Contacts of the helix formed by residues 267 - 284 (chain B) in PDB entry 4OSV
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 GLY 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ILE 2.7 14.4 + - - -
266B ARG* 1.3 76.0 - - - +
268B GLY* 1.3 63.8 + - - +
270B THR* 4.0 7.6 - - - -
271B ALA* 3.4 28.0 + - - +
298B ALA 3.7 1.8 - - - -
300B HIS 3.1 22.3 + - - +
301B ASP* 4.7 0.9 - - - -
302B GLY 5.0 0.4 - - - -
303B GLY 4.7 1.5 + - - -
-1G G 5.7 0.7 - - - +
0G T 4.3 8.7 + - - -
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Residues in contact with GLY 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE 3.1 6.7 + - - -
264B ALA* 3.2 23.6 + - - -
266B ARG 3.2 5.3 - - - -
267B GLY* 1.3 77.3 - - - +
269B VAL* 1.3 66.0 + - - -
270B THR* 3.1 3.4 - - - -
271B ALA* 3.3 6.2 + - - +
272B VAL* 3.3 15.6 + - - +
-1G G 6.0 1.1 - - - -
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ALA* 3.8 38.4 - - + +
240B ALA* 4.5 0.2 - - + -
241B LEU* 3.8 28.5 - - + +
264B ALA* 4.8 2.0 - - - +
268B GLY* 1.3 72.2 - - - -
270B THR* 1.3 63.2 + - - +
272B VAL* 3.1 8.5 + - - +
273B GLU* 2.9 54.7 + - + +
-1G G 4.7 11.5 + - - +
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Residues in contact with THR 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLY 4.0 8.3 - - - -
268B GLY 4.8 0.2 - - - -
269B VAL* 1.3 81.3 - - - +
271B ALA* 1.3 57.8 + - - +
273B GLU* 3.3 13.2 + - - +
274B ALA* 3.0 25.3 + - - +
304B LYS* 3.6 33.6 - - + +
-1G G 4.0 27.0 + - - +
0G T 3.8 17.7 - - - +
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE* 3.7 7.9 - - + -
267B GLY* 3.4 23.3 + - - +
268B GLY 3.3 2.2 + - - -
270B THR* 1.3 75.9 - - - +
272B VAL* 1.3 61.8 + - - +
274B ALA* 3.1 8.1 + - - +
275B VAL* 2.8 35.8 + - - +
298B ALA* 3.4 28.7 - - + +
303B GLY* 4.5 0.4 - - - -
304B LYS* 4.2 15.9 - - - +
307B LEU* 4.2 0.2 - - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 3.6 33.7 - - + -
244B VAL* 3.6 22.3 - - + +
248B LEU* 4.3 3.8 - - + -
260B LEU* 4.1 25.8 - - + +
263B ILE* 3.6 25.4 - - + -
264B ALA* 4.3 2.5 - - - +
268B GLY 3.4 15.5 - - - +
269B VAL* 3.1 6.8 + - + +
271B ALA* 1.3 75.6 - - - +
273B GLU* 1.3 58.0 + - - +
275B VAL* 3.3 8.1 + - - +
276B HIS* 3.0 26.0 + - - +
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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
----------------------------------------------------------
240B ALA* 3.3 29.1 - - - +
244B VAL* 4.0 19.9 - - + +
269B VAL* 2.9 33.8 + - + +
270B THR* 3.7 13.2 + - - +
272B VAL* 1.3 74.6 - - - +
274B ALA* 1.3 59.8 + - - +
276B HIS* 3.7 7.8 + - - +
277B ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 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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270B THR 3.0 8.9 + - - +
271B ALA 3.1 7.8 + - - +
273B GLU* 1.3 73.9 - - - +
275B VAL* 1.3 66.8 + - - +
277B ALA* 3.2 4.5 + - - +
278B TRP* 3.0 49.6 + - + +
304B LYS* 3.6 41.1 - - + +
307B LEU* 4.0 4.7 - - + -
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 4.4 5.8 - - + -
253B LEU* 3.5 26.2 - - + -
255B LEU* 4.1 18.6 - - + -
263B ILE* 4.3 9.0 - - + -
271B ALA 2.8 19.2 + - - +
272B VAL* 3.4 9.0 - - - +
274B ALA* 1.3 76.7 - - - +
276B HIS* 1.3 62.2 + - - +
278B TRP 3.8 0.5 - - - -
279B ARG* 3.0 25.6 + - - +
