Contacts of the helix formed by residues 263 - 274 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B ASN 3.5 2.0 + - - -
262B THR* 1.3 72.9 - - - +
264B ILE* 1.3 60.9 + - - +
265B GLU* 2.9 17.3 - - - +
266B MET* 2.9 38.2 + - + +
267B ILE* 3.6 15.2 + - - +
286C LYS* 3.6 13.0 - - - +
287C TYR* 3.8 9.3 + - - +
192D PHE* 4.1 1.2 - - - -
222D MET* 5.0 0.8 - - - +
228D TYR* 3.0 44.1 + - - -
229D SER* 3.6 14.2 - - - -
233D GLN* 5.2 6.9 + - + +
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Residues in contact with ILE 264 (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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253B VAL* 4.1 14.6 - - + -
255B LEU* 3.2 39.7 - - + +
258B HIS* 3.7 36.6 - - + +
262B THR* 3.2 14.9 + - + +
263B ASN* 1.3 69.0 + - - +
265B GLU* 1.3 72.8 + - - +
266B MET 3.1 2.0 - - - -
267B ILE* 3.0 18.8 + - + +
268B VAL* 3.0 11.3 + - + +
280B PHE* 4.2 16.8 - - + -
301B ARG* 4.3 20.4 - - - +
305B VAL* 4.8 5.8 - - + -
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Residues in contact with GLU 265 (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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263B ASN* 2.9 23.5 - - - +
264B ILE* 1.3 80.1 + - - +
266B MET* 1.3 59.9 + - - +
268B VAL* 3.3 10.1 + - - +
269B ALA* 3.1 17.3 + - - +
301B ARG* 4.2 19.4 - - - +
304B LEU* 3.6 45.0 - - + +
305B VAL* 4.1 11.2 - - - +
308B GLU* 3.6 13.9 - - + +
286C LYS* 4.8 6.4 + - - -
192D PHE* 3.8 8.5 - - + -
228D TYR* 2.5 37.9 + - - +
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Residues in contact with MET 266 (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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263B ASN* 2.9 29.9 + - + +
264B ILE 3.1 0.2 - - - -
265B GLU* 1.3 75.6 - - - +
267B ILE* 1.3 60.1 + - - +
269B ALA* 3.1 2.3 + - - +
270B ARG* 2.9 57.4 + - + +
192D PHE* 3.6 38.4 - - + -
229D SER* 3.9 15.0 - - - +
230D THR 3.2 31.0 - - - +
231D VAL* 4.5 1.6 - - - -
233D GLN* 3.4 32.5 - - - +
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TRP* 3.5 57.0 - - + +
253B VAL* 4.5 12.1 - - + -
258B HIS* 3.6 29.2 - - + +
262B THR* 3.7 20.6 - - + -
263B ASN 3.6 8.5 + - - +
264B ILE* 3.0 10.0 + - + +
266B MET* 1.3 77.2 - - - +
268B VAL* 1.3 62.9 - - - +
270B ARG* 3.3 7.6 + - - +
271B LEU* 3.0 34.7 + - + +
233D GLN* 4.6 6.5 - - - +
234D ASP* 4.9 1.8 - - - +
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL* 4.4 9.9 - - + -
264B ILE 3.0 13.9 + - - +
265B GLU* 3.4 10.1 - - - +
266B MET 3.1 0.2 - - - -
267B ILE* 1.3 78.9 - - - +
269B ALA* 1.3 62.9 + - - +
271B LEU* 3.4 1.6 + - - +
272B ILE* 3.0 45.4 + - + +
277B LEU* 3.9 20.1 - - + +
280B PHE* 3.8 33.0 - - + -
305B VAL* 4.3 9.0 - - + +
308B GLU* 4.3 10.8 - - + -
309B LEU* 4.0 14.6 - - + -
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Residues in contact with ALA 269 (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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265B GLU 3.1 11.2 + - - +
266B MET 3.1 7.6 + - - +
268B VAL* 1.3 79.0 - - - +
270B ARG* 1.3 58.5 + - - +
272B ILE* 3.2 10.3 + - - +
273B GLN* 2.9 29.8 + - - +
308B GLU* 3.5 24.8 - - - +
192D PHE* 3.9 22.4 - - + -
193D THR* 3.8 13.6 + - - +
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Residues in contact with ARG 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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235B TRP* 3.7 31.2 - - + -
266B MET* 2.9 43.1 + - + +
267B ILE 3.7 3.6 - - - +
269B ALA* 1.3 76.1 - - - +
271B LEU* 1.3 62.1 + - - +
273B GLN* 3.4 6.4 + - - -
274B PHE* 3.2 30.9 + - - +
192D PHE* 3.3 35.6 + - - +
193D THR* 4.3 3.2 - - - +
196D PHE* 3.6 41.2 - - - +
231D VAL* 2.8 32.9 + - - +
237D THR* 3.1 25.2 + - - +
240D LEU* 4.6 4.0 - - + -
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Residues in contact with LEU 271 (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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220B HIS* 5.3 0.4 - - + -
235B TRP* 3.9 27.1 - - + +
239B TYR* 4.5 10.8 - - + -
251B CYS* 4.0 35.0 - - + -
253B VAL* 3.5 31.9 - - + -
267B ILE* 3.0 26.9 + - + +
268B VAL 3.9 3.4 - - - +
270B ARG* 1.3 74.6 - - - +
272B ILE* 1.3 61.9 + - - +
274B PHE* 3.3 3.7 + - - +
275B GLY 3.0 4.3 + - - -
276B LYS* 2.8 38.6 + - + +
277B LEU* 3.9 19.7 - - + +
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Residues in contact with ILE 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 VAL* 3.0 39.4 + - + +
269B ALA* 3.5 7.9 - - - +
271B LEU* 1.3 77.6 - - - +
273B GLN* 1.3 63.0 + - - +
275B GLY* 3.0 14.2 + - - -
277B LEU* 3.5 21.1 - - + -
308B GLU 4.1 10.5 - - - +
309B LEU* 4.4 2.0 - - + -
312B ALA* 3.9 21.1 - - + -
315B ARG* 4.5 8.3 - - - +
317B VAL* 3.4 32.9 - - + +
318B LYS* 4.6 2.8 - - - +
320B PHE* 3.7 27.8 - - + -
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Residues in contact with GLN 273 (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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269B ALA 2.9 15.7 + - - +
270B ARG* 3.6 10.6 + - - +
271B LEU 3.3 0.2 - - - -
272B ILE* 1.3 80.4 - - - +
274B PHE* 1.3 83.9 + - + +
275B GLY 3.3 0.6 + - - -
315B ARG* 5.2 3.8 - - - +
317B VAL* 5.3 2.8 - - - +
318B LYS* 4.7 7.3 + - - -
193D THR* 3.7 30.0 + - + +
196D PHE* 3.4 25.9 - - - -
197D GLU* 3.7 27.6 + - - +
200D LEU* 4.5 7.5 - - - +
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Residues in contact with PHE 274 (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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239B TYR* 4.0 31.8 - - + +
243B GLN* 4.9 2.4 - - - +
270B ARG* 3.2 19.4 + - - +
271B LEU* 3.3 2.9 + - - +
272B ILE 3.2 0.6 - - - -
273B GLN* 1.3 106.9 - - + +
275B GLY* 1.3 62.2 + - - +
276B LYS* 3.3 14.6 + - - +
318B LYS* 4.7 6.7 + - - +
196D PHE* 3.9 14.8 - + - -
200D LEU* 4.7 8.3 - - + -
240D LEU* 3.6 39.3 - - + -
244D THR* 4.7 11.9 - - - -
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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