Contacts of the helix formed by residues 262 - 279 (chain V) in PDB entry 6QY3
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 LEU 262 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248V ILE* 4.5 16.2 - - + +
249V PHE* 5.3 7.6 + - - +
251V GLU 4.5 7.1 + - - +
253V TYR* 5.2 7.0 - - + +
260V MET 4.0 0.4 + - - -
261V TYR* 1.3 74.7 - - - +
263V SER* 1.3 57.5 + - - +
265V ILE* 3.3 6.2 + - - +
266V VAL* 2.9 30.8 + - - +
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Residues in contact with SER 263 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39V ASP* 6.1 5.4 - - - -
261V TYR* 3.3 5.4 - - - +
262V LEU* 1.3 79.8 - - - +
264V ASN* 1.3 56.4 + - - +
266V VAL* 3.4 4.9 + - - +
267V SER* 2.9 30.3 + - - -
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Residues in contact with ASN 264 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260V MET* 4.5 13.5 - - + -
261V TYR* 3.4 15.4 + - + +
262V LEU 3.3 0.6 - - - -
263V SER* 1.3 75.1 - - - +
265V ILE* 1.3 62.0 + - - +
267V SER* 3.9 5.0 - - - -
268V ASP* 2.9 32.4 + - - +
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Residues in contact with ILE 265 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253V TYR* 6.1 5.4 - - + +
255V TYR* 5.3 11.4 - - + -
260V MET* 4.9 7.8 - - + +
261V TYR 3.0 17.5 + - - +
262V LEU* 3.7 7.2 - - - +
263V SER 3.3 0.2 - - - -
264V ASN* 1.3 77.6 - - - +
266V VAL* 1.3 58.2 + - - +
268V ASP* 4.4 2.9 - - - +
269V TYR* 2.9 32.8 + - - +
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Residues in contact with VAL 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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187V MET* 5.8 7.9 - - + +
188V PHE* 5.8 8.1 - - + -
191V GLU* 4.7 8.0 - - + +
262V LEU 2.9 17.2 + - - +
263V SER* 3.8 6.1 - - - +
265V ILE* 1.3 76.1 - - - +
267V SER* 1.3 59.5 + - - +
269V TYR* 3.9 3.8 - - - +
270V THR* 2.9 31.2 + - - -
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Residues in contact with SER 267 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191V GLU* 5.0 8.7 - - - +
263V SER 2.9 18.7 + - - -
264V ASN* 3.9 6.1 - - - -
266V VAL* 1.3 78.0 - - - +
268V ASP* 1.3 57.6 + - - +
270V THR* 3.4 4.5 + - - -
271V LYS* 2.9 28.8 + - - +
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Residues in contact with ASP 268 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264V ASN 2.9 17.9 + - - +
265V ILE* 4.4 2.9 - - - +
267V SER* 1.3 77.1 - - - +
269V TYR* 1.3 57.4 + - - +
271V LYS* 3.6 6.5 - - - +
272V LYS* 2.9 30.1 + - - +
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Residues in contact with TYR 269 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265V ILE 2.9 22.2 + - - +
266V VAL* 3.9 4.7 - - - +
268V ASP* 1.3 77.6 - - - +
270V THR* 1.3 56.2 + - - +
272V LYS* 3.4 6.0 + - - +
273V VAL* 2.9 29.2 + - - +
285V PRO* 4.7 14.9 - - + +
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Residues in contact with THR 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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188V PHE 5.9 0.2 - - - -
191V GLU* 4.2 25.1 - - - -
192V VAL* 5.4 1.6 - - - -
218V ILE* 5.9 8.5 - - - -
266V VAL 2.9 19.4 + - - -
267V SER 3.8 2.9 - - - -
269V TYR* 1.3 76.0 - - - +
271V LYS* 1.3 57.2 + - - +
273V VAL* 3.3 7.5 + - - +
274V ILE* 2.9 30.7 + - - +
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Residues in contact with LYS 271 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267V SER 2.9 19.6 + - - +
268V ASP* 3.6 8.3 - - - +
