Contacts of the helix formed by residues 262 - 275 (chain B) in PDB entry 4OL0
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 ASN 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B GLY 4.7 4.5 - - - +
213B VAL* 3.8 23.2 + - - +
256B ILE* 5.3 2.0 - - - +
260B GLU* 4.4 6.0 + - - -
261B THR* 1.3 108.0 + - + +
263B LEU* 1.3 65.7 + - - +
264B PRO* 3.1 11.8 - - + +
265B LEU* 2.9 26.8 + - + +
266B ALA* 3.1 11.7 + - - +
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Residues in contact with LEU 263 (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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260B GLU* 4.4 14.0 + - - +
261B THR 4.2 1.0 - - - +
262B ASN* 1.3 71.8 - - - +
264B PRO* 1.4 75.5 - - + +
266B ALA* 4.0 10.3 - - + -
267B MET* 2.9 47.7 + - + +
318B LEU* 5.3 9.6 - - + -
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Residues in contact with PRO 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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221B ASN* 3.7 16.7 + - - +
262B ASN* 3.1 14.4 - - + +
263B LEU* 1.4 103.4 - - + +
265B LEU* 1.3 57.9 + - - +
267B MET* 3.9 14.7 - - + +
268B GLN* 3.6 16.5 + - - +
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 4.6 21.3 - - + -
212B GLY* 6.4 2.5 - - - -
214B LEU 6.3 2.2 - - - -
215B ASP 5.5 8.3 - - - -
221B ASN* 4.1 12.8 - - - +
225B LEU* 3.9 19.3 - - + -
256B ILE* 4.4 17.9 - - + -
261B THR* 6.1 2.7 - - + -
262B ASN* 2.9 21.1 + - + +
264B PRO* 1.3 77.8 - - - +
266B ALA* 1.3 66.4 + - - +
267B MET 3.2 0.2 - - - -
268B GLN* 2.9 3.6 + - - +
269B LEU* 2.9 44.5 + - + +
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Residues in contact with ALA 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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256B ILE* 4.2 20.3 - - + +
261B THR 6.1 0.7 - - - +
262B ASN 3.1 9.6 + - - +
263B LEU* 3.8 9.4 - - - +
265B LEU* 1.3 79.3 - - - +
267B MET* 1.3 52.0 + - - +
269B LEU* 3.4 2.5 + - - +
270B PHE* 2.7 35.7 + - - +
306B PHE* 3.8 29.9 - - + -
318B LEU* 4.0 17.0 - - + -
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Residues in contact with MET 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 2.9 48.6 + - + +
264B PRO* 3.9 12.1 - - + +
266B ALA* 1.3 77.2 - - - +
268B GLN* 1.3 64.4 + - - +
270B PHE* 3.1 7.2 + - - +
271B GLN* 2.9 52.0 + - - +
317B GLY* 6.5 1.3 - - - -
318B LEU* 4.5 11.2 - - + -
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Residues in contact with GLN 268 (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 ASN* 3.4 42.4 + - + +
225B LEU* 4.7 9.6 - - + -
229B PHE* 4.3 4.9 - - + -
264B PRO 3.6 6.3 + - - +
265B LEU 2.9 9.0 + - - +
267B MET* 1.3 87.2 - - - +
269B LEU* 1.3 57.1 + - - +
271B GLN* 3.6 15.3 + - - +
272B GLY* 2.8 26.9 + - - -
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Residues in contact with LEU 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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209B PHE* 5.7 0.4 - - + -
225B LEU* 4.0 15.7 - - + -
228B LEU* 5.8 2.0 - - + -
229B PHE* 3.6 26.9 - - + -
249B VAL* 5.0 9.4 - - + -
252B ALA* 3.9 27.6 - - + -
253B LEU* 3.9 21.1 - - + -
256B ILE* 3.3 33.0 - - + -
265B LEU* 2.9 26.0 + - + +
266B ALA* 3.8 4.3 - - - +
268B GLN* 1.3 73.2 - - - +
270B PHE* 1.3 60.7 + - - +
273B VAL* 2.8 37.6 + - + +
302B LEU* 4.7 1.3 - - - -
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Residues in contact with PHE 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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266B ALA 2.7 22.6 + - - +
267B MET* 3.1 10.3 + - - +
269B LEU* 1.3 75.3 - - - +
271B GLN* 1.3 63.5 + - + +
273B VAL* 3.1 3.5 + - - +
274B LEU* 2.9 56.4 + - + +
302B LEU* 3.8 12.1 - - + +
306B PHE* 3.5 30.0 - + - -
317B GLY 4.1 10.3 - - - -
318B LEU* 4.0 17.3 - - + -
320B ASP* 3.6 31.9 - - + -
322B ARG* 4.6 1.1 - - - -
323B THR* 3.4 35.9 - - + -
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Residues in contact with GLN 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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267B MET* 2.9 43.6 + - - +
268B GLN* 4.1 18.5 + - - +
270B PHE* 1.3 77.6 - - + +
272B GLY* 1.3 58.0 + - - +
274B LEU* 3.0 18.7 + - + +
275B THR* 2.8 37.6 + - + +
322B ARG* 5.9 1.6 - - - +
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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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229B PHE* 3.6 28.5 - - - -
233B GLN* 5.9 0.2 - - - -
268B GLN 2.8 19.5 + - - -
269B LEU 3.6 1.6 - - - -
271B GLN* 1.3 76.4 - - - +
273B VAL* 1.3 59.6 + - - +
275B THR* 2.5 27.0 + - - -
276B LEU* 3.6 8.0 - - - +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 3.7 9.8 - - + -
249B VAL* 4.2 7.4 - - + -
253B LEU* 4.5 5.4 - - + -
269B LEU 2.8 23.9 + - - +
270B PHE 3.6 3.4 - - - +
272B GLY* 1.3 72.6 - - - +
274B LEU* 1.3 62.9 + - - +
276B LEU* 3.0 27.0 + - - +
298B ILE* 3.7 24.9 - - + -
299B PHE* 3.4 35.1 - - + -
302B LEU* 3.7 33.7 - - + -
326B LEU* 4.6 1.5 - - + +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B PHE* 2.9 45.7 + - + +
271B GLN* 3.0 19.0 + - + +
273B VAL* 1.3 78.6 - - - +
275B THR* 1.3 61.0 + - + +
276B LEU 3.1 1.3 + - - -
277B GLU* 3.6 17.8 + - - +
302B LEU* 4.9 4.9 - - + -
322B ARG* 3.6 57.7 - - + +
326B LEU* 3.9 25.7 - - + +
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Residues in contact with THR 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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233B GLN* 3.1 35.8 + - - +
271B GLN* 2.8 21.1 + - + +
272B GLY* 2.5 23.9 + - - -
274B LEU* 1.3 75.6 - - + +
276B LEU* 1.3 60.5 + - - +
277B GLU* 3.3 1.8 + - - -
278B THR* 4.3 12.0 + - - -
279B ALA* 4.9 1.2 + - - +
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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