Contacts of the helix formed by residues 261 - 280 (chain B) in PDB entry 1UES
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 GLU 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B PHE* 4.3 9.2 - - + -
259B LYS 5.3 1.1 - - - +
260B SER* 1.3 84.5 + - - +
262B GLY* 1.3 70.0 + - - +
264B ILE* 3.2 22.7 - - - +
265B PHE* 3.3 11.1 + - - -
347B ARG* 3.6 12.8 + - - +
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Residues in contact with GLY 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLU* 1.3 78.8 + - - +
263B GLY* 1.3 58.4 + - - -
264B ILE* 5.0 0.7 - - - -
265B PHE* 3.2 5.8 + - - +
266B ASN* 2.9 34.5 + - - -
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Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.9 8.3 - - - -
261B GLU 3.5 0.4 + - - -
262B GLY* 1.3 71.9 - - - -
264B ILE* 1.3 66.0 + - - +
266B ASN* 3.2 11.4 + - - +
267B ASN* 2.9 35.6 + - - -
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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
----------------------------------------------------------
239B LEU* 4.2 13.3 - - + +
242B LEU* 4.1 41.0 - - + +
243B ILE* 5.2 4.0 - - + +
246B THR* 4.9 14.4 - - + +
248B PHE* 4.4 18.2 - - + -
256B ILE* 4.3 12.3 - - + -
260B SER* 3.9 16.4 - - - -
261B GLU 3.2 16.6 - - - +
262B GLY* 5.0 0.7 - - - -
263B GLY* 1.3 79.4 - - - +
265B PHE* 1.3 58.7 + - - +
267B ASN* 3.5 1.2 + - - -
268B ALA* 3.0 30.3 + - - +
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Residues in contact with PHE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 3.4 38.4 - - + -
260B SER* 3.1 18.5 + - - +
261B GLU* 3.3 18.2 + - - -
262B GLY 3.2 9.3 + - - +
264B ILE* 1.3 76.5 - - - +
266B ASN* 1.3 71.6 + - - +
268B ALA* 4.5 0.9 - - - +
269B GLY* 2.8 30.2 + - - -
342B ALA* 3.8 32.3 - - + -
343B GLY* 4.1 10.5 - - - -
344B ASN 4.6 1.8 - - - -
347B ARG* 3.3 41.5 - - + -
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Residues in contact with ASN 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.5 50.4 - - + +
262B GLY 2.9 19.1 + - - +
263B GLY* 3.2 15.8 + - - +
265B PHE* 1.3 84.6 - - - +
267B ASN* 1.3 59.7 + - - +
270B GLN* 3.1 34.7 + - - +
341B ASN* 5.6 0.3 - - - +
342B ALA* 3.5 11.4 + - - +
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Residues in contact with ASN 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 5.6 1.7 - - - -
235B TYR* 3.4 35.1 - - - +
238B ASN* 3.3 33.0 + - - +
239B LEU* 4.0 13.9 - - + +
242B LEU* 3.6 17.7 - - + +
263B GLY* 2.9 29.7 + - - +
264B ILE 4.2 2.0 - - - +
266B ASN* 1.3 78.5 - - - +
268B ALA* 1.3 61.5 + - - +
270B GLN* 3.9 1.0 - - - +
271B THR* 2.8 33.5 + - - -
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Residues in contact with ALA 268 (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 LEU* 3.9 16.8 - - + +
253B LEU* 3.7 6.2 - - + +
256B ILE* 3.6 28.7 - - + -
257B VAL* 3.5 17.8 - - + +
264B ILE 3.0 19.5 + - - +
265B PHE* 4.0 2.0 - - - +
267B ASN* 1.3 74.7 - - - +
269B GLY* 1.3 61.2 + - - +
271B THR* 3.2 2.3 + - - -
272B LEU* 2.9 32.2 + - - +
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Residues in contact with GLY 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 3.8 20.5 - - - +
265B PHE* 2.8 18.2 + - - -
268B ALA* 1.3 79.2 - - - +
270B GLN* 1.3 55.7 + - - +
272B LEU* 3.5 1.6 + - - +
273B ASN* 2.9 33.1 + - - -
342B ALA 3.8 18.8 - - - -
344B ASN* 4.8 2.1 - - - +
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Residues in contact with GLN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 4.0 3.4 - - + -
235B TYR* 3.0 53.7 + - + -
266B ASN 3.1 22.3 + - - +
267B ASN 4.0 0.7 - - - +
268B ALA 3.3 0.2 - - - -
269B GLY* 1.3 73.9 - - - +
271B THR* 1.3 64.6 - - - +
273B ASN* 3.4 5.6 + - - -
274B HIS* 2.5 45.6 + - - -
323B TRP* 2.8 26.7 + - - +
341B ASN 3.4 4.4 - - - +
342B ALA* 3.4 13.7 - - + -
359B TRP* 3.4 24.9 - - - +
361B HIS* 5.1 0.2 - - - -
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Residues in contact with THR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B HIS* 5.4 5.6 - - + -
204B GLU 5.1 2.2 - - - +
232B LEU* 4.0 8.7 - - + +
235B TYR* 3.7 21.8 + - - +
236B VAL* 3.8 21.3 + - + +
239B LEU* 4.0 12.0 - - + +
253B LEU* 4.0 11.4 - - + -
267B ASN 2.8 21.8 + - - -
268B ALA 3.2 4.7 + - - -
270B GLN* 1.3 76.4 - - - +
