Contacts of the helix formed by residues 264 - 280 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A THR* 3.4 18.9 + - - +
262A MET 5.8 0.9 - - - +
263A TRP* 1.3 83.4 - - - +
265A SER* 1.3 58.5 + - - +
266A THR 3.4 2.2 - - - -
267A GLU* 3.1 33.9 + - + +
268A LYS* 3.0 46.9 + - + +
288A LYS* 5.8 3.6 - - - +
701A FMN 3.4 0.4 + - - -
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TRP* 3.5 3.2 + - - +
264A LEU* 1.3 71.9 - - - +
266A THR* 1.3 66.7 + - - +
267A GLU 3.0 1.1 - - - -
268A LYS* 3.2 9.7 + - - +
269A MET* 3.1 27.3 + - - +
344A ALA* 4.0 9.9 - - - -
376A TRP 2.9 26.6 + - - -
377A VAL* 3.7 10.4 - - - +
378A PRO* 3.7 19.7 - - - +
701A FMN 3.0 16.6 + - - -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A TYR* 4.2 4.0 - - + -
260A ASP 3.6 16.8 - - - +
261A THR* 3.0 14.8 - - + -
265A SER* 1.3 73.6 - - - +
267A GLU* 1.3 56.3 + - - +
269A MET* 3.4 9.2 + - - +
270A ALA* 2.9 22.7 + - - +
310A GLY 3.9 1.6 - - - -
311A SER 3.7 21.5 - - - +
312A PRO* 3.3 12.3 - - - +
342A PHE* 3.4 23.3 - - + -
343A GLY* 4.2 1.8 - - - -
344A ALA 3.3 15.6 + - - -
701A FMN 2.6 23.2 + - - -
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A TYR* 2.2 48.2 + - + +
261A THR* 3.0 12.8 + - + +
264A LEU* 3.1 37.1 - - - +
265A SER 3.0 0.2 - - - -
266A THR* 1.3 75.5 - - - +
268A LYS* 1.3 61.5 + - + +
269A MET 3.1 0.2 - - - -
270A ALA* 3.1 3.0 + - - +
271A HIS* 2.8 28.4 + - + +
288A LYS* 4.3 15.6 + - - +
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Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TRP 5.1 1.4 + - - -
264A LEU* 3.0 37.4 + - + +
265A SER* 3.2 15.0 + - - +
267A GLU* 1.3 77.9 - - + +
269A MET* 1.3 57.7 + - - +
271A HIS* 3.4 9.6 - - - +
272A ALA* 3.1 20.6 + - - +
377A VAL* 5.7 4.4 - - - +
378A PRO* 4.6 12.1 - - + +
383A LEU* 3.6 27.9 - - + +
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Residues in contact with MET 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER 3.1 17.9 + - - +
266A THR* 3.5 9.4 - - - +
268A LYS* 1.3 75.2 - - - +
270A ALA* 1.3 66.1 + - - +
271A HIS 3.1 0.2 - - - -
272A ALA* 3.2 2.6 + - - +
273A LEU* 2.9 29.3 + - + +
342A PHE* 4.0 9.4 - - + -
343A GLY* 3.4 42.4 - - - +
344A ALA* 3.4 12.8 - - + +
372A PRO 4.5 7.2 - - - +
373A THR 4.8 0.4 - - - -
374A VAL* 3.2 42.4 - - + -
378A PRO* 4.2 10.1 - - + -
383A LEU* 4.2 7.4 - - + -
386A CYS* 3.9 23.3 - - - -
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.0 12.4 - - + +
259A TYR* 4.1 24.9 - - + -
266A THR 2.9 14.9 + - - +
267A GLU* 3.1 10.3 + - - +
269A MET* 1.3 75.7 - - - +
271A HIS* 1.3 57.3 + - - +
273A LEU* 3.6 4.7 + - - +
274A MET* 3.0 28.1 + - - +
286A LEU* 4.6 6.0 - - + +
342A PHE* 3.7 24.0 - - + -
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 2.8 15.0 + - + +
268A LYS* 3.4 13.9 - - - +
270A ALA* 1.3 74.0 - - - +
272A ALA* 1.3 61.4 + - - +
274A MET* 3.0 33.4 + - + +
275A ASP* 2.9 45.1 + - - +
286A LEU* 4.9 3.4 - - + +
601A ZN 2.5 32.5 - - - -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LYS 3.1 11.1 + - - +
269A MET 3.2 7.2 + - - +
271A HIS* 1.3 76.1 - - - +
273A LEU* 1.3 68.2 + - - +
275A ASP* 3.0 19.8 + - - +
