Contacts of the helix formed by residues 271 - 288 (chain B) in PDB entry 3UMO
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 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ALA* 1.3 77.9 - - - +
272B LEU* 1.3 65.2 + - - +
273B GLU* 3.6 7.7 + - - +
274B GLU* 3.0 28.6 + - - +
275B MET* 2.9 22.2 + - - +
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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
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220B ARG* 4.7 22.9 - - + +
222B VAL* 4.9 2.7 - - + -
232B GLY* 3.8 17.5 - - - +
233B VAL 4.6 6.7 - - - +
234B ASP* 3.7 52.7 + - + +
237B ASN* 3.9 18.8 - - + +
239B ILE* 4.2 7.4 - - + -
270B ALA 4.0 0.2 + - - -
271B SER* 1.3 71.9 - - - +
273B GLU* 1.3 58.3 + - - +
275B MET* 3.3 13.5 + - - +
276B VAL* 2.9 50.0 + - + +
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ILE* 3.5 34.3 - - + +
241B VAL* 5.5 1.1 - - + -
271B SER* 3.3 7.5 + - - +
272B LEU* 1.3 80.0 - - - +
274B GLU* 1.3 56.1 + - - +
276B VAL* 4.0 0.7 - - - +
277B ARG* 2.9 78.8 + - + +
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LYS* 2.5 37.9 + - + +
268B GLU* 4.5 2.3 - - - +
270B ALA* 3.8 14.6 - - + +
271B SER* 3.0 22.8 + - - +
273B GLU* 1.3 76.7 - - - +
275B MET* 1.3 58.0 + - - +
277B ARG* 3.8 6.8 - - - +
278B PHE* 2.9 30.1 + - - +
304B TYR* 3.1 26.0 + - - +
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Residues in contact with MET 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.1 28.3 - - - -
220B ARG* 4.0 21.3 - - - +
222B VAL* 5.2 0.9 - - - -
262B MET* 3.4 37.6 - - + +
265B LYS* 3.8 14.3 - - + +
266B LEU* 3.7 41.5 - - + +
270B ALA* 4.4 13.7 - - + +
271B SER 2.9 15.2 + - - +
272B LEU* 3.5 13.9 - - - +
274B GLU* 1.3 77.8 - - - +
276B VAL* 1.3 58.8 + - + +
278B PHE* 3.9 1.9 - - - +
279B GLY 2.9 22.9 + - - -
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B VAL* 4.1 19.5 - - + -
230B ALA* 4.1 27.1 - - + +
232B GLY* 3.9 22.0 - - - +
239B ILE* 3.5 22.0 - - + -
241B VAL* 3.7 22.2 - - + -
258B MET* 4.8 0.6 - - + +
262B MET* 4.4 5.2 - - - -
272B LEU* 2.9 24.3 + - + +
275B MET* 1.3 73.1 - - + +
277B ARG* 1.3 61.2 + - - +
279B GLY* 3.2 1.3 + - - +
280B VAL* 2.8 28.8 + - + +
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Residues in contact with ARG 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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241B VAL* 3.8 29.6 - - + +
273B GLU* 2.9 61.6 + - - +
274B GLU* 3.8 5.8 - - - +
276B VAL* 1.3 77.1 - - - +
278B PHE* 1.3 57.7 + - - +
281B ALA* 2.9 28.6 + - - +
304B TYR* 3.9 14.1 - - + -
307B LEU* 3.3 42.4 + - + +
308B SER* 4.0 18.8 + - - +
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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
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51B LEU* 4.1 19.5 - - + -
261B ALA* 3.4 46.0 - - + +
264B LEU* 4.6 11.2 - - + -
265B LYS* 3.6 33.4 - - + -
268B GLU* 6.1 0.7 - - - -
274B GLU 2.9 18.5 + - - +
275B MET 3.9 0.4 - - - +
277B ARG* 1.3 77.0 - - - +
279B GLY* 1.3 57.4 + - - +
281B ALA* 3.3 2.4 + - - +
282B ALA* 3.0 24.4 + - - +
300B THR* 3.7 25.6 - - + -
301B GLN* 5.4 2.5 - - - -
304B TYR* 3.7 28.2 - + + -
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Residues in contact with GLY 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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258B MET* 3.4 29.0 - - - +
261B ALA* 4.0 2.9 - - - -
262B MET* 3.6 25.7 - - - +
275B MET 2.9 11.1 + - - -
276B VAL 3.2 2.4 + - - -
278B PHE* 1.3 76.1 - - - +
280B VAL* 1.3 56.2 + - - +
282B ALA 3.4 0.3 + - - -
283B GLY 2.9 24.6 + - - -
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ALA* 3.8 15.0 - - + +
241B VAL* 3.8 32.1 - - + +
243B PRO* 3.8 35.4 - - + -
258B MET* 3.6 15.0 - - + -
