Contacts of the helix formed by residues 260 - 274 (chain B) in PDB entry 6TXA
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 ILE 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B ARG* 3.4 32.3 - - - +
258B GLY 4.6 3.8 - - - +
259B LEU* 1.3 78.1 - - - +
261B PRO* 1.3 67.1 - - + +
262B GLU* 3.0 9.7 + - + +
263B GLU* 3.1 24.2 + - + +
264B ASP* 2.8 33.1 + - - +
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Residues in contact with PRO 261 (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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251B LYS* 3.9 41.3 - - + +
254B MET* 4.3 13.5 - - + -
255B GLU* 3.7 22.9 - - + +
259B LEU 3.5 11.7 - - - +
260B ILE* 1.3 84.4 - - + +
262B GLU* 1.3 65.0 + - - +
265B ILE* 3.1 48.5 + - + +
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Residues in contact with GLU 262 (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 ILE* 3.0 10.3 + - + +
261B PRO* 1.3 81.1 - - - +
263B GLU* 1.3 64.6 + - + +
265B ILE* 4.9 0.3 - - - +
266B CYS* 3.9 14.6 + - - +
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Residues in contact with GLU 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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194B ARG* 2.9 30.4 + - - +
260B ILE* 3.1 22.1 + - + +
262B GLU* 1.3 82.9 - - + +
264B ASP* 1.3 59.2 + - - +
266B CYS* 3.5 7.6 - - - +
267B PHE* 3.2 23.3 + - - +
288B LYS 5.8 3.1 - - - +
289B GLY* 4.0 17.4 - - - +
290B ARG* 4.7 0.4 - - - -
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Residues in contact with ASP 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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194B ARG* 3.0 26.4 + - - -
198B CYS* 3.6 18.8 - - - -
254B MET* 4.6 3.4 - - + -
259B LEU* 3.4 16.7 - - + +
260B ILE 2.8 43.7 + - - +
263B GLU* 1.3 68.0 - - - +
265B ILE* 1.3 60.4 + - - +
266B CYS 3.1 1.8 - - - -
267B PHE* 3.1 6.6 + - - +
268B ILE* 2.8 34.5 + - + +
290B ARG* 3.0 27.4 + - - -
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Residues in contact with ILE 265 (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 PHE* 4.1 15.9 - - + -
242B GLU* 4.2 8.7 - - - +
245B ILE* 4.1 20.4 - - + -
251B LYS* 3.9 28.7 - - + +
254B MET* 3.8 22.7 - - + -
261B PRO* 3.1 30.5 + - + +
262B GLU 4.9 0.2 - - - +
264B ASP* 1.3 76.0 - - - +
266B CYS* 1.3 61.0 + - - +
268B ILE* 3.7 7.0 + - - +
269B LYS* 3.2 46.4 + - + +
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Residues in contact with CYS 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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262B GLU 3.9 12.0 + - - +
263B GLU* 3.5 10.9 + - - +
264B ASP 3.1 0.2 - - - -
265B ILE* 1.3 78.8 - - - +
267B PHE* 1.3 52.6 + - - +
269B LYS* 3.2 9.5 + - - +
270B GLU* 2.8 65.6 + - - +
276B LEU* 5.3 10.1 - - + -
288B LYS* 4.1 11.9 - - - -
289B GLY* 3.8 11.7 - - - -
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Residues in contact with PHE 267 (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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195B ASP 4.4 5.2 - - - -
198B CYS* 3.5 34.8 - - + -
199B VAL* 4.4 0.4 - - + -
263B GLU 3.2 7.3 + - - +
264B ASP 3.1 7.4 + - - +
266B CYS* 1.3 79.7 - - - +
268B ILE* 1.3 56.4 + - - +
270B GLU* 3.4 8.4 + - - +
271B GLN* 3.0 52.0 + - + +
289B GLY* 4.1 3.6 - - - +
290B ARG* 3.6 48.5 - - + +
297B LEU* 3.7 31.4 - - + -
298B TYR* 3.4 35.2 - + - -
