Contacts of the helix formed by residues 262 - 279 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248O ILE 4.6 15.7 - - - +
249O PHE* 5.3 6.5 + - - +
251O GLU 4.6 6.5 + - - +
253O TYR* 5.2 8.8 - - + +
260O MET 4.0 0.4 + - - -
261O TYR* 1.3 74.1 - - - +
263O SER* 1.3 57.7 + - - +
265O ILE* 3.8 6.3 - - - +
266O VAL* 2.9 32.4 + - - +
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Residues in contact with SER 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187O MET* 6.4 1.3 - - - -
261O TYR* 3.2 6.1 - - - +
262O LEU* 1.3 79.9 - - - +
264O ASN* 1.3 57.2 + - - +
266O VAL* 3.5 4.1 + - - +
267O SER* 2.9 29.5 + - - -
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Residues in contact with ASN 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260O MET* 4.7 11.7 - - + -
261O TYR* 3.5 12.3 + - + +
262O LEU 3.4 0.4 - - - -
263O SER* 1.3 79.1 - - - +
265O ILE* 1.3 57.6 + - - +
267O SER* 3.3 7.3 + - - -
268O ASP* 2.9 30.0 + - - +
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Residues in contact with ILE 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253O TYR* 6.3 2.9 - - + -
255O TYR* 4.8 18.8 - - + +
260O MET* 5.0 5.1 - - + +
261O TYR 3.2 17.9 + - - +
262O LEU* 3.8 6.5 - - - +
263O SER 3.3 0.2 - - - -
264O ASN* 1.3 76.7 - - - +
266O VAL* 1.3 57.2 + - - +
268O ASP* 3.4 5.1 + - - +
269O TYR* 2.9 31.1 + - - +
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Residues in contact with VAL 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187O MET* 5.4 12.1 - - + +
188O PHE* 5.5 8.3 - - + +
191O GLU* 4.4 8.5 - - + +
262O LEU 2.9 17.8 + - - +
263O SER* 4.0 5.2 - - - +
265O ILE* 1.3 76.3 - - - +
267O SER* 1.3 58.1 + - - +
269O TYR* 3.9 5.3 - - - +
270O THR* 2.9 31.7 + - - -
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Residues in contact with SER 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191O GLU* 4.8 7.4 - - - +
263O SER 2.9 19.4 + - - -
264O ASN* 3.5 9.2 - - - -
266O VAL* 1.3 78.1 - - - +
268O ASP* 1.3 58.5 + - - +
270O THR* 3.4 5.0 + - - -
271O LYS* 2.9 30.6 + - - +
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Residues in contact with ASP 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264O ASN 2.9 16.9 + - - +
265O ILE* 4.0 4.5 - - - +
267O SER* 1.3 75.9 - - - +
269O TYR* 1.3 58.2 + - - +
271O LYS* 3.4 5.5 + - - +
272O LYS* 2.9 30.5 + - - +
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Residues in contact with TYR 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265O ILE 2.9 18.4 + - - +
266O VAL* 3.9 6.5 - - - +
268O ASP* 1.3 78.3 - - - +
270O THR* 1.3 57.0 + - - +
272O LYS* 3.4 2.4 + - - +
273O VAL* 2.9 30.1 + - - +
285O PRO* 4.3 19.5 - - + +
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Residues in contact with THR 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188O PHE* 5.6 0.7 - - - -
191O GLU* 3.9 27.6 - - - -
192O VAL* 5.0 3.1 - - - -
195O CYS* 5.5 4.2 - - - +
218O ILE* 6.2 5.8 - - - -
266O VAL 2.9 19.0 + - - -
267O SER* 3.8 3.1 - - - -
269O TYR* 1.3 77.3 - - - +
271O LYS* 1.3 56.5 + - - +
273O VAL* 3.2 6.8 + - - +
274O ILE* 2.9 31.2 + - - +
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Residues in contact with LYS 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195O CYS* 6.1 1.8 - - - -
267O SER 2.9 18.7 + - - +
268O ASP* 3.8 6.5 - - - +
270O THR* 1.3 77.4 - - - +
272O LYS* 1.3 57.5 + - - +
274O ILE* 3.4 4.6 + - - +
275O LYS* 2.9 32.8 + - - +
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Residues in contact with LYS 272 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268O ASP 2.9 18.5 + - - +
269O TYR 3.8 3.8 - - - +
271O LYS* 1.3 76.7 - - - +
273O VAL* 1.3 57.5 + - - +
275O LYS* 4.2 3.8 - - - +
276O ALA* 2.9 31.7 + - - +
283O GLU 4.2 4.2 - - - +
285O PRO* 3.8 24.0 - - + -
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Residues in contact with VAL 273 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O ILE* 5.9 7.0 - - + -
269O TYR 2.9 17.5 + - - +
270O THR* 3.2 7.8 + - - +
272O LYS* 1.3 74.6 - - - +
274O ILE* 1.3 59.0 + - - +
276O ALA* 3.4 4.8 + - - +
277O LEU* 2.9 29.8 + - - +
285O PRO* 5.2 3.3 - - + +
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Residues in contact with ILE 274 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195O CYS* 4.5 20.6 - - + -
197O CYS* 5.9 4.7 - - + -
270O THR 2.9 16.5 + - - +
271O LYS* 4.0 4.0 - - - +
273O VAL* 1.3 77.7 - - - +
275O LYS* 1.3 58.8 + - - +
277O LEU* 3.1 6.9 + - - +
278O ASN* 2.9 30.0 + - - +
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Residues in contact with LYS 275 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271O LYS 2.9 18.4 + - - +
272O LYS* 4.2 4.3 - - - +
274O ILE* 1.3 77.5 - - - +
276O ALA* 1.3 56.6 + - - +
278O ASN* 3.9 5.5 - - - +
279O GLN* 3.0 32.4 + - - +
282O GLU* 6.1 0.2 - - - -
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Residues in contact with ALA 276 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272O LYS 2.9 22.6 + - - +
273O VAL* 3.7 5.6 - - - +
274O ILE 3.2 0.2 - - - -
275O LYS* 1.3 77.2 - - - +
277O LEU* 1.3 57.4 + - - +
279O GLN* 4.8 0.9 - - - -
280O LEU 3.0 7.8 + - - -
281O GLY* 2.6 34.4 + - - +
282O GLU* 4.4 12.1 - - - +
283O GLU 3.2 25.1 - - - +
284O ILE* 5.3 1.6 - - - -
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Residues in contact with LEU 277 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O ARG 5.6 1.3 - - - +
97O TRP* 5.3 17.9 - - + +
101O VAL* 5.1 11.2 - - + +
273O VAL 2.9 17.2 + - - +
274O ILE* 3.1 6.7 + - - +
276O ALA* 1.3 79.0 - - - +
278O ASN* 1.3 60.9 + - - +
280O LEU* 3.5 9.8 + - - +
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Residues in contact with ASN 278 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O ARG* 4.6 23.5 - - + +
274O ILE 2.9 15.6 + - - +
275O LYS* 4.1 5.6 - - - +
277O LEU* 1.3 78.3 - - - +
279O GLN* 1.3 59.3 + - - +
280O LEU* 3.3 2.4 + - - +
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Residues in contact with GLN 279 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275O LYS 3.0 19.4 + - - +
276O ALA 4.4 1.1 - - - +
278O ASN* 1.3 75.1 - - - +
280O LEU* 1.3 71.2 + - - +
281O GLY 3.6 0.4 - - - -
282O GLU* 4.5 18.9 + - + +
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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