269V TYR 3.2 0.2 - - - -
270V THR* 1.3 77.2 - - - +
272V LYS* 1.3 55.9 + - - +
274V ILE* 3.4 4.3 + - - +
275V LYS* 2.9 31.4 + - - +
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Residues in contact with LYS 272 (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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268V ASP 2.9 17.8 + - - +
269V TYR 3.8 3.6 - - - +
271V LYS* 1.3 76.1 - - - +
273V VAL* 1.3 57.9 + - - +
275V LYS* 4.0 5.3 - - - +
276V ALA* 2.9 30.3 + - - +
283V GLU 4.3 4.0 - - - +
285V PRO* 4.0 23.6 - - + -
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Residues in contact with VAL 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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218V ILE* 6.0 6.1 - - + -
269V TYR 2.9 18.4 + - - +
270V THR* 3.6 8.1 - - - +
271V LYS 3.2 0.2 - - - -
272V LYS* 1.3 74.8 - - - +
274V ILE* 1.3 60.5 + - - +
276V ALA* 3.3 6.0 + - - +
277V LEU* 2.9 28.6 + - - +
285V PRO* 5.5 1.8 - - + +
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Residues in contact with ILE 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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195V CYS* 4.7 18.6 - - + -
270V THR 2.9 16.8 + - - +
271V LYS* 4.0 4.7 - - - +
273V VAL* 1.3 75.8 - - - +
275V LYS* 1.3 58.8 + - - +
277V LEU* 3.2 7.0 + - - +
278V ASN* 2.9 30.1 + - - +
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Residues in contact with LYS 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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271V LYS 2.9 18.8 + - - +
272V LYS* 4.0 6.3 - - - +
274V ILE* 1.3 76.7 - - - +
276V ALA* 1.3 57.4 + - - +
278V ASN* 3.9 5.3 - - - +
279V GLN* 2.9 33.1 + - - +
282V GLU* 6.1 0.4 - - - -
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Residues in contact with ALA 276 (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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272V LYS 2.9 20.3 + - - +
273V VAL* 3.7 7.0 - - - +
275V LYS* 1.3 76.3 - - - +
277V LEU* 1.3 57.7 + - - +
279V GLN* 4.8 0.4 - - - -
280V LEU 3.0 6.9 + - - -
281V GLY* 2.6 38.6 + - - +
282V GLU* 4.4 7.2 - - - +
283V GLU 3.3 24.9 - - - +
284V ILE* 5.3 2.0 - - - -
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Residues in contact with LEU 277 (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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97V TRP* 5.7 5.5 - - - +
101V VAL* 5.1 11.6 - - + +
273V VAL 2.9 17.0 + - - +
274V ILE* 3.2 8.5 + - - +
276V ALA* 1.3 79.0 - - - +
278V ASN* 1.3 60.5 + - - +
280V LEU* 3.5 10.0 + - - +
281V GLY 5.0 0.2 - - - +
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Residues in contact with ASN 278 (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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93V ARG* 5.3 15.0 - - + -
274V ILE 2.9 16.1 + - - +
275V LYS* 4.1 5.4 - - - +
277V LEU* 1.3 77.9 - - - +
279V GLN* 1.3 59.3 + - - +
280V LEU* 3.3 2.2 + - - +
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Residues in contact with GLN 279 (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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279P GLN* 4.3 12.3 - - + +
280P LEU* 5.3 5.7 - - - +
282P GLU* 5.7 8.5 - - + -
275V LYS 2.9 19.5 + - - +
276V ALA 4.5 0.4 - - - +
278V ASN* 1.3 75.5 - - - +
280V LEU* 1.3 71.2 + - - +
281V GLY 3.6 0.2 - - - -
282V GLU* 4.2 22.1 + - + +
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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