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Residues in contact with ILE 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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198B CYS* 3.6 30.5 - - + +
201B ILE* 3.7 32.1 - - + +
202B ALA* 4.0 18.6 - - - +
241B PHE* 3.5 34.8 - - + -
254B MET* 4.4 12.1 - - + -
264B ASP 2.8 26.9 + - - +
265B ILE* 3.9 4.3 - - - +
267B PHE* 1.3 70.9 - - - +
269B LYS* 1.3 64.3 + - - +
271B GLN* 3.2 17.7 + - - +
272B ILE* 3.4 21.1 + - + +
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Residues in contact with LYS 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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238B VAL* 3.7 45.6 - - + +
241B PHE* 4.2 14.1 - - + -
242B GLU* 2.8 38.2 + - - +
265B ILE* 3.2 30.4 + - + +
266B CYS* 3.6 5.6 - - - +
268B ILE* 1.3 76.8 - - - +
270B GLU* 1.3 62.6 + - - +
272B ILE* 3.1 15.1 + - - +
273B VAL* 3.1 20.5 + - - +
276B LEU* 4.5 20.5 - - + +
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Residues in contact with GLU 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 CYS* 2.8 35.3 + - - +
267B PHE* 3.6 1.8 - - - +
269B LYS* 1.3 75.4 - - - +
271B GLN* 1.3 64.1 + - - +
273B VAL* 4.9 0.2 - - - -
274B GLY* 3.0 38.0 + - - +
276B LEU* 4.6 16.8 + - + +
286B PRO 4.5 1.9 - - - +
287B TYR* 3.6 21.3 + - + -
288B LYS* 2.9 23.7 + - - +
289B GLY* 2.9 15.2 + - - -
298B TYR* 2.7 40.8 + - + -
304B LYS* 5.3 0.3 - - - -
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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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198B CYS 3.3 13.2 - - - +
199B VAL* 3.2 37.0 - - - +
202B ALA* 3.1 28.2 - - + +
267B PHE* 3.0 41.5 + - + +
268B ILE* 3.2 9.7 + - - +
270B GLU* 1.3 76.8 - - - +
272B ILE* 1.3 61.4 + - - +
274B GLY 4.8 0.3 + - - -
297B LEU 3.5 17.5 + - - +
298B TYR* 4.1 15.7 - - + +
301B VAL* 4.4 11.9 - - + +
302B SER* 3.6 26.9 + - - +
304B LYS* 5.1 1.2 - - - -
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Residues in contact with ILE 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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202B ALA* 4.1 13.7 - - + +
205B CYS* 3.9 23.3 - - + +
206B HIS* 3.7 33.0 - - + +
234B GLU* 4.0 24.0 - - + +
237B SER* 3.9 20.2 - - - +
238B VAL* 4.4 5.4 - - + -
241B PHE* 5.3 4.9 - - + -
268B ILE* 3.5 28.3 - - + +
269B LYS* 3.1 10.2 + - - +
271B GLN* 1.3 82.2 - - - +
273B VAL* 1.3 60.9 + - + +
301B VAL* 5.4 1.1 - - + -
302B SER* 3.8 9.5 + - - -
304B LYS* 3.7 11.4 + - - -
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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
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234B GLU* 3.3 44.2 - - + +
235B GLN* 3.7 12.6 - - + +
238B VAL* 3.4 18.8 - - + -
269B LYS 3.1 13.2 + - - +
272B ILE* 1.3 75.3 - - + +
274B GLY* 1.3 68.8 + - - +
275B PRO 5.1 1.3 - - - +
276B LEU* 3.7 21.8 - - + -
304B LYS* 3.7 14.6 + - - +
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Residues in contact with GLY 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 GLU* 3.0 32.7 + - - +
272B ILE 3.6 0.8 - - - -
273B VAL* 1.3 85.9 - - - +
275B PRO* 1.3 76.8 - - - +
276B LEU* 3.4 1.7 + - - +
287B TYR* 4.0 7.6 - - - -
304B LYS* 3.7 17.8 - - - +
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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
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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