276B VAL 2.8 22.5 + - - +
277B ARG 3.9 1.6 - - - +
279B GLY* 1.3 69.6 - - - +
281B ALA* 1.3 60.7 + - - +
284B SER* 2.8 31.2 + - - +
303B ILE* 5.4 0.4 - - + -
307B LEU* 4.0 9.6 - - + -
313B ATP 3.5 16.4 - - - +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ARG 2.9 17.8 + - - +
278B PHE 3.5 5.6 - - - +
280B VAL* 1.3 77.1 - - - +
282B ALA* 1.3 56.9 + - - +
285B ALA* 2.8 30.7 + - - +
300B THR* 3.5 28.4 - - + +
303B ILE* 3.7 18.5 - - + +
304B TYR* 3.6 23.6 - - + +
307B LEU* 4.0 0.4 - - + +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.1 1.8 - - + -
257B SER* 3.5 15.4 - - - +
261B ALA* 3.4 31.6 - - + -
278B PHE 3.0 7.9 + - - +
279B GLY 4.1 0.4 - - - +
281B ALA* 1.3 73.5 - - - +
283B GLY* 1.3 67.2 + - - +
286B ALA 3.0 18.0 + - - -
295B CYS* 3.2 20.2 - - - +
300B THR* 3.6 22.0 - - + +
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ALA* 3.4 22.4 - - - +
257B SER* 4.2 0.7 - - - -
258B MET 4.0 2.5 - - - +
279B GLY 2.9 16.3 + - - -
280B VAL 3.9 0.4 - - - -
282B ALA* 1.3 75.9 - - - +
284B SER* 1.3 61.7 + - - +
286B ALA* 3.2 17.5 + - - +
287B THR* 3.4 11.6 + - - +
313B ATP 3.4 20.6 - - - -
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PRO* 3.2 21.9 - - - +
244B PRO* 5.0 1.3 - - - -
280B VAL* 2.8 15.7 + - - -
281B ALA 4.2 1.3 - - - -
283B GLY* 1.3 72.2 - - - +
285B ALA* 1.3 65.1 + - - +
287B THR* 2.7 21.5 + - - -
288B LEU* 3.6 9.4 + - - +
303B ILE* 4.1 13.0 - - - -
313B ATP 2.9 43.7 + - - -
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Residues in contact with ALA 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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281B ALA 2.8 20.7 + - - +
282B ALA 3.6 2.7 - - - +
284B SER* 1.3 78.4 - - - +
286B ALA* 1.3 62.3 + - - +
288B LEU* 3.1 23.6 + - - +
289B ASN* 4.0 9.4 + - - -
295B CYS* 4.0 7.4 - - + -
296B SER 5.0 0.2 + - - -
299B ASP* 3.8 13.1 - - + +
300B THR* 3.4 34.3 - - - +
303B ILE* 3.7 8.2 - - + +
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Residues in contact with ALA 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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250B SER 4.2 0.4 - - - -
252B VAL 4.6 0.7 - - - +
253B GLY 3.8 14.4 - - - +
254B ALA* 3.8 6.1 - - - +
257B SER* 3.5 25.1 - - - +
282B ALA 3.0 8.2 + - - +
283B GLY 3.2 12.3 - - - +
285B ALA* 1.3 78.6 - - - +
287B THR* 1.3 61.3 + - - +
288B LEU 3.1 1.0 + - - -
289B ASN* 3.3 7.1 + - - +
293B ARG 3.8 3.9 - - - +
294B LEU* 4.1 4.9 - - - -
295B CYS* 3.9 13.8 - - - +
314B K 2.9 21.3 - - - -
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Residues in contact with THR 287 (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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246B VAL 5.6 0.5 + - - -
248B SER* 3.3 26.7 - - - +
249B GLN 2.7 30.5 + - - -
250B SER 3.1 16.3 + - - -
251B THR* 4.1 7.4 - - - -
254B ALA* 4.1 7.9 - - + -
283B GLY 3.4 15.0 - - - +
284B SER* 2.7 18.3 + - - -
286B ALA* 1.3 76.8 - - - +
288B LEU* 1.3 59.4 + - - +
289B ASN 3.2 0.4 - - - -
313B ATP 3.6 39.8 - - + +
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Residues in contact with LEU 288 (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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246B VAL* 3.8 31.2 - - + +
247B LYS 3.8 12.3 - - - +
249B GLN* 3.4 21.4 - - + +
284B SER 3.6 12.6 - - - +
285B ALA* 3.4 13.2 - - - +
286B ALA 3.1 1.0 - - - -
287B THR* 1.3 80.8 - - - +
289B ASN* 1.3 63.8 + - - +
290B GLN* 4.2 1.0 + - - +
299B ASP* 3.9 33.7 - - + +
303B ILE* 4.2 12.8 - - + -
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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
------------------------------------------------------------
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