Contacts of the helix formed by residues 262 - 275 (chain V) in PDB entry 3MQT
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 262 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95V ARG* 3.4 13.2 - - - +
96V GLY* 3.0 33.7 + - - +
99V LEU* 3.9 13.0 - - - -
100V PHE* 4.0 17.0 - - + -
260V MET 4.3 6.1 - - - +
261V SER* 1.3 80.1 - - - +
263V THR* 1.3 77.1 + - - +
266V GLU* 3.2 19.7 + - - +
285V ARG* 3.5 20.9 - - + +
286V CYS* 3.8 4.5 - - - +
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Residues in contact with THR 263 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82V TYR* 4.8 0.2 - - - +
86V TYR* 4.2 7.9 - - + -
94V MET 3.3 26.2 - - - +
95V ARG* 3.7 9.0 + - - +
99V LEU* 3.6 23.1 - - + -
261V SER* 4.9 1.9 + - - -
262V THR* 1.3 84.6 + - - +
264V ARG* 1.3 64.8 + - - +
265V PHE* 3.3 26.9 + - - +
266V GLU 3.6 4.5 + - - -
267V ALA* 3.4 17.5 + - - +
281V SER* 5.3 0.3 + - - -
286V CYS* 2.9 18.4 + - - +
291V GLU* 3.3 11.9 - - - +
295V ILE* 4.0 7.2 - - - +
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Residues in contact with ARG 264 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300N GLU* 3.2 27.5 + - - +
82V TYR* 4.7 10.7 - - - -
83V ASN* 5.2 6.3 + - - -
86V TYR* 6.4 0.2 - - - -
263V THR* 1.3 72.0 - - - +
265V PHE* 1.3 98.1 + - + +
267V ALA* 3.8 1.4 - - - +
268V GLN* 2.9 34.5 + - - +
291V GLU* 2.7 36.9 + - - +
294V ARG* 3.1 55.7 - - + +
295V ILE* 3.7 25.1 - - + -
298V ILE* 4.1 15.6 - - + +
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Residues in contact with PHE 265 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M ASP* 3.5 44.4 - - + -
269M GLU* 5.6 0.5 - - - +
300N GLU* 5.6 1.3 - - + -
301N HIS* 6.1 2.5 - - - -
86V TYR* 3.7 13.9 - + - -
95V ARG* 3.4 29.2 - - - +
263V THR* 3.1 22.6 - - - +
264V ARG* 1.3 122.3 - - + +
266V GLU* 1.3 58.5 + - - +
268V GLN* 4.0 5.7 - - - +
269V GLU* 3.1 27.0 + - - +
291V GLU* 5.0 0.2 - - - -
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Residues in contact with GLU 266 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94M MET* 5.3 4.6 - - - +
95M ARG* 3.5 30.6 + - - +
266M GLU* 4.5 1.2 - - - +
95V ARG* 3.3 30.3 + - - +
238V HIS* 5.4 0.7 - - - -
261V SER* 3.2 30.9 - - - -
262V THR* 3.2 25.1 + - - +
263V THR* 3.5 2.2 + - - -
265V PHE* 1.3 76.3 - - - +
267V ALA* 1.3 64.0 + - - +
269V GLU* 3.1 18.5 + - - +
270V TRP* 3.0 32.7 + - + +
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Residues in contact with ALA 267 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258V ALA* 4.9 5.6 - - - -
261V SER* 4.7 2.1 + - - +
263V THR 3.4 12.4 + - - +
264V ARG 3.8 6.3 - - - +
266V GLU* 1.3 76.3 - - - +
268V GLN* 1.3 62.2 + - - +
270V TRP* 3.4 10.3 + - - +
271V LEU* 3.1 30.4 + - + +
279V VAL* 4.4 8.1 - - + +
281V SER* 4.1 11.4 - - - +
295V ILE* 4.1 31.2 - - + -
298V ILE* 6.0 1.8 - - + -
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Residues in contact with GLN 268 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301N HIS* 3.3 42.6 + - + +
264V ARG* 2.9 19.2 + - - +
265V PHE* 4.0 6.6 - - - +
267V ALA* 1.3 74.2 - - - +
