Contacts of the helix formed by residues 264 - 280 (chain B) in PDB entry 1YCH
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 LEU 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B THR* 2.5 26.1 + - + -
262B MET 3.7 1.5 - - - +
263B TRP* 1.3 75.3 - - - +
265B SER* 1.3 57.1 + - - +
266B THR 3.4 2.2 - - - -
267B GLU* 3.2 40.1 + - + +
268B LYS* 2.9 50.9 + - - +
288B LYS* 5.8 2.9 - - - +
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Residues in contact with SER 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B TRP* 3.5 4.0 + - - +
264B LEU* 1.3 73.6 - - - +
266B THR* 1.3 66.2 + - - +
268B LYS* 3.1 8.9 + - - +
269B MET* 3.1 26.8 + - - +
344B ALA* 3.9 10.8 - - - -
374B VAL* 4.8 0.2 - - - -
376B TRP 2.7 28.3 + - - -
377B VAL* 3.9 8.0 - - - +
378B PRO* 3.9 21.2 - - - +
711B FMN 3.0 17.2 + - - -
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TYR* 4.4 3.8 - - + -
260B ASP 3.7 18.2 - - - +
261B THR* 4.0 1.1 - - - -
265B SER* 1.3 73.4 - - - +
267B GLU* 1.3 57.5 + - - +
269B MET* 3.4 9.8 + - - +
270B ALA* 2.9 23.2 + - - +
310B GLY 3.9 1.3 - - - -
311B SER 3.6 27.4 - - - +
312B PRO* 3.5 9.5 - - - +
342B PHE* 3.4 23.5 - - + -
343B GLY* 4.0 3.4 - - - -
344B ALA 3.4 15.9 + - - -
711B FMN 2.4 28.8 + - - -
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Residues in contact with GLU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TYR* 3.2 40.8 + - + +
261B THR* 3.7 15.5 - - + +
264B LEU* 3.2 36.2 + - - +
265B SER 3.0 0.4 - - - -
266B THR* 1.3 78.0 - - - +
268B LYS* 1.3 61.0 + - - +
270B ALA* 3.0 4.1 + - + +
271B HIS* 2.8 30.0 + - + +
286B LEU* 5.9 1.5 - - + +
288B LYS* 4.4 10.7 + - - +
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B TRP 4.7 2.6 + - - -
264B LEU* 2.9 40.2 + - - +
265B SER* 3.5 11.1 + - - +
267B GLU* 1.3 77.4 - - + +
269B MET* 1.3 56.9 + - - +
271B HIS* 3.4 8.1 + - - +
272B ALA* 3.1 20.6 + - - +
377B VAL* 4.9 12.9 - - + +
378B PRO* 4.2 18.2 - - + -
383B LEU* 3.5 21.6 - - + +
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Residues in contact with MET 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B SER 3.1 19.9 + - - +
266B THR* 3.5 9.6 - - - +
267B GLU 3.1 0.4 - - - -
268B LYS* 1.3 75.4 - - - +
270B ALA* 1.3 66.0 + - - +
271B HIS 3.1 0.2 - - - -
272B ALA* 3.2 1.6 + - - +
273B LEU* 3.0 29.2 + - - +
342B PHE* 4.1 9.4 - - + -
343B GLY* 3.6 39.7 - - - +
344B ALA* 3.7 7.6 - - + +
372B PRO* 4.4 8.7 - - - +
373B THR 4.8 0.2 - - - -
374B VAL* 3.4 41.1 - - + -
378B PRO* 4.6 10.8 - - + -
382B ASP* 6.2 0.7 - - + -
383B LEU* 4.2 8.3 - - + -
386B CYS* 3.9 24.2 - - - +
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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
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257B ILE* 3.9 16.5 - - + +
259B TYR* 4.2 16.4 - - + -
266B THR 2.9 14.9 + - - +
267B GLU* 3.0 12.5 + - - +
269B MET* 1.3 75.9 - - - +
271B HIS* 1.3 57.5 + - - +
273B LEU* 3.6 5.7 - - - +
274B MET* 3.0 28.1 + - - +
286B LEU* 4.6 7.4 - - + +
342B PHE* 3.9 23.1 - - + -
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU* 2.8 13.2 + - + +
268B LYS* 3.5 12.8 - - - +
269B MET 3.1 0.2 - - - -
270B ALA* 1.3 74.2 - - - +
272B ALA* 1.3 61.8 + - - +
274B MET* 3.0 34.0 + - + +
275B ASP* 2.9 43.7 + - - -
286B LEU* 4.9 3.6 - - + +
611B ZN 2.5 30.6 - - - -
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Residues in contact with ALA 272 (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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268B LYS 3.1 11.8 + - - +
269B MET 3.2 3.6 + - - +
271B HIS* 1.3 78.6 - - - +