272B LEU* 1.3 58.6 + - - +
274B HIS* 3.8 1.2 - - - +
275B ASN* 2.9 52.9 + - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.7 24.7 - - + +
254B ASN* 4.0 19.3 - - - +
257B VAL* 3.8 20.6 - - + -
268B ALA 2.9 16.6 + - - +
269B GLY 3.9 3.4 - - - +
271B THR* 1.3 75.5 - - - +
273B ASN* 1.3 66.1 + - - +
275B ASN* 3.3 4.6 + - + +
276B LEU* 3.1 47.9 + - + +
344B ASN* 3.8 25.8 - - - +
346B VAL* 4.0 15.9 - - + -
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Residues in contact with ASN 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLY 2.9 21.9 + - - +
270B GLN* 3.4 4.0 + - - +
272B LEU* 1.3 77.2 - - - +
274B HIS* 1.3 57.4 + - - +
276B LEU* 3.5 2.4 + - - +
277B TYR* 2.9 28.6 + - - +
323B TRP* 3.1 47.2 - - + +
325B TRP* 3.0 20.6 + - - -
342B ALA 3.3 8.3 + - - -
343B GLY 2.9 22.1 + - - +
344B ASN* 2.9 21.2 - - - +
355B THR* 4.2 2.3 - - - +
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Residues in contact with HIS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B HIS* 3.1 20.0 + + - -
231B HIS* 5.3 0.4 - - - +
232B LEU* 3.7 28.9 - - + -
235B TYR* 3.5 29.3 - + - -
270B GLN* 2.5 38.8 + - - +
273B ASN* 1.3 73.2 - - - +
275B ASN* 1.3 63.6 + - - +
277B TYR* 3.9 5.6 - + - -
278B PHE* 2.8 46.6 + + + -
323B TRP* 3.4 21.7 - + - -
357B ASP* 3.7 0.2 + - - -
361B HIS* 3.9 0.8 + - - -
392B MN 2.2 34.6 + - - -
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Residues in contact with ASN 275 (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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204B GLU 5.2 2.7 + - - +
206B ILE* 3.0 46.3 + - + +
232B LEU* 3.8 8.5 - - - +
253B LEU* 3.7 15.2 - - - +
271B THR* 2.9 38.3 + - - +
272B LEU* 3.3 7.6 + - + +
274B HIS* 1.3 76.3 - - - +
276B LEU* 1.3 58.8 + - + +
278B PHE* 4.2 0.3 - - - -
279B THR* 2.7 38.7 + - + +
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Residues in contact with LEU 276 (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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272B LEU* 3.1 41.3 + - + +
273B ASN 3.9 2.9 - - - +
275B ASN* 1.3 75.2 - - + +
277B TYR* 1.3 64.8 + - - +
279B THR* 3.7 4.5 - - - +
280B GLN* 3.2 13.7 + - - +
325B TRP* 3.5 31.9 - - + -
344B ASN* 4.3 0.2 - - - +
352B PRO* 3.8 22.2 - - + +
390B ARG* 2.9 45.7 + - - +
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Residues in contact with TYR 277 (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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219B ILE* 3.5 20.3 - - + +
227B HIS* 3.6 23.2 + + - -
273B ASN 2.9 19.4 + - - +
274B HIS* 3.2 6.9 + - - +
276B LEU* 1.3 76.7 - - - +
278B PHE* 1.3 89.9 + + - +
280B GLN* 3.2 17.7 - - - +
281B PHE* 3.1 47.9 - + - -
323B TRP* 4.0 9.6 - + + -
355B THR* 3.6 21.2 - - + +
356B PHE* 4.4 1.3 - - - -
357B ASP* 3.6 31.1 - - + +
362B ALA* 4.1 16.3 + - - +
374B HIS* 4.3 9.0 + - - -
378B LEU* 4.7 2.6 - - + +
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 4.0 8.7 - - + -
208B LEU* 3.9 18.8 - - + -
209B PRO* 5.2 1.3 - - - -
210B TYR* 2.7 43.9 + + - +
215B LEU* 6.0 0.9 - - + -
219B ILE* 5.5 6.3 - - + -
224B VAL* 5.0 12.3 - - + -
227B HIS* 3.6 33.2 - + + -
228B HIS* 3.7 39.9 - + + -
232B LEU* 4.2 6.1 - - + -
274B HIS* 2.8 51.1 + + + +
277B TYR* 1.3 93.1 - + - +
279B THR* 1.3 60.0 + - - +
280B GLN 3.5 0.5 + - - -
281B PHE* 3.6 6.6 + + - +
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 4.3 18.4 - - + -
207B SER 5.2 2.7 - - - +
209B PRO* 4.8 12.6 - - + -
275B ASN* 2.7 24.4 + - + +
276B LEU* 3.3 9.4 + - - +
278B PHE* 1.3 73.6 - - - +
280B GLN* 1.3 58.6 + - - +
281B PHE 3.2 2.5 - - - -
282B ARG* 2.8 27.5 + - - +
386B ILE* 3.1 14.8 - - - +
390B ARG* 3.3 10.8 + - - -
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Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU 3.2 12.5 + - - +
277B TYR* 3.2 19.5 + - - +
278B PHE 3.3 0.2 - - - -
279B THR* 1.3 78.1 - - - +
281B PHE* 1.3 85.8 + - + +
354B LEU* 3.7 16.6 - - + +
355B THR* 2.6 44.3 + - - +
382B VAL* 3.8 2.1 - - + +
383B ASP* 2.9 31.3 + - - +
386B ILE* 4.3 6.1 - - + -
387B VAL* 4.7 9.2 - - + -
390B ARG* 3.3 30.5 + - - +
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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
------------------------------------------------------------
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