Contacts of the helix formed by residues 263 - 274 (chain D) in PDB entry 3ITX
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 ASN 263 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A LYS* 3.7 7.4 - - - +
287A TYR* 3.8 14.5 + - - +
192B PHE* 4.1 1.4 - - - -
222B MET* 5.0 1.4 - - - +
228B TYR* 3.0 45.1 + - - -
229B SER* 3.7 12.8 - - - -
233B GLN* 5.2 7.3 + - + +
261D ASN 3.5 1.6 + - - -
262D THR* 1.3 75.0 - - - +
264D ILE* 1.3 58.6 + - - +
265D GLU* 3.0 17.0 - - - +
266D MET* 2.9 38.6 + - + +
267D ILE* 3.6 14.2 + - - +
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Residues in contact with ILE 264 (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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253D VAL* 4.2 9.6 - - + -
255D LEU* 3.2 49.1 - - + +
258D HIS* 3.6 36.8 - - + +
262D THR* 3.2 15.0 + - + +
263D ASN* 1.3 67.8 - - - +
265D GLU* 1.3 73.5 + - - +
266D MET 3.1 2.0 - - - -
267D ILE* 2.9 20.7 + - + +
268D VAL* 3.1 14.1 + - + +
301D ARG* 4.1 30.5 - - - +
305D VAL* 4.6 5.6 - - + -
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Residues in contact with GLU 265 (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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286A LYS* 5.0 5.4 + - - -
192B PHE* 3.7 8.5 - - + -
228B TYR* 2.5 38.6 + - - +
263D ASN* 3.0 19.9 - - - +
264D ILE* 1.3 79.0 + - - +
266D MET* 1.3 60.4 + - - +
268D VAL* 3.3 13.0 + - - +
269D ALA* 3.1 17.2 + - - +
301D ARG* 4.2 19.3 - - - +
304D LEU* 3.5 45.3 - - + +
305D VAL* 4.2 8.0 - - - +
308D GLU* 3.5 15.1 - - + +
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Residues in contact with MET 266 (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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192B PHE* 3.7 39.5 - - + +
229B SER* 3.8 15.7 - - - +
230B THR 3.3 30.7 - - - +
231B VAL* 4.5 1.8 - - - -
233B GLN* 3.4 32.5 - - - +
263D ASN* 2.9 28.4 + - + +
264D ILE 3.1 0.2 - - - -
265D GLU* 1.3 74.6 - - - +
267D ILE* 1.3 66.1 + - - +
269D ALA* 3.2 2.1 + - - +
270D ARG* 2.9 50.8 + - + +
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Residues in contact with ILE 267 (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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233B GLN* 4.7 5.8 - - - +
234B ASP* 5.0 1.1 - - - +
235D TRP* 3.6 52.9 - - + +
253D VAL* 4.5 10.8 - - + -
258D HIS* 3.5 33.0 - - + +
262D THR* 3.7 21.3 - - + -
263D ASN 3.6 8.9 + - - +
264D ILE* 2.9 10.4 + - + +
266D MET* 1.3 77.2 - - - +
268D VAL* 1.3 62.9 + - - +
270D ARG* 3.3 7.7 + - - +
271D LEU* 3.0 34.6 + - + +
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Residues in contact with VAL 268 (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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253D VAL* 4.7 6.7 - - + -
264D ILE* 3.1 21.2 + - + +
265D GLU* 3.4 13.5 - - - +
267D ILE* 1.3 77.8 - - - +
269D ALA* 1.3 63.6 + - - +
271D LEU* 3.4 2.4 + - - +
272D ILE* 3.0 36.6 + - + +
277D LEU* 3.8 17.2 - - + +
280D PHE* 3.4 44.4 - - + -
305D VAL* 4.3 9.0 - - + +
308D GLU* 4.3 9.9 - - + -
309D LEU* 4.0 5.4 - - + -
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Residues in contact with ALA 269 (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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192B PHE* 3.8 16.6 - - + -
193B THR* 3.7 18.9 + - - +
265D GLU 3.1 11.7 + - - +
266D MET 3.2 7.4 + - - +
268D VAL* 1.3 78.1 - - - +
270D ARG* 1.3 64.0 + - - +
272D ILE* 3.3 11.6 + - - +
273D GLN* 2.9 23.4 + - - +
308D GLU* 3.5 25.5 - - - +
315D ARG* 6.1 0.4 - - - +
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Residues in contact with ARG 270 (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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192B PHE* 3.4 35.0 + - - +
193B THR* 4.4 1.8 - - - +
196B PHE* 3.6 40.3 - - - +
231B VAL* 2.8 33.7 + - - +
237B THR* 3.1 24.8 + - - +
240B LEU* 4.5 4.0 - - + -
235D TRP* 3.6 31.9 - - + -
266D MET* 2.9 42.7 + - + +
267D ILE* 3.7 3.6 - - - +
269D ALA* 1.3 75.6 - - - +
271D LEU* 1.3 64.0 + - - +
273D GLN* 3.2 7.7 + - - -
274D PHE* 3.2 29.6 + - - +
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Residues in contact with LEU 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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220D HIS* 5.3 0.2 - - + -
235D TRP* 3.9 28.7 - - + +
239D TYR* 4.6 9.6 - - + -
251D CYS* 4.0 35.7 - - + -
253D VAL* 3.6 30.7 - - + -
267D ILE* 3.0 28.5 + - + +
268D VAL 3.8 3.8 - - - +
270D ARG* 1.3 74.4 - - - +
272D ILE* 1.3 62.5 + - - +
274D PHE* 3.3 3.8 + - - -
275D GLY 3.1 4.0 + - - -
276D LYS* 2.8 37.6 + - + +
277D LEU* 3.9 19.5 - - + +
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Residues in contact with ILE 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 VAL* 3.0 33.3 + - + +
269D ALA* 3.6 8.7 - - - +
271D LEU* 1.3 76.6 - - - +
273D GLN* 1.3 64.2 + - - +
275D GLY* 3.0 15.0 + - - -
277D LEU* 3.4 31.9 - - + +
308D GLU* 4.1 10.5 - - + +
309D LEU* 4.2 1.8 - - + -
312D ALA* 4.0 25.1 - - + -
315D ARG* 4.3 9.4 - - - +
317D VAL* 4.3 24.4 - - + +
320D PHE* 3.8 26.5 - - + -
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Residues in contact with GLN 273 (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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193B THR* 3.6 36.7 + - + +
196B PHE* 3.3 26.7 - - - +
197B GLU* 3.7 23.6 + - - +
200B LEU* 4.3 8.1 - - - +
269D ALA 2.9 13.5 + - - +
270D ARG* 3.2 13.2 + - - +
272D ILE* 1.3 77.6 - - - +
274D PHE* 1.3 81.8 + - + +
275D GLY 3.7 0.5 + - - -
315D ARG* 5.7 1.8 - - - +
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Residues in contact with PHE 274 (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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196B PHE* 3.8 15.3 - + - -
200B LEU* 4.6 6.5 - - + -
240B LEU* 3.6 40.8 - - + -
244B THR* 4.4 16.2 - - + -
239D TYR* 3.9 32.4 - - + +
243D GLN* 5.0 2.4 - - - +
270D ARG* 3.2 19.0 + - - +
271D LEU* 4.2 1.8 - - - +
272D ILE 3.1 0.8 - - - -
273D GLN* 1.3 106.8 - - + +
275D GLY* 1.3 63.2 + - - +
276D LYS* 3.3 13.5 + - - +
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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
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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