Contacts of the helix formed by residues 266 - 286 (chain B) in PDB entry 5H1Y
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 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B CYS* 3.4 2.7 - - - +
265B PRO* 1.3 80.5 - - - +
267B ARG* 1.3 62.6 + - - +
268B GLU* 3.3 20.9 - - - +
269B LEU* 3.3 24.6 + - - +
270B ALA* 3.1 18.0 + - - +
320B THR* 3.5 14.4 - - - +
323B ARG* 5.9 0.2 - - - +
348B ARG* 4.5 18.0 + - - -
352B MET* 5.7 2.5 - - - -
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Residues in contact with ARG 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B SER* 1.3 71.2 - - - +
268B GLU* 1.3 70.3 + - - +
270B ALA* 3.2 8.0 + - - +
271B ARG* 2.9 39.4 + - - +
298B ILE* 4.1 14.3 - - + +
299B GLY* 3.3 32.0 + - - +
300B GLY* 3.3 23.2 - - - +
320B THR* 4.0 2.6 - - - +
323B ARG* 2.8 48.8 - - - +
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B SER* 3.3 21.0 - - - +
267B ARG* 1.3 92.4 + - - +
269B LEU* 1.3 59.5 + - + +
271B ARG* 3.7 7.9 + - - +
272B GLN* 3.2 23.6 + - - +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B THR* 6.5 1.3 - - + -
232B THR* 5.9 2.7 - - - +
264B CYS* 4.2 17.7 - - + -
265B PRO* 4.2 2.7 - - + -
266B SER* 3.3 18.9 + - - +
267B ARG 3.2 0.6 - - - -
268B GLU* 1.3 77.4 - - + +
270B ALA* 1.3 66.3 + - - +
272B GLN* 3.2 22.5 + - - +
273B THR* 3.0 32.2 + - - +
344B ASP* 3.6 21.8 - - - +
345B GLU* 3.4 40.6 - - + +
348B ARG* 6.2 0.2 - - - +
502B MG 4.6 0.2 - - - -
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B CYS* 3.7 9.5 - - + -
266B SER 3.1 12.9 + - - +
267B ARG 3.5 8.1 - - - +
269B LEU* 1.3 77.6 - - - +
271B ARG* 1.3 57.4 + - - +
273B THR 3.2 0.3 + - - -
274B HIS* 2.8 31.2 + - - +
296B LEU* 3.9 5.4 - - + -
298B ILE* 3.5 29.4 - - + -
318B VAL* 3.5 25.5 - - + +
319B ALA 4.7 3.1 - - - +
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Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ARG* 2.9 23.8 + - - +
268B GLU* 4.0 7.0 - - - +
270B ALA* 1.3 76.0 - - - +
272B GLN* 1.3 56.4 + - - +
274B HIS* 3.8 4.3 + - - +
275B GLY* 3.0 23.9 + - - -
296B LEU* 3.7 28.6 - - + +
298B ILE* 3.7 22.0 - - + +
299B GLY 4.5 1.8 + - - -
300B GLY* 4.1 19.2 + - - -
301B MET* 4.3 13.9 - - - +
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Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B THR* 6.1 0.9 - - - +
232B THR* 5.4 3.5 + - - -
268B GLU 3.2 14.7 + - - +
269B LEU* 3.2 23.1 + - + +
270B ALA 3.2 0.6 - - - -
271B ARG* 1.3 77.4 - - - +
273B THR* 1.3 64.3 + - - +
275B GLY* 3.4 2.2 + - - -
276B ILE* 3.1 38.0 + - + +
501B SO4 5.3 5.2 + - - -
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 4.5 10.7 + - + +
235B PHE* 4.0 13.7 - - + -
236B THR* 4.1 8.1 - - + -
262B ILE* 3.9 31.9 - - + -
264B CYS* 4.9 2.3 - - - -
269B LEU* 3.0 29.0 + - - +
270B ALA 3.8 2.5 - - - -
272B GLN* 1.3 76.2 + - - +
274B HIS* 1.3 61.1 + - - +
276B ILE* 3.2 10.8 + - - +
277B LEU* 2.9 26.4 + - + +
318B VAL* 4.3 11.4 - - + -
344B ASP* 4.5 7.4 + - - -
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Residues in contact with HIS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA 2.8 17.5 + - - +
271B ARG 3.8 4.6 + - - +
273B THR* 1.3 78.4 - - - +
275B GLY* 1.3 65.5 + - - +
277B LEU* 3.2 6.0 + - - +
278B GLU* 3.0 59.5 + - - +
294B CYS* 3.5 31.8 + - + -
295B ALA* 4.0 8.1 + - - -
296B LEU* 3.5 38.8 + - + +
318B VAL* 3.9 13.7 - - + +
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Residues in contact with GLY 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG 3.0 17.1 + - - -
272B GLN* 3.8 2.9 - - - -
273B THR 3.2 0.4 - - - -
274B HIS* 1.3 81.8 + - - +
276B ILE* 1.3 56.6 + - - +
278B GLU* 3.4 7.1 + - - +
279B TYR* 3.0 28.4 + - - +
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Residues in contact with ILE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LYS* 4.8 15.7 - - - +
232B THR* 3.9 28.5 - - + +
233B LEU* 4.3 16.4 - - + -
