Contacts of the helix formed by residues 263 - 275 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B SER* 4.3 2.7 - - - -
239B GLY 5.4 0.4 - - - -
262B HIS* 1.3 95.9 - - - +
264B GLU* 1.3 64.2 + - - +
265B MET 3.2 1.1 + - - -
266B LEU* 3.4 10.2 + - - +
267B PRO* 4.5 0.7 - - - +
283B ASN* 4.2 1.2 + - - +
284B TYR 4.8 0.2 + - - -
286B ASN 3.6 13.8 + - - -
287B ALA* 3.7 3.6 - - - -
288B TRP* 3.1 19.1 + - - -
427B CYS* 3.9 4.9 - - - +
429B LYS* 5.5 0.9 + - - -
430B TYR* 2.8 36.4 + - - -
1546B FSO 3.4 18.1 - - - -
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Residues in contact with GLU 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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239B GLY 2.9 17.9 + - - +
240B HIS* 3.0 18.0 + - + +
262B HIS 3.0 1.6 + - - -
263B SER* 1.3 78.7 - - - +
265B MET* 1.3 58.1 + - - +
266B LEU 3.4 0.7 - - - -
267B PRO* 3.3 11.5 - - - +
426B GLY* 3.3 22.8 + - - -
427B CYS* 3.6 5.4 + - + -
429B LYS* 4.5 4.7 + - - -
450B GLY 4.0 1.9 - - - +
451B GLN* 2.9 38.5 - - - +
452B CYS 2.8 18.1 + - - -
1545B SF3 3.3 0.2 - - - -
1546B FSO 2.0 58.6 + - - +
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Residues in contact with MET 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ILE* 3.4 39.7 - - + +
238B SER 3.5 13.9 - - - +
239B GLY 3.2 20.2 - - - +
240B HIS* 3.5 22.4 - - - +
241B ASP 3.5 23.3 - - - +
242B LEU* 4.1 10.8 - - + -
245B LEU* 3.8 26.0 - - + -
261B THR* 3.3 16.7 - - + +
262B HIS 3.0 5.7 + - - +
264B GLU* 1.3 75.7 - - - +
266B LEU* 1.3 66.3 + - - +
267B PRO* 3.2 3.6 - - - -
268B ALA* 2.9 22.1 + - + +
305B THR* 4.3 0.2 - - - -
451B GLN* 4.4 1.6 - - - +
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Residues in contact with LEU 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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225B VAL* 3.9 21.8 - - + -
261B THR* 3.7 3.1 - - - -
262B HIS 4.3 0.2 + - - -
263B SER 3.4 3.8 + - - +
264B GLU 3.4 0.2 - - - -
265B MET* 1.3 75.8 - - - +
267B PRO* 1.3 68.4 - - + +
269B HIS* 3.1 23.4 + - - +
270B TYR* 3.7 24.2 - - - +
283B ASN* 3.3 40.6 + - + +
365B ILE* 4.2 20.0 - - + -
429B LYS* 3.8 25.4 - - + +
430B TYR* 3.4 24.2 - - + +
433B ASN* 4.3 2.0 - - - +
448B ASP* 3.9 1.3 - - - +
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Residues in contact with PRO 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 5.3 0.2 - - - -
263B SER 4.5 0.7 - - - +
264B GLU* 3.3 13.9 - - - +
265B MET 3.3 4.7 - - - -
266B LEU* 1.3 91.6 - - + +
268B ALA* 1.3 64.0 + - - +
269B HIS 3.0 0.7 - - - -
270B TYR* 2.9 30.7 + - + +
271B TYR* 3.3 19.1 - - + -
429B LYS* 3.7 12.3 - - - +
450B GLY* 3.4 42.0 - - - -
451B GLN* 3.5 16.8 - - + +
454B ASP* 4.8 1.8 - - - +
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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
----------------------------------------------------------
242B LEU* 3.7 19.3 - - + +
245B LEU* 3.2 33.7 - - + -
261B THR* 4.5 0.9 - - + -
265B MET* 2.9 17.9 + - + +
267B PRO* 1.3 77.6 - - - +
269B HIS* 1.3 61.9 + - - +
270B TYR 3.1 1.4 + - - -
271B TYR* 3.2 18.7 + - - -
274B PHE* 3.3 20.8 - - + +
280B PHE* 4.1 6.7 - - + -
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Residues in contact with HIS 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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223B THR* 3.4 16.3 - - + +
225B VAL* 3.6 34.4 - - + +
