Contacts of the helix formed by residues 263 - 277 (chain A) in PDB entry 1UPX
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A SER* 4.3 3.4 - - - -
239A GLY 5.4 0.2 - - - -
262A HIS* 1.3 93.9 - - - +
264A GLU* 1.3 62.5 + - - +
265A MET 3.3 3.6 + - - -
266A LEU* 3.4 9.2 + - - +
267A PRO* 4.4 0.7 - - - +
283A ASN* 4.2 1.2 + - - +
286A ASN 3.6 14.6 + - - -
287A ALA* 3.7 3.8 - - - -
288A TRP* 3.1 20.5 + - - -
427A CYS* 3.8 4.7 - - - +
429A LYS* 5.5 0.9 + - - -
430A TYR* 2.8 36.6 + - - -
1546A FSO 3.4 18.4 - - - -
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Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLY 2.9 18.1 + - - +
240A HIS* 2.9 22.6 + - + +
262A HIS 3.0 1.4 + - - -
263A SER* 1.3 79.7 - - - +
265A MET* 1.3 57.8 + - - +
266A LEU 3.4 0.7 - - - -
267A PRO* 3.4 10.5 - - - +
426A GLY* 3.4 21.2 + - - -
427A CYS* 3.8 5.4 - - + -
429A LYS* 4.4 5.0 + - - +
450A GLY 4.0 1.9 - - - +
451A GLN* 2.9 40.0 + - - +
452A CYS 2.8 20.6 + - - -
1546A FSO 2.1 55.3 + - - +
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Residues in contact with MET 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ILE* 3.4 39.9 - - + +
238A SER 3.5 14.6 - - - +
239A GLY 3.2 19.7 - - - +
240A HIS 3.5 23.1 - - - +
241A ASP 3.5 21.1 - - - +
242A LEU* 4.2 10.3 - - + -
245A LEU* 3.8 26.9 - - + -
261A THR* 3.3 15.3 - - + +
262A HIS 2.9 5.9 + - - +
264A GLU* 1.3 76.2 - - - +
266A LEU* 1.3 66.2 + - - +
267A PRO* 3.2 3.1 - - - -
268A ALA* 3.0 21.8 + - + +
305A THR* 4.3 0.7 - - - -
451A GLN* 4.5 2.2 - - - +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A VAL* 3.9 19.5 - - + -
261A THR* 3.7 3.1 - - - -
263A SER 3.4 3.8 + - - +
265A MET* 1.3 76.4 - - - +
267A PRO* 1.3 69.1 - - + +
268A ALA 3.1 1.4 + - - -
269A HIS* 3.1 23.4 + - - +
270A TYR* 3.7 24.1 - - - +
283A ASN* 3.3 39.9 + - + +
365A ILE* 3.9 23.3 - - + -
429A LYS* 3.8 25.8 - - + +
430A TYR* 3.4 21.8 - - + +
433A ASN* 4.2 1.1 - - - +
448A ASP* 3.8 1.8 - - - +
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Residues in contact with PRO 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A SER 4.4 0.7 - - - +
264A GLU* 3.4 15.0 - - - +
265A MET 3.3 4.7 - - - -
266A LEU* 1.3 89.5 - - + +
268A ALA* 1.3 63.4 + - - +
269A HIS 3.0 0.7 - - - -
270A TYR* 2.9 35.1 + - + +
271A TYR* 3.3 15.4 - - + -
429A LYS* 3.7 12.6 - - - +
450A GLY* 3.3 42.4 - - - -
451A GLN* 3.5 15.9 - - + +
454A ASP* 4.8 1.8 - - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A LEU* 3.7 20.0 - - + +
245A LEU* 3.2 33.9 - - + -
261A THR* 4.5 0.7 - - + -
265A MET* 3.0 18.4 + - + +
267A PRO* 1.3 77.2 - - - +
269A HIS* 1.3 60.8 + - - +
270A TYR 3.1 1.4 + - - -
271A TYR* 3.2 19.5 + - - +
274A PHE* 3.3 19.9 - - + +
280A PHE* 4.1 6.1 - - + -
451A GLN* 5.7 0.2 - - - +
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Residues in contact with HIS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A THR* 3.4 6.9 - - + +
225A VAL* 3.6 34.5 - - + +
226A ASN 5.9 0.2 - - - -
261A THR* 2.8 37.7 + - + +
266A LEU* 3.1 22.1 + - - +
267A PRO 3.0 0.2 - - - -
268A ALA* 1.3 77.7 - - - +
270A TYR* 1.3 61.7 + - + +
271A TYR 3.5 0.6 + - - -
274A PHE* 5.4 0.7 - - - -
275A LYS* 3.3 25.5 - - - +
280A PHE* 3.7 22.6 - + - -
281A LYS 2.6 28.7 + - - -
282A GLY 3.3 16.8 + - - -