282B LEU* 4.8 4.8 - - - +
294B VAL* 4.2 11.4 - - + -
298B ALA* 3.4 29.2 - - + -
307B LEU* 3.6 10.3 - - + -
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 3.5 36.5 - - + +
247B GLU* 3.3 39.3 + - + -
248B LEU* 4.0 16.6 - - + +
272B VAL 3.0 8.4 + - - +
273B GLU* 3.7 6.5 + - - +
275B VAL* 1.3 76.7 - - - +
277B ALA* 1.3 65.5 + - - +
279B ARG* 3.1 57.6 + - - +
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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 GLU 2.9 19.6 + - - +
274B ALA* 3.6 7.6 - - - +
276B HIS* 1.3 82.1 + - - +
278B TRP* 1.3 78.2 + - + +
279B ARG* 4.0 1.2 + - - +
280B ASN 5.5 0.2 + - - -
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Residues in contact with TRP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ALA* 3.0 33.8 + - + +
275B VAL 3.8 1.1 - - - -
277B ALA* 1.3 93.0 - - + +
279B ARG* 1.3 65.3 + - - +
280B ASN 3.2 2.8 + - - -
281B ALA* 3.2 9.1 + - + +
282B LEU* 3.0 29.5 + - + +
304B LYS* 3.5 42.6 - - + -
307B LEU* 3.9 11.4 - - + -
308B GLU* 3.5 35.7 - - + -
311B GLN* 3.3 33.0 - - - +
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLU* 3.5 28.3 + - - -
248B LEU* 4.3 8.5 - - + +
251B PRO 4.5 4.6 + - - -
252B PRO* 3.6 27.8 - - - +
253B LEU* 3.5 29.0 + - + +
275B VAL 3.0 14.0 + - - +
276B HIS* 3.1 61.4 + - - +
277B ALA 3.6 1.4 + - - +
278B TRP* 1.3 76.6 - - - +
280B ASN* 1.3 71.0 + - - +
282B LEU* 4.0 4.6 - - - +
283B THR* 2.5 39.4 + - - +
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Residues in contact with ASN 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO* 3.4 28.5 - - - +
277B ALA 5.5 0.2 + - - -
278B TRP 3.3 0.8 - - - -
279B ARG* 1.3 93.9 + - - +
281B ALA* 1.3 53.1 + - - +
283B THR* 3.1 4.1 + - - -
284B GLY* 2.6 36.7 + - - -
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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
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278B TRP* 3.2 10.7 + - + +
280B ASN* 1.3 77.3 - - - +
282B LEU* 1.3 64.2 + - - +
284B GLY* 3.2 18.4 - - - +
285B ALA 4.9 2.3 - - - +
287B LEU* 3.5 15.2 - - + +
311B GLN* 3.5 19.5 - - - +
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 4.8 7.2 - - - +
278B TRP* 3.0 38.3 + - + +
279B ARG* 4.0 5.6 - - - +
281B ALA* 1.3 75.6 - - - +
283B THR* 1.3 58.3 + - + +
287B LEU* 3.5 7.6 - - + +
288B ASN 3.4 6.9 + - - -
289B LEU* 3.0 44.0 + - + +
294B VAL* 3.9 28.0 - - + -
307B LEU* 4.1 30.3 - - + +
310B VAL* 4.3 5.8 - - + -
311B GLN* 3.5 30.3 - - + +
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Residues in contact with THR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO* 3.2 31.9 - - + +
253B LEU* 3.6 29.8 - - + -
279B ARG 2.5 24.1 + - - +
280B ASN* 3.1 6.4 + - - -
282B LEU* 1.3 76.2 - - - +
284B GLY* 1.3 61.8 + - - +
288B ASN* 3.5 16.1 - - - +
289B LEU 3.7 18.9 - - - +
291B PRO* 5.1 2.7 - - + -
294B VAL* 4.7 4.0 - - + -
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Residues in contact with GLY 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ASN 2.6 21.8 + - - -
281B ALA* 3.2 9.9 + - - +
283B THR* 1.3 71.4 + - - +
285B ALA* 1.3 67.9 + - - +
287B LEU 3.1 3.1 + - - -
288B ASN* 3.0 22.8 + - - -
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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