
250B ARG 5.4 0.5 - - - +
251B VAL* 3.9 19.9 - - - +
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Residues in contact with GLU 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 ASP* 3.0 12.5 + - - +
268A GLU* 3.6 40.6 - - - +
270A ASP* 1.3 75.1 + - - +
272A ILE* 1.3 70.3 + - + +
273A ILE 3.1 2.7 - - - -
274A ARG* 3.3 13.3 + - - +
275A ALA* 3.0 29.8 + - - +
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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 GLU 3.2 15.6 + - - +
269A LEU* 3.5 22.2 - - + +
271A GLU* 1.3 89.6 - - + +
273A ILE* 1.3 68.7 + - + +
275A ALA* 4.1 9.6 - - + +
276A TRP* 3.2 24.1 + - - +
272B ILE* 3.6 43.0 - - + +
273B ILE* 5.9 2.9 - - + -
276B TRP* 5.6 6.3 - - + -
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Residues in contact with ILE 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* 3.3 20.4 - - + +
270A ASP* 3.9 7.4 - - - +
271A GLU 3.1 0.4 - - - -
272A ILE* 1.3 86.0 - - + +
274A ARG* 1.3 56.9 + - - +
276A TRP* 2.9 13.6 + - + +
277A ALA* 2.7 33.6 + - - +
290A LEU* 4.1 23.6 - - + -
292A MET* 4.6 14.6 - - + -
251B VAL* 4.0 23.1 - - + -
253B GLU* 3.8 27.6 - - + -
269B LEU* 5.9 3.6 - - + -
272B ILE* 6.1 2.2 - - + -
273B ILE* 5.4 13.0 - - + -
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Residues in contact with ARG 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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270A ASP* 3.6 18.0 + - - +
271A GLU* 3.3 13.2 + - - +
273A ILE* 1.3 82.4 - - - +
275A ALA* 1.3 60.3 + - - +
276A TRP 3.4 0.2 + - - -
277A ALA* 4.1 4.4 - - - +
278A ASP* 2.9 41.6 + - - +
253B GLU* 5.1 6.7 - - - +
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Residues in contact with ALA 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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271A GLU 3.0 16.8 + - - +
272A ILE* 4.3 12.6 - - + +
274A ARG* 1.3 78.1 - - - +
276A TRP* 1.3 60.4 + - - +
278A ASP* 4.6 3.6 - - - +
279A LYS* 3.7 19.2 + - - +
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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
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272A ILE 3.2 18.3 + - - +
273A ILE* 2.9 19.1 + - + +
275A ALA* 1.3 80.5 - - - +
277A ALA* 1.3 86.8 + - + +
279A LYS* 3.4 9.3 + - + +
280A TYR* 3.2 56.9 - + - -
290A LEU* 4.4 16.2 - - + -
253B GLU* 5.7 0.9 - - + -
255B LEU* 5.2 9.9 - - + -
257B ILE* 4.7 7.6 - - + -
265B ALA* 3.9 16.9 + - + -
268B GLU* 4.3 6.0 - - + -
269B LEU* 3.5 61.4 - - + +
272B ILE* 5.1 8.3 - - + -
294B PHE* 4.2 18.4 - + - -
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Residues in contact with ALA 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 ILE 2.7 18.9 + - - +
274A ARG* 4.1 4.3 - - - +
275A ALA 3.5 0.2 - - - -
276A TRP* 1.3 85.6 - - + +
278A ASP* 1.3 66.6 + - - +
279A LYS 3.2 0.2 + - - -
280A TYR* 3.3 2.3 + - - +
281A HIS* 3.1 19.0 + - - +
253B GLU* 3.5 34.5 - - + +
255B LEU* 3.2 23.9 - - + +
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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 ARG* 2.9 32.4 + - - +
275A ALA* 4.6 4.3 - - - +
277A ALA* 1.3 78.8 - - - +
279A LYS* 1.3 62.3 + - - +
280A TYR 3.6 0.2 + - - -
281A HIS* 3.7 25.2 + - - +
253B GLU* 5.7 0.2 - - - +
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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 ALA 3.7 13.6 + - - +
276A TRP* 3.5 13.2 - - + +
277A ALA 3.1 0.6 - - - -
278A ASP* 1.3 81.7 - - - +
280A TYR* 1.3 91.5 + - + +
281A HIS 3.7 2.9 + - - +
282A GLN* 6.1 0.2 - - - +
268B GLU* 5.4 4.2 - - - +
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Residues in contact with TYR 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 TRP* 3.2 57.2 - + + +
277A ALA 3.3 4.0 + - - +
279A LYS* 1.3 106.7 + - + +
281A HIS* 1.3 64.5 + - - +
282A GLN* 3.3 5.9 + - - +
255B LEU* 5.0 0.2 - - + -
256B ASP 3.5 6.6 - - - +
257B ILE* 3.6 35.4 - - + +
258B LEU* 4.6 3.8 + - - +
261B LYS* 4.9 17.9 - - + -
264B GLN* 4.3 19.3 + - + +
265B ALA* 4.0 27.8 - - + -
268B GLU* 3.3 28.8 - - - +
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Residues in contact with HIS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ALA 3.1 16.8 + - - +
278A ASP* 3.8 21.8 + - - +
279A LYS 3.4 3.8 - - - +
280A TYR* 1.3 77.4 - - - +
282A GLN* 1.3 92.8 + - - +
283A ASP* 4.0 6.8 + - - +
254B GLU 5.6 0.9 - - - -
255B LEU* 4.3 18.3 - - + +
256B ASP* 3.5 35.0 + - + -
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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