283A ASN 3.9 1.8 - - - -
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PRO* 3.2 14.5 - - + +
221A GLU* 3.0 32.6 + - - +
223A THR* 3.5 18.8 - - - -
225A VAL* 3.8 22.1 - - + +
266A LEU* 3.7 18.7 - - + +
267A PRO* 2.9 37.5 + - + +
269A HIS* 1.3 79.5 - - + +
271A TYR* 1.3 60.8 - + - +
275A LYS* 4.4 0.7 - - - -
365A ILE* 5.2 2.3 - - - +
366A ILE 4.4 2.3 + - - -
367A GLY* 3.5 23.0 + - - -
368A GLY* 3.4 33.2 - - - -
448A ASP* 2.6 37.2 + - - +
449A ALA 5.0 2.0 - - - -
450A GLY* 4.3 4.9 - - - -
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Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ASN* 3.4 40.0 + - + +
214A THR* 4.3 2.6 - - - +
217A TYR* 3.6 20.6 - - + +
218A GLY 3.0 26.0 - - - -
220A PRO* 3.8 25.2 - - + +
242A LEU* 3.6 20.8 - - + +
267A PRO* 3.3 28.3 - - + -
268A ALA* 3.2 14.7 + - - +
269A HIS 4.1 0.2 - - - +
270A TYR* 1.3 80.7 - + - +
272A PRO* 1.3 70.4 - - - +
273A ALA 3.2 0.7 + - - -
274A PHE* 3.2 23.6 + + + +
275A LYS* 3.7 10.5 + - - +
451A GLN* 5.1 3.0 + - - -
454A ASP* 4.4 15.5 + - - -
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Residues in contact with PRO 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A TYR 3.4 13.0 - - - +
218A GLY* 3.9 8.5 - - - -
219A HIS 3.2 29.4 - - - +
221A GLU* 4.1 17.9 - - - +
270A TYR 3.7 3.6 - - - +
271A TYR* 1.3 83.5 - - - +
273A ALA* 1.3 60.1 + - - +
275A LYS* 3.2 28.7 + - + +
276A LYS* 4.0 12.1 - - - +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A THR 4.7 2.2 - - - +
217A TYR* 3.1 44.9 + - + +
271A TYR 3.2 0.2 + - - -
272A PRO* 1.3 77.8 - - - +
274A PHE* 1.3 64.4 + - + +
275A LYS 3.4 0.7 + - - -
276A LYS* 3.5 19.0 + - - +
277A TYR* 3.6 14.6 - - + -
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A TYR* 3.5 39.9 - + + -
242A LEU* 3.6 31.6 - - + -
245A LEU* 4.0 16.2 - - + -
246A GLU* 3.8 30.5 - - + -
249A LEU* 3.7 16.8 - - + -
268A ALA 3.3 23.1 - - - +
269A HIS* 5.4 0.4 - - - -
271A TYR* 3.2 15.3 + + + +
273A ALA* 1.3 75.8 - - + +
275A LYS* 1.3 60.8 + - - +
276A LYS 3.1 6.4 + - - -
277A TYR* 3.4 22.7 + + - +
280A PHE* 3.5 35.2 - - + -
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLU* 2.7 36.3 + - - +
222A ILE 3.6 6.9 + - - -
223A THR* 2.8 37.9 + - - +
269A HIS 3.3 16.8 - - - +
270A TYR 4.3 4.0 - - - -
271A TYR 3.7 10.1 - - - +
272A PRO* 3.2 12.7 + - + +
274A PHE* 1.3 76.8 - - - +
276A LYS* 1.3 59.4 + - + +
277A TYR 3.3 7.2 + - - +
278A ALA* 5.6 0.3 - - - -
280A PHE* 5.4 1.1 - - - -
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Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A GLU* 5.3 1.4 - - - +
272A PRO* 4.0 11.7 - - - +
273A ALA* 3.7 17.7 - - - +
274A PHE 3.1 1.4 - - - -
275A LYS* 1.3 80.1 - - + +
277A TYR* 1.3 66.8 + - + +
278A ALA 3.9 1.8 + - - -
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Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A GLU* 4.5 5.5 - - + +
249A LEU* 3.8 39.9 - - + -
250A LYS* 3.5 40.9 - - + +
253A GLU* 4.0 11.9 - - + -
273A ALA* 3.6 17.9 - - + -
274A PHE* 3.6 24.2 - + - +
275A LYS* 3.3 5.8 - - - +
276A LYS* 1.3 81.4 - - + +
278A ALA* 1.3 64.6 + - - +
279A HIS* 3.2 24.9 - + + +
280A PHE* 3.1 25.8 + - + +
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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