261B THR* 2.8 39.8 + - + +
266B LEU* 3.1 22.2 + - - +
267B PRO 3.0 0.4 - - - -
268B ALA* 1.3 76.7 - - - +
270B TYR* 1.3 61.8 + - + +
271B TYR 3.3 1.2 + - - -
275B LYS* 3.4 15.2 - - - +
280B PHE* 3.7 23.5 - + - -
281B LYS 2.7 29.0 + - - -
282B GLY* 3.3 14.5 + - - -
283B ASN 4.0 1.6 - - - -
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Residues in contact with TYR 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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220B PRO* 3.2 13.7 - - + +
221B GLU* 2.9 32.7 + - - +
223B THR* 3.5 18.6 - - - -
225B VAL* 3.8 22.7 - - + -
266B LEU* 3.7 17.8 - - + +
267B PRO* 2.9 35.9 + - + +
269B HIS* 1.3 81.7 - - + +
271B TYR* 1.3 61.6 + - - +
275B LYS* 4.3 0.7 - - - -
365B ILE* 4.2 5.2 - - - +
367B GLY* 3.5 22.8 + - - -
368B GLY* 3.3 31.9 - - - -
448B ASP* 2.6 36.9 + - - +
449B ALA 5.0 2.0 - - - -
450B GLY* 4.4 4.7 - - - -
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Residues in contact with TYR 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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213B ASN* 3.4 38.9 + - + +
214B THR* 4.3 3.4 - - + +
217B TYR* 3.7 20.2 - - + +
218B GLY 3.1 27.6 - - - -
220B PRO* 3.7 24.8 - - + +
242B LEU* 3.6 20.7 - - + +
267B PRO* 3.3 33.9 - - + -
268B ALA* 3.2 16.0 + - - +
270B TYR* 1.3 79.5 - - - +
272B PRO* 1.3 70.0 - - - +
273B ALA 3.1 0.9 + - - -
274B PHE* 3.2 23.5 + + + +
275B LYS* 3.7 12.7 + - - +
451B GLN* 5.2 2.2 + - - -
454B ASP* 4.4 16.0 + - - -
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Residues in contact with PRO 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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217B TYR 3.4 12.3 - - - +
218B GLY* 3.8 8.7 - - - -
219B HIS 3.1 31.2 - - - +
221B GLU* 3.9 25.1 - - - +
270B TYR 3.7 3.8 - - - +
271B TYR* 1.3 84.0 - - - +
273B ALA* 1.3 62.3 + - - +
274B PHE 3.2 0.9 + - - -
275B LYS* 3.2 19.4 + - + +
276B LYS* 4.3 2.9 + - - +
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Residues in contact with ALA 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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216B THR 4.6 2.5 - - - +
217B TYR* 3.0 51.8 + - + +
271B TYR 3.1 0.4 + - - -
272B PRO* 1.3 76.2 - - - +
274B PHE* 1.3 63.4 + - + +
276B LYS* 2.7 40.8 + - - +
277B TYR* 3.5 4.2 - - - -
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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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217B TYR* 3.5 46.7 - + + -
242B LEU* 3.7 24.5 - - + -
245B LEU* 4.0 16.6 - - + -
246B GLU* 3.9 27.4 - - + -
249B LEU* 3.7 15.7 - - + -
268B ALA* 3.3 25.6 - - + +
269B HIS* 5.5 0.7 - - - -
271B TYR* 3.2 14.3 + + + +
273B ALA* 1.3 78.8 - - + +
275B LYS* 1.3 64.4 + - - +
276B LYS 3.2 3.2 + - - -
277B TYR* 3.5 22.4 + + - +
280B PHE* 3.5 34.7 - - + -
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Residues in contact with LYS 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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221B GLU* 3.0 37.8 + - - +
222B ILE 3.6 7.7 + - - -
223B THR* 2.8 36.1 + - - +
269B HIS 3.4 17.3 - - - +
270B TYR 4.2 4.9 - - - -
271B TYR 3.7 9.6 - - - +
272B PRO* 3.2 10.7 + - + +
274B PHE* 1.3 79.6 - - - +
276B LYS* 1.3 61.0 + - - +
277B TYR 3.2 5.5 + - - +
280B PHE* 5.6 0.7 - - - -
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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