Contacts of the helix formed by residues 260 - 274 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ARG* 3.4 35.9 - - - +
258A GLY 4.7 3.6 - - - +
259A LEU* 1.3 77.3 - - - +
261A PRO* 1.3 66.7 - - + +
262A GLU* 3.0 8.8 + - + +
263A GLU* 3.1 28.7 + - + +
264A ASP* 2.8 30.9 + - - -
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Residues in contact with PRO 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LYS* 3.9 40.2 - - + +
254A MET* 4.3 14.1 - - + -
255A GLU* 3.7 22.7 - - + +
259A LEU* 3.5 11.4 - - - +
260A ILE* 1.3 82.9 - - + +
262A GLU* 1.3 67.4 + - + +
265A ILE* 3.1 49.4 + - + +
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LYS* 5.5 6.4 - - - -
260A ILE* 3.0 9.0 + - + +
261A PRO* 1.3 81.8 - - + +
263A GLU* 1.3 65.1 + - + +
265A ILE* 4.9 0.2 - - - +
266A CYS* 3.9 14.4 + - - +
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Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ARG* 2.9 30.2 + - - +
260A ILE* 3.1 24.0 + - + +
262A GLU* 1.3 82.4 - - + +
264A ASP* 1.3 61.1 + - - +
266A CYS* 3.5 8.3 - - - +
267A PHE* 3.2 23.4 + - - +
288A LYS 5.7 3.6 - - - +
289A GLY* 4.0 16.1 - - - +
290A ARG* 4.6 1.0 + - - -
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Residues in contact with ASP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ARG* 3.0 24.7 + - - -
198A CYS* 3.6 18.6 - - - -
254A MET* 4.5 3.8 - - + -
259A LEU* 3.4 16.5 - - + +
260A ILE 2.8 44.9 + - - +
263A GLU* 1.3 68.9 - - - +
265A ILE* 1.3 60.2 + - - +
266A CYS 3.1 1.3 - - - -
267A PHE* 3.1 6.5 + - - +
268A ILE* 2.8 33.8 + - + +
290A ARG* 3.0 26.9 + - - -
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A PHE* 4.1 16.2 - - + -
242A GLU* 4.3 7.4 - - - +
245A ILE* 4.1 20.0 - - + -
251A LYS* 3.9 29.2 - - + +
254A MET* 3.8 24.0 - - + -
261A PRO* 3.1 29.4 + - + +
262A GLU 4.9 0.4 - - - +
264A ASP* 1.3 75.8 - - - +
266A CYS* 1.3 60.5 + - - +
268A ILE* 3.9 6.7 - - - +
269A LYS* 3.2 47.3 + - + +
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Residues in contact with CYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A GLU 3.9 12.4 + - - +
263A GLU* 3.5 10.9 + - - +
264A ASP 3.1 0.6 - - - -
265A ILE* 1.3 78.3 - - - +
267A PHE* 1.3 52.1 + - - +
269A LYS* 3.2 7.8 + - - +
270A GLU* 2.8 66.0 + - - +
276A LEU* 4.3 13.6 - - + +
288A LYS* 4.1 11.9 - - - -
289A GLY* 3.8 11.9 - - - -
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Residues in contact with PHE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ASP 4.4 1.3 - - - -
198A CYS* 3.5 34.3 - - + -
199A VAL* 4.3 4.0 - - + -
263A GLU 3.2 5.6 + - - +
264A ASP 3.1 7.3 + - - +
266A CYS* 1.3 78.0 - - - +
268A ILE* 1.3 56.6 + - - +
270A GLU* 3.4 8.7 + - - +
271A GLN* 3.0 53.1 + - + +
289A GLY* 4.1 4.2 - - - +
290A ARG* 3.6 48.2 - - + +
297A LEU* 3.7 32.3 - - + -
298A TYR* 3.4 34.5 - + - -
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A CYS* 3.6 29.8 - - + +
201A ILE* 3.7 32.3 - - + +
202A ALA* 4.0 19.3 - - - +
241A PHE* 3.5 36.3 - - + -
254A MET* 4.4 11.4 - - + -
264A ASP 2.8 27.7 + - - +
265A ILE* 3.9 4.3 - - - +
267A PHE* 1.3 69.9 - - - +
269A LYS* 1.3 64.2 + - - +
271A GLN* 3.2 18.1 + - - +
272A ILE* 3.4 20.8 + - + +
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A VAL* 3.7 45.3 - - + +
241A PHE* 4.2 15.0 - - + -
242A GLU* 2.8 38.2 + - - +
265A ILE* 3.2 30.2 + - + +
266A CYS* 3.6 4.3 - - - +
268A ILE* 1.3 78.1 - - - +
270A GLU* 1.3 62.8 + - - +
272A ILE* 3.1 14.8 + - - +
273A VAL* 3.1 20.5 + - - +
276A LEU* 4.1 21.1 - - + -
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A CYS* 2.8 34.8 + - - +
267A PHE* 3.7 1.7 - - - +
269A LYS* 1.3 75.1 - - - +
271A GLN* 1.3 64.1 + - - +
274A GLY* 3.0 38.2 + - - +
276A LEU* 4.1 18.9 + - + +
286A PRO 4.5 1.7 - - - +
287A TYR* 3.6 23.0 + - + -
288A LYS* 2.9 22.7 + - - +
289A GLY* 2.9 14.9 + - - -
298A TYR* 2.7 41.6 + - + -
304A LYS* 5.3 0.2 - - - -
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Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A CYS 3.3 12.1 - - - +
199A VAL* 3.2 36.8 - - - +
202A ALA* 3.1 28.3 - - + +
267A PHE* 3.0 39.3 + - + +
268A ILE* 3.2 10.3 + - - +
270A GLU* 1.3 77.0 - - - +
272A ILE* 1.3 61.3 + - - +
274A GLY 4.8 0.3 + - - -
297A LEU 3.5 18.4 + - - +
298A TYR* 4.1 16.4 - - + +
301A VAL* 4.4 12.2 - - + +
302A SER* 3.6 27.9 + - - +
304A LYS* 5.1 0.9 - - - -
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA* 4.1 14.1 - - + +
205A CYS* 3.9 23.1 - - + +
206A HIS* 3.7 35.0 - - + +
234A GLU* 4.0 23.9 - - + +
237A SER* 3.9 20.2 - - - +
238A VAL* 4.4 5.8 - - + -
241A PHE* 5.3 4.7 - - + -
268A ILE* 3.4 27.6 - - + +
269A LYS* 3.1 11.1 + - - +
271A GLN* 1.3 80.7 - - - +
273A VAL* 1.3 61.8 + - + +
274A GLY 3.6 0.2 - - - -
301A VAL* 5.4 1.1 - - + -
302A SER* 3.8 9.2 + - - -
304A LYS* 3.7 10.7 + - - -
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.3 43.5 - - + +
235A GLN* 3.7 12.8 - - + +
238A VAL* 3.4 15.0 - - + -
269A LYS 3.1 14.3 + - - +
272A ILE* 1.3 76.1 - - - +
274A GLY* 1.3 68.1 + - - +
275A PRO 5.1 1.8 - - - +
276A LEU* 3.6 20.9 - - + -
304A LYS* 3.7 14.7 + - - +
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Residues in contact with GLY 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLU* 3.0 32.9 + - - +
272A ILE 3.6 1.4 - - - -
273A VAL* 1.3 85.6 - - - +
275A PRO* 1.3 74.2 - - - +
276A LEU 3.4 1.2 + - - -
287A TYR* 4.0 9.0 - - - -
304A LYS* 3.7 17.2 - - - +
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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