236B THR* 4.4 7.9 - - + +
272B GLN* 3.1 26.6 + - + +
273B THR* 3.2 9.2 + - - +
275B GLY* 1.3 75.2 - - - +
277B LEU* 1.3 66.0 + - - +
279B TYR* 3.4 6.5 + - - +
280B TYR* 3.3 43.0 + - + -
501B SO4 6.1 0.7 - - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B THR* 3.6 36.3 - - + +
239B VAL* 4.6 2.0 - - + -
240B ILE* 3.8 25.3 - - + +
262B ILE* 4.1 11.0 - - + -
273B THR 2.9 14.1 + - - +
274B HIS* 3.2 6.9 + - - +
276B ILE* 1.3 78.8 - - - +
278B GLU* 1.3 64.5 + - - +
280B TYR* 3.3 1.2 + - - -
281B CYS* 3.0 24.9 + - - -
294B CYS* 3.7 18.6 - - + -
316B MET* 4.0 28.3 - - + -
317B MET 5.6 0.2 - - - -
318B VAL* 3.8 30.1 - - + -
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B HIS* 3.0 52.1 + - - +
275B GLY* 3.9 6.4 - - - +
277B LEU* 1.3 72.5 - - - +
279B TYR* 1.3 66.0 + - - +
281B CYS* 3.8 6.8 - - - +
282B ARG* 2.9 26.9 + - - +
294B CYS* 3.7 23.9 + - + +
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLY* 2.9 36.4 + - - -
198B LYS* 4.4 8.7 - - - +
199B LYS* 3.6 38.7 - - + +
275B GLY 3.0 17.8 + - - +
276B ILE* 3.6 7.4 - - - +
277B LEU 3.2 0.2 - - - -
278B GLU* 1.3 78.6 - - - +
280B TYR* 1.3 94.8 - + - +
282B ARG* 3.3 34.5 + - - +
283B LEU* 3.3 37.0 + - + +
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ILE* 4.1 25.5 - - + +
195B GLY 3.8 16.3 + - - -
196B LEU* 3.2 34.0 - - + +
199B LYS* 4.8 4.5 - - + +
201B ILE* 4.0 8.8 - - - +
233B LEU* 3.8 24.7 - - + +
236B THR* 6.2 0.2 - - - -
237B LEU* 3.9 20.9 - - + -
240B ILE* 3.7 20.4 - - + -
276B ILE* 3.3 30.0 + - + -
277B LEU 3.3 2.6 + - - -
279B TYR* 1.3 106.9 - + - +
281B CYS* 1.3 62.4 + - - +
283B LEU* 3.3 9.9 + - + +
284B LEU* 3.1 26.9 + - - +
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Residues in contact with CYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE* 3.9 14.6 - - - -
277B LEU 3.0 21.4 + - - +
278B GLU* 3.9 6.7 - - - +
280B TYR* 1.3 76.7 - - - +
282B ARG* 1.3 57.4 + - - +
284B LEU* 3.2 10.8 + - - +
285B GLN* 3.0 26.2 + - - +
290B PRO 5.1 2.3 - - - +
291B LEU* 5.2 5.5 - - + +
292B LEU* 3.8 45.4 + - + +
294B CYS* 4.0 8.5 - - - -
316B MET* 3.9 17.0 - - - -
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B GLU 2.9 18.1 + - - +
279B TYR* 3.5 39.7 + - - +
280B TYR 3.2 0.2 - - - -
281B CYS* 1.3 75.8 - - - +
283B LEU* 1.3 67.1 + - - +
285B GLN* 2.9 21.9 + - - +
286B GLU* 2.9 64.3 + - + +
291B LEU* 5.5 1.8 - - + -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA* 3.4 28.8 - - + +
192B ILE* 5.6 0.2 - - - -
194B ARG* 5.4 1.3 + - + -
195B GLY* 3.4 33.7 - - - +
198B LYS* 5.8 7.0 - - + -
279B TYR* 3.3 37.5 + - + +
280B TYR* 3.3 13.0 + - + +
282B ARG* 1.3 85.8 - - - +
284B LEU* 1.3 61.0 + - - +
286B GLU* 3.4 24.6 + - + +
287B ASP* 3.2 17.0 + - - +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PRO* 4.1 22.4 - - + -
191B ALA* 4.0 17.9 - - + -
192B ILE* 4.2 13.7 - - + -
240B ILE* 3.6 31.4 - - + -
244B LEU* 4.3 20.2 - - + -
280B TYR 3.1 17.1 + - - +
281B CYS* 3.4 12.6 - - - +
282B ARG 3.1 0.6 - - - -
283B LEU* 1.3 76.7 - - - +
285B GLN* 1.3 61.2 + - - +
287B ASP 3.3 8.6 + - - +
289B SER* 2.9 50.2 + - - +
290B PRO 5.1 1.8 - - - +
292B LEU* 4.8 4.5 - - + -
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B CYS 3.0 12.0 + - - +
282B ARG* 2.9 23.1 + - - +
284B LEU* 1.3 77.4 - - - +
286B GLU* 1.3 63.2 + - + +
287B ASP 3.2 1.3 + - - -
288B SER* 3.7 7.6 + - - -
289B SER 3.5 17.5 - - - +
290B PRO 4.7 0.9 + - - -
291B LEU* 3.4 47.5 - - + +
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ARG* 2.9 54.8 + - + +
283B LEU* 3.6 23.7 - - + +
284B LEU 3.2 0.2 - - - -
285B GLN* 1.3 79.3 - - + +
287B ASP* 1.3 56.6 + - + +
288B SER 3.7 1.5 + - - -
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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) + - + + + + + -
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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