273B LEU* 1.3 63.9 + - - +
275B ASP* 2.9 21.5 + - - +
276B GLY 3.0 10.7 + - - -
383B LEU* 3.4 37.9 - - + +
386B CYS* 3.7 10.8 - - + -
387B TYR* 3.7 10.2 - - + +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 4.5 3.1 - - + -
269B MET 3.0 24.5 + - - +
270B ALA* 3.6 5.6 - - - +
272B ALA* 1.3 76.0 - - - +
274B MET* 1.3 62.2 + - - +
276B GLY 3.3 0.5 + - - -
277B LEU* 3.0 28.5 + - - +
308B LEU* 4.0 16.8 - - + -
340B LEU* 3.6 23.8 - - + -
342B PHE* 3.5 45.5 - - + -
372B PRO* 4.9 0.9 - - + -
386B CYS* 3.6 35.0 - - + +
389B LEU* 4.3 8.7 - - + -
390B GLY* 3.6 9.1 - - - +
393B ILE* 5.0 0.4 - - + -
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Residues in contact with MET 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 3.9 13.2 - - + +
270B ALA 3.0 12.8 + - - +
271B HIS* 3.0 39.5 + - + +
273B LEU* 1.3 78.4 - - - +
275B ASP* 1.3 65.2 + - - +
277B LEU* 3.1 5.3 + - - +
278B VAL* 3.0 29.8 + - + +
284B VAL* 3.5 32.8 - - + +
286B LEU* 3.5 28.0 - - + -
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B HIS* 2.9 29.8 + - - +
272B ALA* 2.9 10.7 + - - +
274B MET* 1.3 79.1 - - - +
276B GLY* 1.3 57.7 + - - +
278B VAL* 3.4 6.6 + - - +
279B ALA* 2.9 30.5 + - - +
387B TYR* 3.7 15.9 - - + -
611B ZN 2.6 34.6 - - - -
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Residues in contact with GLY 276 (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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272B ALA 3.0 10.5 + - - -
273B LEU 3.8 2.5 - - - -
274B MET 3.2 0.2 - - - -
275B ASP* 1.3 76.2 - - - +
277B LEU* 1.3 57.3 + - - +
279B ALA* 3.3 2.4 + - - +
280B GLY 2.9 24.6 + - - -
387B TYR* 3.3 38.4 - - - -
390B GLY 3.6 6.5 - - - -
391B ARG* 3.7 10.6 - - - +
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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
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255B ALA* 3.6 34.3 - - + -
257B ILE* 4.0 22.7 - - + -
273B LEU 3.0 17.1 + - - +
274B MET 3.1 7.4 + - - +
276B GLY* 1.3 77.5 - - - +
278B VAL* 1.3 55.7 + - - +
280B GLY* 3.4 6.8 + - - -
281B GLY 3.6 0.3 + - - -
282B CYS* 2.8 45.0 + - - +
284B VAL* 3.7 12.1 - - + -
306B ALA* 5.3 0.2 - - + -
308B LEU* 4.3 14.6 - - + -
390B GLY* 3.5 21.7 + - - +
393B ILE* 4.1 14.1 - - + -
394B ALA* 3.9 12.5 - - - +
397B ILE* 5.7 0.7 - - + -
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Residues in contact with VAL 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 MET* 3.0 30.6 + - + +
275B ASP* 3.8 6.5 - - - +
277B LEU* 1.3 72.3 - - - +
279B ALA* 1.3 62.0 + - - +
280B GLY 3.2 0.2 - - - -
281B GLY* 3.0 20.3 + - - -
282B CYS 3.6 13.1 + - - +
284B VAL* 3.8 20.4 - - + +
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Residues in contact with ALA 279 (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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275B ASP 2.9 17.7 + - - +
276B GLY 3.7 4.0 - - - +
278B VAL* 1.3 78.2 - - - +
280B GLY* 1.3 58.4 + - - +
281B GLY* 3.0 4.9 + - - -
387B TYR* 3.4 26.0 - - + +
391B ARG* 5.2 5.6 - - + -
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Residues in contact with GLY 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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276B GLY 2.9 11.8 + - - -
277B LEU 3.4 1.5 + - - -
278B VAL 3.2 0.6 - - - -
279B ALA* 1.3 75.1 - - - +
281B GLY* 1.3 59.9 + - - +
282B CYS* 3.5 2.4 - - - +
391B ARG* 4.7 10.3 - - - +
394B ALA* 3.6 32.9 - - - +
395B ALA* 5.7 0.3 - - - -
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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