Contacts of the helix formed by residues 264 - 280 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261D THR* 3.4 21.9 + - - +
262D MET 5.2 2.0 - - - +
263D TRP* 1.3 82.4 - - - +
265D SER* 1.3 64.6 + - - +
266D THR 3.4 2.0 - - - -
267D GLU* 3.2 27.3 + - + +
268D LYS* 3.0 45.2 + - + +
288D LYS* 6.3 1.6 - - - -
731D FMN 3.3 0.6 + - - -
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Residues in contact with SER 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D TRP 3.5 2.8 + - - -
264D LEU* 1.3 68.6 - - - +
266D THR* 1.3 67.7 + - - +
268D LYS* 3.1 17.6 + - - +
269D MET* 3.2 17.8 + - - +
344D ALA* 3.9 12.1 - - - -
374D VAL* 5.4 0.2 - - - -
376D TRP 2.7 27.0 + - - -
377D VAL* 3.6 7.1 - - - +
378D PRO* 3.6 24.8 - - - +
731D FMN 2.9 22.2 + - - -
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Residues in contact with THR 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D TYR* 4.4 3.6 - - + -
260D ASP 3.7 11.0 - - - +
261D THR* 3.0 14.6 - - + -
265D SER* 1.3 73.7 - - - +
267D GLU* 1.3 54.9 + - - +
269D MET* 3.4 11.2 + - - +
270D ALA* 3.0 23.0 + - - +
310D GLY 3.9 1.6 - - - -
311D SER 3.6 26.7 - - - +
312D PRO* 3.2 12.6 - - - +
342D PHE* 3.5 22.0 - - + -
343D GLY* 4.0 3.4 - - - -
344D ALA 3.4 13.9 + - - -
731D FMN 2.6 23.8 + - - -
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Residues in contact with GLU 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D TYR* 2.8 41.9 + - + +
261D THR* 3.0 12.1 + - + +
264D LEU* 3.4 34.4 - - - +
265D SER 3.0 0.4 - - - -
266D THR* 1.3 75.2 - - - +
268D LYS* 1.3 61.5 + - + +
270D ALA* 3.2 3.7 + - - +
271D HIS* 2.9 28.2 + - + +
286D LEU* 6.0 1.1 - - + +
288D LYS* 4.2 15.8 - - - +
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Residues in contact with LYS 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D TRP 5.0 2.4 + - - -
264D LEU* 3.0 41.4 + - + +
265D SER* 3.1 10.0 + - - +
267D GLU* 1.3 77.5 - - + +
269D MET* 1.3 56.8 + - - +
271D HIS* 3.5 7.6 + - - +
272D ALA* 3.2 20.4 + - - +
377D VAL* 4.9 13.3 - - + +
378D PRO* 4.3 19.3 - - + -
383D LEU* 3.7 21.9 - - + +
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Residues in contact with MET 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D SER* 3.2 20.1 + - - +
266D THR* 3.5 13.2 - - - +
267D GLU 3.1 0.4 - - - -
268D LYS* 1.3 74.7 - - - +
270D ALA* 1.3 65.4 + - - +
271D HIS 3.1 0.2 - - - -
272D ALA* 3.2 2.1 + - - +
273D LEU* 2.9 29.8 + - + +
342D PHE* 4.1 9.4 - - + -
343D GLY 3.6 43.7 - - - +
344D ALA* 3.6 8.7 - - + +
372D PRO 4.3 9.4 - - - +
374D VAL* 3.9 32.5 - - + -
378D PRO* 4.6 1.8 - - + -
383D LEU* 4.3 10.8 - - + -
386D CYS* 3.7 26.3 - - - +
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Residues in contact with ALA 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ILE* 4.2 10.5 - - + +
259D TYR* 4.0 25.1 - - + -
266D THR 3.0 15.1 + - - +
267D GLU* 3.4 9.6 - - - +
269D MET* 1.3 75.9 - - - +
271D HIS* 1.3 63.3 + - - +
273D LEU* 3.6 5.0 + - - +
274D MET* 3.0 23.2 + - - +
286D LEU* 4.8 7.4 - - + +
342D PHE* 3.8 23.5 - - + -
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Residues in contact with HIS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D GLU* 2.9 18.0 + - + +
268D LYS* 3.6 9.2 - - - +
269D MET 3.1 0.2 - - - -
270D ALA* 1.3 75.5 - - - +
272D ALA* 1.3 65.2 + - - +
274D MET* 3.2 30.1 + - + +
275D ASP* 3.0 40.4 + - - +
286D LEU* 5.0 4.8 - - + +
631D ZN 2.7 29.0 - - - -
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Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D LYS 3.2 12.3 + - - +
