Contacts of the helix formed by residues 264 - 280 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C THR* 3.5 21.1 - - - +
262C MET 5.1 3.1 - - - +
263C TRP* 1.3 82.4 - - - +
265C SER* 1.3 59.5 + - - +
266C THR 3.4 1.8 - - - -
267C GLU* 3.3 28.3 + - + +
268C LYS* 3.0 50.1 + - + +
288C LYS* 6.3 1.1 - - - +
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Residues in contact with SER 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C TRP 3.5 3.1 + - - -
264C LEU* 1.3 74.4 - - - +
266C THR* 1.3 66.3 + - - +
268C LYS* 3.1 16.0 + - - +
269C MET* 3.1 18.3 + - - +
344C ALA* 3.9 11.0 - - - -
374C VAL* 5.2 0.2 - - - -
376C TRP 2.7 27.2 + - - -
377C VAL* 3.7 5.7 - - - +
378C PRO* 3.6 25.2 - - - +
721C FMN 3.1 17.4 + - - -
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Residues in contact with THR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C TYR* 4.5 4.3 - - + -
260C ASP 3.7 8.5 - - - +
261C THR* 3.0 15.2 - - - +
265C SER* 1.3 73.1 - - - +
267C GLU* 1.3 55.5 + - - +
269C MET* 3.3 12.6 + - - +
270C ALA* 2.9 25.8 + - - +
310C GLY 3.9 1.6 - - - -
311C SER 3.6 26.0 - - - +
312C PRO* 3.5 12.5 - - - +
342C PHE* 3.6 20.2 - - + -
343C GLY* 3.9 4.7 - - - -
344C ALA 3.6 12.6 + - - -
721C FMN 2.6 25.6 + - - -
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Residues in contact with GLU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C TYR* 2.6 43.2 + - + +
261C THR* 3.3 12.3 + - - +
264C LEU* 3.3 35.4 - - + +
265C SER 3.0 0.2 - - - -
266C THR* 1.3 78.0 - - - +
268C LYS* 1.3 61.2 + - + +
270C ALA* 3.5 3.1 - - - +
271C HIS* 2.9 28.0 + - + +
288C LYS* 4.4 11.8 + - - +
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Residues in contact with LYS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C TRP 4.9 2.2 + - - -
264C LEU* 3.0 40.9 + - + +
265C SER* 3.1 8.8 + - - +
267C GLU* 1.3 77.7 - - + +
269C MET* 1.3 61.8 + - - +
271C HIS* 3.5 7.9 + - - +
272C ALA* 3.1 17.0 + - - +
377C VAL* 5.7 5.4 - - + +
378C PRO* 4.3 23.4 - - + +
383C LEU* 3.7 22.2 - - + +
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Residues in contact with MET 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C SER 3.1 11.3 + - - +
266C THR* 3.5 22.2 - - - +
268C LYS* 1.3 76.3 - - - +
270C ALA* 1.3 65.1 + - - +
271C HIS 3.1 0.2 - - - -
272C ALA* 3.1 3.2 + - - +
273C LEU* 3.0 29.8 + - - +
342C PHE* 4.2 9.2 - - + -
343C GLY* 3.1 47.8 - - - +
344C ALA* 3.3 13.5 - - + +
372C PRO 4.3 8.5 - - - +
374C VAL* 3.8 30.3 - - + -
378C PRO* 4.5 6.7 - - + -
383C LEU* 4.3 6.1 - - + -
386C CYS* 4.0 24.8 - - - +
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 3.9 12.5 - - + +
259C TYR* 4.1 25.4 - - + -
266C THR 2.9 15.4 + - - +
267C GLU* 3.2 9.8 + - - +
269C MET* 1.3 74.7 - - - +
271C HIS* 1.3 56.8 + - - +
273C LEU* 3.6 5.2 + - - +
274C MET* 3.1 28.1 + - - +
286C LEU* 4.7 6.3 - - + +
342C PHE* 3.9 23.5 - - + -
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Residues in contact with HIS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C GLU* 2.9 17.5 + - + +
268C LYS* 3.6 9.4 - - - +
269C MET 3.1 0.2 - - - -
270C ALA* 1.3 75.8 - - - +
272C ALA* 1.3 65.0 - - - +
274C MET* 3.3 29.9 + - + +
275C ASP* 3.0 30.0 + - - -
286C LEU* 5.0 6.1 - - + +
621C ZN 2.5 30.5 - - - -
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LYS 3.1 13.3 + - - +