276A GLY 3.1 10.4 + - - -
383A LEU* 3.6 37.5 - - + +
386A CYS* 3.6 8.3 - - + -
387A TYR* 3.6 12.2 - - + +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.5 7.4 - - + -
269A MET 2.9 20.2 + - - +
270A ALA* 3.7 4.3 - - - +
272A ALA* 1.3 78.0 - - - +
274A MET* 1.3 62.2 + - - +
276A GLY 3.4 0.7 + - - -
277A LEU* 3.1 28.7 + - - +
308A LEU* 4.4 10.8 - - + -
340A LEU* 3.7 26.2 - - + -
342A PHE* 3.6 48.0 - - + -
372A PRO* 4.8 2.0 - - + -
386A CYS* 3.5 33.8 - - + +
389A LEU* 4.1 4.5 - - + -
390A GLY* 3.6 15.0 - - - +
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.1 14.6 - - + +
270A ALA 3.0 13.1 + - - +
271A HIS* 3.0 38.0 + - + +
273A LEU* 1.3 74.6 - - - +
275A ASP* 1.3 70.1 + - - +
277A LEU* 3.1 6.0 + - - +
278A VAL* 2.9 32.1 + - + +
284A VAL* 3.8 23.6 - - + +
286A LEU* 3.5 32.1 - - + -
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Residues in contact with ASP 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 HIS* 2.9 30.7 + - - +
272A ALA* 3.0 9.8 + - - +
274A MET* 1.3 80.8 - - - +
276A GLY* 1.3 57.4 + - - +
278A VAL* 3.4 7.2 + - - +
279A ALA* 2.9 31.0 + - - +
387A TYR* 3.8 15.1 - - + -
601A ZN 3.0 31.3 - - - -
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Residues in contact with GLY 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 ALA 3.1 10.3 + - - -
273A LEU 3.4 2.9 + - - -
274A MET 3.2 0.2 - - - -
275A ASP* 1.3 76.5 - - - +
277A LEU* 1.3 57.7 + - - +
279A ALA* 3.4 2.1 + - - +
280A GLY 2.9 23.9 + - - -
387A TYR* 3.3 39.1 - - - -
390A GLY 3.6 7.1 - - - +
391A ARG* 3.7 10.8 - - - -
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Residues in contact with LEU 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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255A ALA* 3.7 30.3 - - + -
257A ILE* 3.8 22.7 - - + -
273A LEU 3.1 17.8 + - - +
274A MET 3.1 8.6 + - - +
276A GLY* 1.3 76.9 - - - +
278A VAL* 1.3 59.5 + - - +
280A GLY* 3.3 6.9 + - - -
281A GLY 3.6 0.2 + - - -
282A CYS* 2.8 38.3 + - - +
284A VAL* 3.7 11.2 - - + -
308A LEU* 4.3 15.0 - - + -
390A GLY* 3.5 23.1 + - - +
393A ILE* 3.8 23.1 - - + -
394A ALA* 4.0 6.9 - - - +
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 2.9 31.8 + - + +
275A ASP* 3.9 7.0 - - - +
277A LEU* 1.3 72.1 - - - +
279A ALA* 1.3 62.1 + - - +
281A GLY* 3.0 19.4 + - - -
282A CYS 3.6 12.8 + - - +
284A VAL* 3.9 20.2 - - + +
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Residues in contact with ALA 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 ASP 2.9 19.1 + - - +
276A GLY 3.6 4.7 - - - +
278A VAL* 1.3 75.1 - - - +
280A GLY* 1.3 58.7 + - - +
281A GLY 3.0 5.8 + - - -
387A TYR* 3.3 27.6 - - + +
391A ARG* 4.2 15.3 + - - +
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Residues in contact with GLY 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 GLY 2.9 11.5 + - - -
277A LEU 3.3 1.8 + - - -
278A VAL 3.2 0.8 - - - -
279A ALA* 1.3 75.6 - - - +
281A GLY* 1.3 59.1 + - - +
282A CYS* 3.5 2.0 - - - +
391A ARG* 3.5 25.7 - - - +
394A ALA* 3.6 28.1 - - - +
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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