Contacts of the helix formed by residues 268 - 279 (chain B) in PDB entry 6O81
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 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PHE* 6.3 4.3 - - + -
130B SER* 4.4 3.1 - - - +
131B LEU* 4.5 13.2 - - + +
132B GLY 4.8 0.2 - - - +
152B TYR* 4.7 13.0 - - - +
260B PHE* 3.4 10.9 - - - -
267B GLN* 1.3 93.1 - - + +
269B ARG* 1.3 63.3 + - - +
270B ASP* 3.6 19.6 + - - -
271B ASP* 2.8 21.2 + - - +
272B PHE* 3.3 14.2 - - - +
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Residues in contact with ARG 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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131B LEU* 4.5 15.8 - - + +
150B LEU* 4.4 16.4 - - + -
152B TYR* 5.2 8.2 + - + +
181B MET* 5.0 6.7 - - + -
183B MET* 3.4 30.9 - - - +
215B PHE* 4.8 7.5 - - - -
217B LYS* 5.9 0.4 - - - +
246B ASP* 2.4 38.3 + - - -
248B HIS* 3.3 39.7 + - + +
250B SER* 3.8 30.6 - - - +
260B PHE* 5.0 1.3 - - + -
268B THR* 1.3 80.0 - - - +
270B ASP* 1.3 60.3 + - + +
272B PHE* 3.2 11.0 + - + +
273B VAL* 2.9 40.5 + - + +
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Residues in contact with ASP 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 3.7 28.6 - - + -
217B LYS* 3.6 26.1 - - + +
248B HIS* 6.5 1.1 - - + -
268B THR* 3.7 12.9 + - - -
269B ARG* 1.3 81.6 - - + +
271B ASP* 1.3 75.4 + - - +
273B VAL* 3.3 2.8 + - - +
274B ARG* 2.9 53.8 + - - +
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP 4.1 4.5 - - - +
266B TYR* 3.9 10.9 - - + -
267B GLN* 3.0 31.8 + - - +
268B THR* 2.8 33.6 + - - +
270B ASP* 1.3 79.8 + - - +
272B PHE* 1.3 58.6 + - - -
274B ARG* 3.4 28.2 + - - +
275B GLY* 2.9 25.5 + - - -
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Residues in contact with PHE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B MET* 3.7 32.1 - - + -
256B VAL* 4.0 20.9 - - + -
259B LEU* 4.1 28.5 - - + -
260B PHE* 3.6 26.9 - + + -
266B TYR* 3.5 32.4 - + + -
268B THR 3.3 18.4 - - - +
269B ARG* 3.2 10.9 + - + +
271B ASP* 1.3 83.4 + - - +
273B VAL* 1.3 65.5 + - + +
275B GLY* 3.4 0.9 + - - -
276B LEU* 2.9 48.5 + - + +
287B ILE* 4.9 0.9 - - + -
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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
----------------------------------------------------------
181B MET* 4.4 6.7 - - - -
183B MET* 4.3 21.8 - - + -
212B VAL* 5.4 1.1 - - + -
215B PHE* 3.7 26.9 - - + -
269B ARG* 2.9 27.7 + - + +
270B ASP* 3.3 4.9 + - - +
272B PHE* 1.3 88.1 - - + +
274B ARG* 1.3 57.9 + - - +
276B LEU* 3.3 0.9 + - - +
277B LEU* 2.9 46.0 + - + +
287B ILE* 3.9 26.5 - - + -
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Residues in contact with ARG 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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214B HIS* 6.4 0.4 - - + -
215B PHE* 3.5 29.1 - - + +
216B GLN* 5.0 9.2 - - - +
217B LYS 6.0 0.2 - - - +
270B ASP* 2.9 44.6 + - - +
271B ASP* 3.4 22.2 + - - +
273B VAL* 1.3 76.3 - - - +
275B GLY* 1.3 58.5 + - - +
277B LEU* 4.0 5.5 + - + +
278B VAL* 3.3 30.7 + - - +
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Residues in contact with GLY 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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266B TYR* 3.2 24.9 + - - -
271B ASP 2.9 16.2 + - - -
272B PHE 3.9 0.2 - - - -
274B ARG* 1.3 77.2 - - - +
276B LEU* 1.3 58.4 + - - +
277B LEU 3.3 0.7 - - - -
278B VAL* 3.4 8.8 - - - +
279B ASN* 3.1 30.7 + - - +
446S ARG* 5.7 0.2 - - - -
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Residues in contact with LEU 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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180B VAL* 4.3 5.6 - - + -
259B LEU* 4.4 5.4 - - + -
266B TYR* 3.8 4.4 + - + +
272B PHE* 2.9 41.5 + - + +
273B VAL* 3.9 4.9 - - - +
275B GLY* 1.3 75.9 - - - +
277B LEU* 1.3 64.1 + - + +
279B ASN* 3.4 19.1 - - - +
280B GLU* 4.1 5.5 - - - +
283B LEU* 3.5 39.9 - - + +
284B GLY 3.6 8.1 - - - +
285B ASN* 3.6 29.4 - - + +
287B ILE* 3.8 22.9 - - + -
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Residues in contact with LEU 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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212B VAL* 3.4 31.4 - - + +
213B LEU* 3.4 25.7 - - - +
214B HIS* 3.8 5.6 - - - +
215B PHE* 3.8 27.1 - - + +
230B LEU* 5.7 3.3 - - - +
273B VAL* 2.9 39.2 + - + +
274B ARG* 4.4 6.1 - - - +
275B GLY 3.3 0.2 - - - -
276B LEU* 1.3 79.1 - - + +
278B VAL* 1.3 60.9 + - + +
280B GLU* 3.3 28.8 - - - +
286B GLN* 6.4 0.4 - - - -
287B ILE* 5.1 12.1 - - + +
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B HIS* 6.0 6.5 - - + +
274B ARG 3.3 21.5 + - - +
275B GLY* 3.4 12.6 - - - +
277B LEU* 1.3 80.4 - - + +
279B ASN* 1.3 63.8 + - + +
280B GLU* 3.4 6.3 + - - +
281B GLU* 4.2 10.6 - - - +
449S LYS* 4.8 16.8 - - + +
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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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266B TYR* 5.1 2.9 - - - +
275B GLY 3.1 18.5 + - - +
276B LEU* 3.4 13.9 + - - +
277B LEU 3.5 0.2 - - - -
278B VAL* 1.3 75.0 - - - +
280B GLU* 1.3 58.6 + - - +
281B GLU* 3.6 7.6 - - - +
282B ILE* 3.0 28.6 - - + +
283B LEU* 3.5 15.3 - - + +
446S ARG* 6.6 0.4 - - - -
449S LYS* 4.8 16.2 - - + +
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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