269C MET 3.1 7.2 + - - +
271C HIS* 1.3 73.4 - - - +
273C LEU* 1.3 67.6 + - - +
275C ASP* 3.0 20.6 + - - +
276C GLY 3.0 10.7 + - - -
383C LEU* 3.5 37.5 - - + +
386C CYS* 3.7 7.2 - - + -
387C TYR* 3.6 12.3 - - + +
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Residues in contact with LEU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 4.3 2.0 - - + -
269C MET 3.0 21.3 + - - +
270C ALA* 3.7 4.9 - - - +
272C ALA* 1.3 75.0 - - - +
274C MET* 1.3 63.3 + - - +
276C GLY 3.3 1.6 + - - -
277C LEU* 3.0 27.6 + - - +
308C LEU* 4.3 18.8 - - + -
340C LEU* 3.8 23.8 - - + -
342C PHE* 3.5 49.1 - - + -
372C PRO* 4.8 2.0 - - + -
386C CYS* 3.6 37.4 - - + +
389C LEU* 4.2 7.2 - - + -
390C GLY* 3.7 6.9 - - - +
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Residues in contact with MET 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 4.0 13.4 - - + +
270C ALA 3.1 16.4 + - - +
271C HIS* 3.4 40.6 - - + +
272C ALA 3.1 0.2 - - - -
273C LEU* 1.3 77.5 - - - +
275C ASP* 1.3 63.5 + - - +
277C LEU* 3.1 6.6 + - - +
278C VAL* 2.9 38.5 + - + +
284C VAL* 3.8 25.4 - - + +
286C LEU* 3.8 27.8 - - + -
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Residues in contact with ASP 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C HIS* 3.0 28.7 + - - +
272C ALA* 3.0 11.7 + - - +
274C MET* 1.3 82.3 - - - +
276C GLY* 1.3 57.1 + - - +
278C VAL* 3.8 6.8 - - - +
279C ALA* 2.9 30.8 + - - +
387C TYR* 3.9 16.9 - - + -
621C ZN 3.0 31.0 - - - -
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ALA 3.0 10.9 + - - -
273C LEU 3.7 2.2 - - - -
275C ASP* 1.3 76.5 - - - +
277C LEU* 1.3 57.7 + - - +
279C ALA 3.4 0.2 + - - -
280C GLY 2.9 23.4 + - - -
387C TYR* 3.3 36.5 - - - -
390C GLY 3.6 8.5 - - - +
391C ARG* 3.2 13.0 - - - -
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Residues in contact with LEU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ALA* 3.9 23.3 - - + -
257C ILE* 3.8 26.2 - - + -
273C LEU 3.0 19.9 + - - +
274C MET* 3.3 7.0 - - - +
276C GLY* 1.3 77.4 - - - +
278C VAL* 1.3 62.4 + - - +
280C GLY* 3.2 8.8 + - - -
281C GLY 3.5 0.3 + - - -
282C CYS* 3.1 31.0 + - + +
284C VAL* 3.6 12.6 - - + -
308C LEU* 3.8 16.8 - - + -
390C GLY* 3.4 19.3 - - - +
393C ILE* 3.7 24.0 - - + -
394C ALA* 3.8 10.2 - - + +
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Residues in contact with VAL 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C MET* 2.9 30.8 + - + +
275C ASP* 3.9 6.5 - - - +
277C LEU* 1.3 75.4 - - - +
279C ALA* 1.3 58.6 + - - +
281C GLY* 3.0 20.6 + - - -
282C CYS 3.6 13.8 + - - +
284C VAL* 3.9 18.6 - - + +
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ASP 2.9 18.7 + - - +
276C GLY 3.5 2.2 - - - +
278C VAL* 1.3 77.2 - - - +
280C GLY* 1.3 58.3 + - - +
281C GLY* 3.1 4.3 + - - -
387C TYR* 3.2 26.5 - - + +
391C ARG* 3.4 20.9 + - - +
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Residues in contact with GLY 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C GLY 2.9 12.4 + - - -
277C LEU 3.2 1.3 + - - -
278C VAL 3.2 0.6 - - - -
279C ALA* 1.3 74.8 - - - +
281C GLY* 1.3 59.0 + - - +
282C CYS* 3.6 2.4 - - - -
391C ARG* 3.8 17.4 - - - +
394C ALA* 3.6 30.8 - - - +
395C ALA* 5.6 0.7 - - - -
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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