Contacts of the helix formed by residues 262 - 279 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248P ILE* 4.5 15.9 - - + +
249P PHE* 5.3 7.2 + - - -
251P GLU 4.5 6.2 + - - +
253P TYR* 5.2 7.2 - - + +
260P MET 4.0 0.4 + - - -
261P TYR* 1.3 75.1 - - - +
263P SER* 1.3 58.7 + - - +
265P ILE* 3.3 6.2 + - - +
266P VAL* 2.9 30.5 + - - +
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Residues in contact with SER 263 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P ASP* 6.1 4.9 - - - -
261P TYR* 3.3 5.6 - - - +
262P LEU* 1.3 78.8 - - - +
264P ASN* 1.3 57.1 + - - +
266P VAL* 3.4 5.6 + - - +
267P SER* 2.9 30.4 + - - -
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Residues in contact with ASN 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260P MET* 4.5 14.1 - - + -
261P TYR* 3.4 15.6 + - + +
262P LEU 3.3 0.2 - - - -
263P SER* 1.3 76.0 - - - +
265P ILE* 1.3 60.9 + - - +
267P SER* 3.9 5.4 - - - -
268P ASP* 2.9 32.7 + - - +
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Residues in contact with ILE 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253P TYR* 6.1 4.7 - - + +
255P TYR* 5.3 11.9 - - + -
260P MET* 4.9 8.0 - - + +
261P TYR 3.0 16.8 + - - +
262P LEU* 3.7 7.0 - - - +
263P SER 3.3 0.2 - - - -
264P ASN* 1.3 77.1 - - - +
266P VAL* 1.3 57.9 + - - +
268P ASP* 4.4 2.6 - - - +
269P TYR* 2.9 32.4 + - - +
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Residues in contact with VAL 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187P MET* 5.8 7.9 - - + +
188P PHE* 5.8 7.9 - - + -
191P GLU* 4.7 8.2 - - + +
262P LEU 2.9 16.8 + - - +
263P SER* 3.8 6.1 - - - +
265P ILE* 1.3 75.4 - - - +
267P SER* 1.3 58.8 + - - +
269P TYR* 3.9 4.2 - - - +
270P THR* 2.9 31.7 + - - -
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Residues in contact with SER 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191P GLU* 5.0 8.5 - - - +
263P SER 2.9 18.3 + - - -
264P ASN* 3.9 5.6 - - - -
265P ILE 3.4 0.2 - - - -
266P VAL* 1.3 77.4 - - - +
268P ASP* 1.3 57.9 + - - +
270P THR* 3.8 4.6 - - - -
271P LYS* 2.9 28.8 + - - +
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Residues in contact with ASP 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264P ASN 2.9 17.9 + - - +
265P ILE* 4.4 2.9 - - - +
267P SER* 1.3 77.3 - - - +
269P TYR* 1.3 57.4 + - - +
271P LYS* 3.3 7.3 + - - +
272P LYS* 2.9 30.0 + - - +
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Residues in contact with TYR 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265P ILE 2.9 22.0 + - - +
266P VAL* 3.9 4.7 - - - +
268P ASP* 1.3 76.7 - - - +
270P THR* 1.3 56.1 + - - +
272P LYS* 3.4 6.4 + - - +
273P VAL* 2.9 28.8 + - - +
285P PRO* 4.7 15.1 - - + +
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Residues in contact with THR 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188P PHE 5.9 0.2 - - - -
191P GLU* 4.2 25.6 - - - -
192P VAL* 5.4 1.6 - - - -
195P CYS* 5.6 4.1 - - - +
218P ILE* 5.9 8.3 - - - -
266P VAL 2.9 18.8 + - - -
267P SER* 3.8 3.1 - - - -
269P TYR* 1.3 77.6 - - - +
271P LYS* 1.3 58.7 + - - +
273P VAL* 3.6 7.2 - - - +
274P ILE* 2.9 30.1 + - - +
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Residues in contact with LYS 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267P SER 2.9 17.6 + - - +
268P ASP* 3.6 9.2 - - - +
270P THR* 1.3 78.0 - - - +
272P LYS* 1.3 56.6 + - - +
274P ILE* 3.4 4.6 + - - +
275P LYS* 2.9 31.6 + - - +
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Residues in contact with LYS 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268P ASP 2.9 17.1 + - - +
269P TYR 3.8 3.8 - - - +
271P LYS* 1.3 75.7 - - - +
273P VAL* 1.3 58.7 + - - +
275P LYS* 3.9 6.0 - - - +
276P ALA* 2.9 30.0 + - - +
283P GLU 4.3 4.5 - - - +
285P PRO* 4.0 24.0 - - + -
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Residues in contact with VAL 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218P ILE* 6.0 6.1 - - + -
269P TYR 2.9 17.7 + - - +
270P THR* 3.6 7.9 - - - +
271P LYS 3.2 0.2 - - - -
272P LYS* 1.3 76.3 - - - +
274P ILE* 1.3 60.5 + - - +
276P ALA* 3.3 5.3 + - - +
277P LEU* 2.9 28.6 + - - +
285P PRO* 5.5 2.0 - - + +
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Residues in contact with ILE 274 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195P CYS* 4.7 19.3 - - + -
270P THR 2.9 17.0 + - - +
271P LYS* 4.0 4.3 - - - +
273P VAL* 1.3 76.5 - - - +
275P LYS* 1.3 58.0 + - - +
277P LEU* 3.2 7.5 + - - +
278P ASN* 2.9 30.5 + - - +
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Residues in contact with LYS 275 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271P LYS 2.9 18.8 + - - +
272P LYS* 4.0 6.1 - - - +
274P ILE* 1.3 76.9 - - - +
276P ALA* 1.3 57.4 + - - +
278P ASN* 3.9 4.7 - - - +
279P GLN* 2.9 33.1 + - - +
282P GLU* 6.1 0.4 - - - -
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Residues in contact with ALA 276 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272P LYS 2.9 20.1 + - - +
273P VAL* 3.7 6.3 - - - +
275P LYS* 1.3 77.8 - - - +
277P LEU* 1.3 57.2 + - - +
279P GLN* 4.8 0.4 - - - -
280P LEU* 3.0 7.3 + - - -
281P GLY* 2.6 39.4 + - - +
282P GLU* 4.4 7.2 - - - +
283P GLU 3.3 25.1 - - - +
284P ILE* 5.3 1.8 - - - -
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Residues in contact with LEU 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97P TRP* 5.7 8.5 - - + +
101P VAL* 5.1 11.2 - - + +
273P VAL 2.9 17.4 + - - +
274P ILE* 3.2 7.4 + - - +
276P ALA* 1.3 77.1 - - - +
278P ASN* 1.3 61.0 + - - +
280P LEU* 3.5 9.8 + - - +
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Residues in contact with ASN 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93P ARG* 5.3 14.4 - - + -
274P ILE 2.9 16.3 + - - +
275P LYS* 4.1 5.2 - - - +
277P LEU* 1.3 77.1 - - - +
279P GLN* 1.3 59.0 + - - +
280P LEU* 3.3 2.1 + - - +
282V GLU* 5.3 3.1 - - - +
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Residues in contact with GLN 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275P LYS 2.9 18.0 + - - +
276P ALA 4.5 0.4 - - - +
278P ASN* 1.3 74.8 - - - +
280P LEU* 1.3 71.1 - - - +
281P GLY 3.6 0.7 - - - -
282P GLU* 4.2 21.8 + - + +
279V GLN* 4.3 12.0 - - + +
282V GLU* 3.9 16.0 - - - +
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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