Contacts of the helix formed by residues 271 - 286 (chain B) in PDB entry 3UCD
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 THR 271 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254B GLY 5.5 0.9 - - - -
255B LYS* 4.6 25.1 - - + +
256B TYR* 4.2 2.5 - - - -
270B ILE* 1.3 77.8 - - - +
272B GLY* 1.3 65.8 + - - +
273B ASP* 3.2 12.3 + - - +
274B GLN* 2.8 40.4 + - - +
275B LEU* 2.9 22.2 + - - +
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Residues in contact with GLY 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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254B GLY 5.5 2.2 + - - -
256B TYR* 3.9 23.2 - - - -
271B THR* 1.3 74.9 - - - +
273B ASP* 1.3 57.2 + - - +
275B LEU* 3.3 1.1 + - - -
276B GLY* 2.9 24.8 + - - -
295B PHE* 3.3 21.3 - - - -
299B ASP* 4.9 1.3 - - - -
302B ALA* 4.8 10.3 - - - -
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Residues in contact with ASP 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B THR* 3.2 9.6 + - - +
272B GLY* 1.3 72.0 - - - +
274B GLN* 1.3 67.5 + - + +
276B GLY* 3.3 2.4 + - - +
277B ALA* 3.0 22.3 + - - +
305B LYS* 3.0 40.2 + - - +
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Residues in contact with GLN 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TYR 4.6 1.0 - - - +
270B ILE* 3.3 31.0 - - + +
271B THR* 2.8 43.8 + - - +
273B ASP* 1.3 79.4 - - + +
275B LEU* 1.3 61.5 + - - +
277B ALA* 3.2 9.6 + - - +
278B LEU* 3.1 21.1 + - - +
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Residues in contact with LEU 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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164B MET* 4.4 0.2 - - + -
250B PHE* 4.3 5.2 - - + -
256B TYR* 3.7 36.6 - - + -
258B LEU* 4.2 24.2 - - + -
270B ILE* 4.0 19.2 - - + +
271B THR 2.9 14.6 + - - +
272B GLY 3.6 4.9 - - - +
274B GLN* 1.3 76.5 - - - +
276B GLY* 1.3 63.3 + - - +
278B LEU* 3.0 13.1 + - + +
279B TYR* 3.0 62.9 + - + +
294B PRO 3.6 12.1 - - - +
295B PHE* 4.1 5.4 - - + -
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Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLY 2.9 16.3 + - - -
273B ASP* 3.3 4.0 + - - -
275B LEU* 1.3 76.6 - - - +
277B ALA* 1.3 60.5 + - - +
279B TYR* 3.2 13.5 + - - -
280B GLN* 3.0 28.4 + - - +
295B PHE* 4.1 4.2 - - - -
306B PHE* 3.6 18.8 - - - -
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASP 3.0 13.8 + - - +
274B GLN* 3.2 12.3 + - - +
276B GLY* 1.3 75.5 - - - +
278B LEU* 1.3 63.4 + - - +
280B GLN* 3.3 9.9 + - - +
281B ASP* 3.1 29.0 + - - +
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Residues in contact with LEU 278 (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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164B MET* 4.1 11.0 - - + -
219B ASN* 5.5 0.7 - - - +
258B LEU* 3.6 31.2 - - + -
270B ILE* 5.1 2.7 - - + -
274B GLN 3.1 10.7 + - - +
275B LEU* 3.0 15.3 + - + +
277B ALA* 1.3 76.1 - - - +
279B TYR* 1.3 63.4 + - + +
281B ASP* 3.1 18.8 + - + +
282B PHE* 3.0 57.4 + - + -
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Residues in contact with TYR 279 (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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164B MET* 3.8 17.3 - - + -
245B VAL* 3.3 34.3 - - + +
275B LEU* 3.0 42.7 + - + +
276B GLY* 3.2 8.3 + - - +
278B LEU* 1.3 78.0 - - + +
280B GLN* 1.3 56.8 + - - +
282B PHE* 3.1 20.3 + + - +
283B VAL* 2.9 32.8 + - - +
291B ILE* 3.8 17.0 - - + +
294B PRO* 2.7 47.9 + - + -
295B PHE* 3.9 5.8 - + - -
306B PHE* 3.4 30.7 - + + -
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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
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276B GLY 3.0 21.1 + - - +
277B ALA* 3.6 11.2 - - - +
278B LEU 3.3 0.2 - - - -
279B TYR* 1.3 75.5 - - - +
281B ASP* 1.3 63.8 + - - +
283B VAL* 3.3 11.9 + - - +
284B ARG* 3.0 23.2 + - - +
306B PHE* 4.2 9.5 - - + -
309B ASN* 3.8 24.1 + - - +
310B VAL* 3.6 21.1 - - - +
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Residues in contact with ASP 281 (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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277B ALA* 3.1 18.1 + - - +
278B LEU* 3.1 19.3 + - + +
280B GLN* 1.3 78.6 - - - +
282B PHE* 1.4 67.0 + - + +
284B ARG* 3.2 6.8 + - - +
285B ASP* 2.9 39.1 + - - +
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Residues in contact with PHE 282 (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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164B MET* 3.9 17.7 - - + -
219B ASN* 4.0 18.6 - - + -
220B SER* 4.1 22.4 - - - -
223B LEU* 3.7 19.5 - - + -
243B MET* 3.9 35.0 - - + -
278B LEU* 3.0 50.3 + - + -
279B TYR* 3.4 17.7 - + - +
281B ASP* 1.4 79.6 - - + +
283B VAL* 1.3 57.6 + - + +
286B TYR* 3.0 46.0 + + - +
288B VAL* 4.1 10.4 - - + +
291B ILE* 5.4 0.9 - - + -
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 2.9 20.8 + - + +
280B GLN* 3.8 12.6 - - - +
281B ASP 3.3 0.2 - - - -
282B PHE* 1.3 75.1 - - - +
284B ARG* 1.3 60.2 + - - +
286B TYR 3.1 18.0 - - - +
288B VAL* 4.1 19.8 - - + +
291B ILE* 4.5 2.9 - - + -
306B PHE* 5.7 1.3 - - + -
310B VAL* 5.9 3.8 - - + -
312B ILE* 4.0 46.7 - - + -
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Residues in contact with ARG 284 (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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280B GLN 3.0 16.1 + - - +
281B ASP* 3.2 7.8 + - - +
283B VAL* 1.3 80.2 - - - +
285B ASP* 1.3 70.9 + - - +
286B TYR 3.8 0.7 + - - +
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Residues in contact with ASP 285 (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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227B LYS* 4.4 10.7 + - - -
281B ASP* 2.9 27.9 + - - +
284B ARG* 1.3 93.9 - - - +
286B TYR* 1.4 89.6 - - + +
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Residues in contact with TYR 286 (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 SER* 3.4 30.9 + - - -
223B LEU* 3.8 35.9 - - + -
224B GLU* 3.1 45.3 + - - -
227B LYS* 3.8 15.5 - - + +
241B ILE* 4.8 1.3 - - + -
282B PHE* 3.0 24.1 + + - +
283B VAL 3.1 17.7 - - - +
284B ARG 3.5 0.9 + - - -
285B ASP* 1.4 99.4 + - + +
287B PRO* 1.4 68.1 - - + +
288B VAL* 2.8 22.0 + - + -
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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