Contacts of the helix formed by residues 275 - 289 (chain B) in PDB entry 3UXO
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 275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B ARG* 3.3 28.4 - - - +
274B GLY* 1.3 77.3 - - - +
276B ASP* 1.3 64.9 + - - +
277B ILE* 4.0 5.2 - - - -
278B PHE* 3.2 8.8 - - - +
279B ASN* 3.0 20.7 + - - -
333B ARG 2.2 33.1 + - - -
334B SER* 2.8 21.6 + - - -
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Residues in contact with ASP 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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183B ARG* 5.2 1.0 - - - +
274B GLY 3.7 0.2 + - - -
275B SER* 1.3 72.9 - - - +
277B ILE* 1.3 64.8 + - + +
279B ASN* 3.4 9.0 + - - +
280B LYS* 3.0 48.2 + - - +
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Residues in contact with ILE 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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275B SER* 3.2 4.1 - - - -
276B ASP* 1.3 79.7 - - + +
278B PHE* 1.3 60.1 + - - +
280B LYS* 3.1 11.0 + - + +
281B ASN* 2.9 54.4 + - - +
334B SER 4.7 9.6 - - - +
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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
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270B LEU* 4.3 7.9 - - + -
274B GLY* 4.1 5.6 - - - -
275B SER* 3.2 25.5 + - - +
277B ILE* 1.3 78.3 - - - +
279B ASN* 1.3 70.8 + - - +
281B ASN* 3.2 11.2 + - + +
282B MET* 2.9 54.1 + - + +
320B PHE* 3.4 32.3 - + - -
328B ARG* 3.7 40.8 - - - -
333B ARG* 3.3 38.8 - - + +
334B SER 4.1 4.4 + - - +
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Residues in contact with ASN 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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270B LEU* 3.6 19.1 - - - +
271B TYR* 2.5 52.4 + - + -
274B GLY 3.6 11.3 + - - +
275B SER 3.0 16.2 + - - +
276B ASP* 3.6 9.4 + - - +
277B ILE 3.2 0.2 - - - -
278B PHE* 1.3 88.5 - - - +
280B LYS* 1.3 60.3 + - + +
282B MET* 4.1 2.9 - - - +
283B ARG* 2.5 48.7 + - - +
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Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TYR* 6.0 2.2 - - - -
276B ASP* 3.0 37.3 + - - +
277B ILE* 3.1 15.2 + - + +
279B ASN* 1.3 77.4 - - - +
281B ASN* 1.3 55.8 + - - +
282B MET 3.2 0.2 + - - -
283B ARG* 3.2 17.0 + - - +
284B ALA* 2.7 38.0 + - - +
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 2.9 41.7 + - - +
278B PHE* 3.6 11.9 - - + +
280B LYS* 1.3 74.4 - - - +
282B MET* 1.3 59.5 + - - +
284B ALA* 3.7 7.6 - - - +
285B HIS* 3.5 21.8 + - - +
325B TRP* 5.2 2.3 + - - -
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Residues in contact with MET 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.7 21.3 - - + -
278B PHE* 2.9 46.7 + - + +
279B ASN* 4.1 3.8 - - - +
281B ASN* 1.3 76.6 - - - +
283B ARG* 1.3 61.2 + - - +
284B ALA 3.2 0.2 - - - -
285B HIS* 3.7 1.8 + - - -
286B ALA* 3.0 26.5 + - - +
293B ILE* 4.0 6.2 - - + +
319B ILE* 3.5 30.3 - - + -
320B PHE* 3.7 36.6 - - + +
323B ILE* 3.6 25.0 - - + +
325B TRP* 4.8 9.4 - - + +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 5.8 2.4 - - - +
271B TYR* 3.0 45.0 - - - +
279B ASN* 2.5 36.0 + - - +
280B LYS* 3.3 23.6 - - - +
282B MET* 1.3 75.7 - - - +
284B ALA* 1.3 68.4 + - - +
286B ALA* 3.8 8.4 - - - +
287B LEU* 3.4 22.0 + - - +
293B ILE* 3.2 51.6 + - + +
294B ASN* 4.5 6.3 + - - +
295B GLU* 5.0 0.4 - - - +
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Residues in contact with ALA 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 LYS 2.7 17.2 + - - +
281B ASN* 3.7 10.8 - - - +
283B ARG* 1.3 78.4 - - - +
285B HIS* 1.3 58.8 + - - +
286B ALA 3.1 0.2 - - - -
287B LEU* 2.9 26.0 + - - +
288B GLU* 3.0 17.9 + - - +
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Residues in contact with HIS 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 ASN 3.5 13.9 + - - +
282B MET 4.1 3.8 - - - +
284B ALA* 1.3 78.8 - - - +
286B ALA* 1.3 59.9 + - - +
288B GLU* 3.6 25.7 + - + +
289B LYS* 3.2 40.3 + - + +
323B ILE* 3.5 30.2 + - + +
324B GLN* 5.1 4.5 - - + -
325B TRP* 4.4 24.1 + + - +
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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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282B MET 3.0 18.8 + - - +
283B ARG* 4.1 4.5 - - - +
284B ALA 3.0 0.6 + - - -
285B HIS* 1.3 75.9 - - - +
287B LEU* 1.3 61.2 + - - +
289B LYS* 3.3 5.9 + - - -
290B GLY 3.3 0.5 + - - -
291B PHE* 2.6 38.6 + - + +
293B ILE* 3.5 33.9 - - + +
323B ILE* 3.6 18.4 - - + -
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Residues in contact with LEU 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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283B ARG 3.4 12.5 + - - +
284B ALA* 2.9 11.0 + - - +
286B ALA* 1.3 76.6 - - - +
288B GLU* 1.3 64.5 + - - +
289B LYS 3.1 0.7 + - - -
290B GLY 3.3 8.5 + - - -
291B PHE 3.1 7.9 + - - +
292B THR* 3.2 34.8 - - + +
293B ILE 5.2 0.7 - - - +
301B LEU* 4.0 17.8 - - + +
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Residues in contact with GLU 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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284B ALA* 3.0 12.2 + - - +
285B HIS* 3.6 33.6 + - + +
286B ALA 3.2 0.2 - - - -
287B LEU* 1.3 77.9 - - - +
289B LYS* 1.3 69.0 + - + +
290B GLY 3.7 0.3 + - - -
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Residues in contact with LYS 289 (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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285B HIS* 3.2 40.7 + - + +
286B ALA* 3.3 4.4 + - - +
287B LEU 3.1 1.0 - - - -
288B GLU* 1.3 86.4 + - + +
290B GLY* 1.3 60.1 + - - +
291B PHE* 3.6 21.8 - - + -
322B TYR 5.7 0.7 - - - +
323B ILE* 4.4 12.3 - - - +
324B GLN* 4.8 11.0 - - + -
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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