Contacts of the helix formed by residues 266 - 278 (chain F) in PDB entry 1XPU
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 SER 266 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F ILE* 3.7 4.3 + - - +
264F LEU* 3.7 6.7 + - - +
265F ASP* 1.3 87.5 + - - +
267F ILE* 1.3 60.4 + - - +
268F THR* 3.1 20.2 - - - +
269F ARG* 3.2 26.0 - - - +
270F LEU* 3.4 16.5 + - - +
318F THR* 2.6 24.9 + - - -
320F LEU* 3.7 10.1 - - - -
6701F FPD 2.8 20.0 + - - -
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Residues in contact with ILE 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LEU* 5.0 6.5 - - + -
264F LEU* 3.7 26.2 - - + +
266F SER* 1.3 72.7 - - - +
268F THR* 1.3 60.5 + - + +
269F ARG 3.4 0.2 - - - -
270F LEU* 3.5 9.0 + - + +
271F ALA* 2.9 27.4 + - - +
297F PRO* 3.9 27.8 - - + +
300F PHE* 4.3 10.5 - - + -
301F PHE* 4.4 13.2 - - + -
317F ALA* 4.1 9.2 - - + -
318F THR 3.0 22.5 + - - +
319F ALA* 4.3 11.7 - - + -
331F ILE* 4.5 0.6 - - - +
335F PHE* 3.7 36.8 - - + -
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Residues in contact with THR 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266F SER* 3.5 13.2 - - - -
267F ILE* 1.3 79.3 - - + +
269F ARG* 1.3 59.6 + - - +
271F ALA* 3.3 2.4 + - - +
272F ARG* 2.9 34.6 + - - +
319F ALA* 4.0 12.6 - - + -
320F LEU* 3.5 42.9 + - - +
328F ASP* 3.8 17.4 + - - +
331F ILE* 3.7 27.9 - - + +
332F TYR* 4.6 6.7 - - - +
335F PHE* 5.9 0.2 - - + -
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Residues in contact with ARG 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E GLU 5.5 1.2 + - - -
334E GLU 5.7 1.2 + - - -
336E LYS* 3.6 16.6 + - - +
337E GLY* 5.2 0.6 - - - -
338E THR* 5.9 2.0 - - - +
209F ILE* 3.8 16.9 - - + +
210F ASP* 3.5 36.1 + - + +
266F SER* 3.2 23.8 + - - +
267F ILE 3.4 0.4 - - - -
268F THR* 1.3 79.3 + - - +
270F LEU* 1.3 63.9 + - - +
272F ARG* 3.2 41.1 + - - +
273F ALA* 3.2 21.7 + - - +
320F LEU* 5.2 4.6 - - + +
323F THR* 5.6 1.4 - - - +
328F ASP* 3.6 18.8 + - - -
6701F FPD 2.9 57.2 + - - +
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Residues in contact with LEU 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F ILE* 3.6 23.9 - - + +
239F HIS 4.0 13.2 - - - +
240F VAL* 4.6 2.0 - - - +
243F ALA* 3.6 32.3 - - + -
264F LEU* 4.4 2.5 - - + -
266F SER 3.4 7.9 + - - +
267F ILE* 3.7 18.6 - - + +
268F THR 3.3 0.4 - - - -
269F ARG* 1.3 79.2 - - - +
271F ALA* 1.3 57.9 + - - +
273F ALA* 3.3 2.7 + - + +
274F TYR* 3.0 61.0 + - + -
297F PRO* 5.1 1.3 - - + -
300F PHE* 4.1 31.6 - - + -
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Residues in contact with ALA 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F ILE 2.9 18.1 + - - +
268F THR 3.3 5.4 + - - +
270F LEU* 1.3 75.0 - - - +
272F ARG* 1.3 59.3 + - - +
274F TYR* 3.5 1.7 + - - +
275F ASN* 3.0 30.0 + - - +
289F VAL* 5.1 2.1 - - + +
293F ALA* 5.5 1.4 - - - +
294F LEU* 4.8 9.0 - - + -
297F PRO* 3.9 24.2 - - + +
331F ILE* 3.7 28.4 - - + +
335F PHE* 4.8 1.3 - - + -