269V GLU* 1.3 63.2 + - - +
271V LEU* 3.3 6.5 + - - +
272V GLU* 3.0 52.0 + - + +
298V ILE* 3.5 40.7 - - + +
302V HIS* 5.2 3.1 - - + -
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Residues in contact with GLU 269 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95M ARG* 5.9 1.0 + - - -
265M PHE 5.3 2.1 - - - +
269M GLU* 3.8 40.5 - - + +
241V LEU* 3.4 27.7 - - + +
265V PHE 3.1 15.6 + - - +
266V GLU* 3.1 21.4 + - - +
268V GLN* 1.3 72.9 - - - +
270V TRP* 1.3 65.6 + - - +
272V GLU* 3.3 8.6 + - - +
273V LYS* 2.9 40.6 + - + +
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Residues in contact with TRP 270 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238V HIS* 3.0 48.2 + + - -
241V LEU* 3.7 23.1 - - + +
244V HIS* 3.6 47.3 - + + -
257V GLY* 3.8 9.0 - - - -
258V ALA* 3.6 38.7 - - + +
261V SER* 4.4 4.5 - - - -
266V GLU* 3.0 33.3 + - + +
267V ALA 3.5 9.0 - - - +
269V GLU* 1.3 73.1 - - + +
271V LEU* 1.3 58.5 + - - +
274V THR* 2.6 53.7 + - + -
276V ILE* 3.7 25.8 - - + -
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Residues in contact with LEU 271 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246K LYS* 5.7 0.2 + - - -
267V ALA* 3.1 19.3 + - + +
268V GLN 3.6 4.5 - - - +
269V GLU 3.3 0.2 - - - -
270V TRP* 1.3 79.1 - - - +
272V GLU* 1.3 62.1 + - - +
275V GLY* 3.2 21.2 + - - -
276V ILE* 3.7 26.7 - - + +
279V VAL* 3.4 32.5 - - + -
295V ILE* 5.4 0.7 - - + +
298V ILE* 3.9 25.4 - - + +
299V CYS* 4.0 17.9 - - - -
302V HIS* 3.9 33.7 - - + +
304V ALA* 3.7 11.0 - - + -
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Residues in contact with GLU 272 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273M LYS* 4.6 14.6 + - - -
301N HIS* 4.5 5.4 + - - -
268V GLN* 3.0 49.3 + - + +
269V GLU* 4.0 5.2 - - - +
271V LEU* 1.3 78.0 - - - +
273V LYS* 1.3 62.3 + - + +
275V GLY 4.7 1.0 + - - -
302V HIS* 3.9 24.4 - - + +
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Residues in contact with LYS 273 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272M GLU* 4.8 9.7 + - - +
241V LEU* 4.4 27.6 - - + +
242V ILE* 4.3 20.3 - - + +
245V GLN* 3.0 21.3 - - + +
269V GLU* 2.9 25.9 + - + +
272V GLU* 1.3 78.9 - - + +
274V THR* 1.3 64.5 + - + +
301W HIS* 4.3 22.4 + - - -
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Residues in contact with THR 274 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241V LEU* 3.3 46.0 - - + +
244V HIS* 4.0 11.4 - - + -
245V GLN* 3.4 29.1 - - - +
248V ALA* 3.7 10.6 - - - +
270V TRP* 2.6 28.7 + - + +
273V LYS* 1.3 82.8 - - + +
275V GLY* 1.3 61.7 + - - +
276V ILE* 3.1 24.2 + - - +
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Residues in contact with GLY 275 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214K TRP* 5.9 1.4 - - - -
246K LYS* 4.9 20.5 + - - -
248V ALA* 4.4 8.7 - - - +
271V LEU 3.2 18.1 + - - -
272V GLU 4.7 1.2 + - - -
273V LYS 3.9 0.4 - - - -
274V THR* 1.3 78.1 + - - +
276V ILE* 1.3 68.4 + - - +
277V SER* 3.4 8.1 + - - -
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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