269D MET 3.2 6.0 + - - +
271D HIS* 1.3 75.7 - - - +
273D LEU* 1.3 68.0 + - - +
275D ASP* 2.9 23.4 + - - +
276D GLY 3.0 9.4 + - - -
383D LEU* 3.5 38.1 - - + +
386D CYS* 3.7 7.6 - - + -
387D TYR* 3.8 10.6 - - + +
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ILE* 5.3 2.9 - - + -
269D MET 2.9 19.9 + - - +
270D ALA* 3.7 4.7 - - - +
272D ALA* 1.3 75.1 - - - +
274D MET* 1.3 62.6 + - - +
276D GLY 3.3 0.7 + - - -
277D LEU* 3.1 31.8 + - + +
308D LEU* 4.0 12.8 - - + -
340D LEU* 3.7 25.4 - - + -
342D PHE* 3.4 48.2 - - + -
372D PRO* 5.0 1.8 - - + -
386D CYS* 3.7 33.4 - - + +
389D LEU* 4.2 4.7 - - + -
390D GLY* 3.7 14.7 - - - +
393D ILE* 5.1 0.2 - - + -
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Residues in contact with MET 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ILE* 4.6 4.0 - - + +
270D ALA 3.0 14.3 + - - +
271D HIS* 3.4 35.2 - - + +
272D ALA 3.0 0.2 - - - -
273D LEU* 1.3 77.6 - - - +
275D ASP* 1.3 61.5 + - - +
277D LEU* 3.0 11.7 + - - +
278D VAL* 2.9 34.6 + - + +
284D VAL* 3.7 33.2 - - + +
286D LEU* 3.7 31.9 - - + -
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Residues in contact with ASP 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D HIS* 3.0 35.0 + - - +
272D ALA* 2.9 11.8 + - - +
274D MET* 1.3 80.7 - - - +
276D GLY* 1.3 57.8 + - - +
278D VAL* 3.9 5.3 - - - +
279D ALA* 2.9 31.0 + - - +
387D TYR* 3.7 17.3 - - + -
631D ZN 3.0 24.8 - - - -
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Residues in contact with GLY 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D ALA 3.0 10.7 + - - -
273D LEU 3.3 3.1 + - - -
275D ASP* 1.3 77.3 - - - +
277D LEU* 1.3 58.2 + - - +
279D ALA* 3.4 2.3 + - - +
280D GLY* 3.0 22.3 + - - -
387D TYR* 3.3 38.5 - - - -
390D GLY 3.6 10.8 - - - +
391D ARG* 3.7 7.7 - - - -
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ALA* 4.2 18.6 - - + -
257D ILE* 4.0 27.4 - - + -
273D LEU 3.1 22.5 + - - +
274D MET 3.0 6.3 + - - +
276D GLY* 1.3 76.4 - - - +
278D VAL* 1.3 62.4 + - - +
280D GLY* 3.2 8.8 + - - -
281D GLY 3.5 0.2 + - - -
282D CYS* 3.1 27.0 + - + +
284D VAL* 3.6 11.7 - - + -
308D LEU* 4.2 15.0 - - + -
390D GLY* 3.3 21.8 - - - +
393D ILE* 3.6 27.4 - - + -
394D ALA* 3.8 10.4 - - - +
397D ILE* 4.7 2.2 - - + -
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Residues in contact with VAL 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D MET* 2.9 30.1 + - + +
275D ASP* 4.0 5.6 - - - +
277D LEU* 1.3 71.9 - - - +
279D ALA* 1.3 66.9 + - - +
281D GLY* 3.0 14.7 + - - -
282D CYS 3.5 18.7 + - - +
283D GLU* 5.7 0.2 - - - -
284D VAL* 3.8 15.7 - - + +
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Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PRO* 3.0 35.9 - - + +
99A ASP* 3.8 2.8 + - - +
275D ASP 2.9 20.0 + - - +
276D GLY 3.5 4.9 - - - +
278D VAL* 1.3 77.7 - - - +
280D GLY* 1.3 57.9 + - - +
281D GLY* 2.9 6.4 + - - -
387D TYR* 3.2 26.0 - - + +
391D ARG* 4.1 5.8 - - - -
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Residues in contact with GLY 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PRO 4.3 9.5 - - - +
99A ASP* 4.5 10.2 - - - +
122A ASN* 5.8 3.3 - - - +
276D GLY 3.0 12.4 + - - -
277D LEU 3.2 1.7 + - - -
279D ALA* 1.3 75.1 - - - +
281D GLY* 1.3 58.4 + - - +
282D CYS* 3.6 2.7 - - - -
391D ARG* 4.4 10.5 - - - +
394D ALA* 3.6 31.2 - - - +
395D ALA* 5.7 0.2 - - - -
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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