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Residues in contact with ARG 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E LYS* 5.5 1.2 - - - +
333E GLU* 4.5 9.8 + - - +
334E GLU* 3.5 43.1 + - - +
210F ASP* 5.3 4.3 + - - +
268F THR 2.9 16.3 + - - +
269F ARG* 3.2 42.5 - - - +
271F ALA* 1.3 76.2 - - - +
273F ALA* 1.3 58.2 + - - +
275F ASN* 3.8 2.1 + - - +
276F THR* 3.2 29.1 + - - +
325F SER* 3.8 19.8 + - - -
327F MET* 3.7 35.5 - - + +
328F ASP* 3.5 28.9 + - - -
331F ILE* 3.8 4.7 - - + -
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Residues in contact with ALA 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F ASP* 5.5 0.4 - - - +
236F ALA* 3.8 11.9 - - - +
239F HIS* 3.5 41.3 - - + -
240F VAL* 4.1 6.2 - - + +
269F ARG 3.2 14.6 + - - +
270F LEU* 3.6 6.5 - - - +
271F ALA 3.3 0.2 - - - -
272F ARG* 1.3 77.8 - - - +
274F TYR* 1.3 61.8 + - - +
276F THR* 3.0 18.8 + - - -
277F VAL* 3.3 15.4 + - - +
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Residues in contact with TYR 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F VAL* 3.5 23.0 + - + +
243F ALA* 5.0 3.5 - - - +
244F GLU* 3.0 26.5 + - - +
270F LEU* 3.0 53.7 + - + +
271F ALA* 3.9 4.9 - - - +
273F ALA* 1.3 74.7 - - - +
275F ASN* 1.3 65.5 - - - +
277F VAL* 3.0 7.0 + - + -
278F VAL* 3.0 32.1 + - + +
293F ALA* 4.2 14.4 - - - +
296F ARG* 3.4 60.0 + - + +
297F PRO* 3.6 21.3 - - + -
300F PHE* 5.2 6.3 - - + +
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Residues in contact with ASN 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271F ALA 3.0 18.6 + - - +
272F ARG 3.9 5.8 - - - +
273F ALA 3.4 0.4 - - - -
274F TYR* 1.3 75.5 - - - +
276F THR* 1.3 67.3 + - - +
278F VAL 3.3 16.3 - - - +
288F GLY 4.0 6.7 + - - +
289F VAL* 3.5 24.0 - - + +
290F ASP* 2.8 32.6 + - - +
293F ALA* 3.8 12.0 - - + +
327F MET* 3.6 23.8 - - + +
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Residues in contact with THR 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E THR* 5.2 11.2 - - + -
291E ALA* 4.7 24.5 - - + +
334E GLU* 5.9 2.7 - - - +
236F ALA* 3.3 18.9 - - - +
272F ARG 3.2 15.4 + - - +
273F ALA 3.0 15.9 + - - -
275F ASN* 1.3 85.3 - - - +
277F VAL* 1.3 58.2 + - - +
278F VAL 3.6 2.1 - - - +
327F MET* 6.4 0.7 - - + -
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Residues in contact with VAL 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F ALA* 4.9 4.0 - - + +
237F SER* 4.2 29.4 - - - +
240F VAL* 3.7 27.4 - - + -
273F ALA 3.3 9.8 + - - +
274F TYR* 3.0 15.2 + - + +
276F THR* 1.3 78.6 - - - +
278F VAL* 1.3 71.5 + - + +
279F PRO* 3.7 8.1 - - - +
296F ARG* 5.2 2.7 - - - +
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Residues in contact with VAL 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F TYR* 3.0 21.3 + - + +
275F ASN 3.3 14.7 - - - +
276F THR 4.7 1.5 - - - -
277F VAL* 1.3 85.9 - - + +
279F PRO* 1.3 84.1 - - + +
290F ASP* 4.7 3.1 - - - +
292F ASN* 5.1 10.3 - - - +
293F ALA* 4.7 16.6 - - + +
296F ARG* 3.4 37.5 - - + +
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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