Contacts of the helix formed by residues 266 - 279 (chain A) in PDB entry 2QC8
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 GLY 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ALA 3.2 25.8 - - - -
261A MET* 3.3 18.1 - - - -
263A GLU 2.9 7.4 + - - -
265A ASN* 1.3 73.8 - - - +
267A LEU* 1.3 64.9 + - - +
268A LYS 3.0 2.7 - - - -
269A TYR* 2.9 18.1 + - - +
270A ILE* 3.0 14.4 + - - +
333A LYS 3.0 2.6 + - - -
334A LYS* 4.3 0.4 - - - -
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Residues in contact with LEU 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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265A ASN* 3.1 1.1 - - - -
266A GLY* 1.3 77.3 - - - +
268A LYS* 1.3 61.0 + - - +
270A ILE* 3.7 20.2 - - + -
271A GLU* 2.9 47.6 + - + +
325A ILE* 4.2 29.4 - - + -
329A VAL* 4.4 5.4 - - + +
330A GLY* 4.1 13.2 - - - +
333A LYS* 3.1 46.9 + - + +
334A LYS* 3.9 0.6 - - - +
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Residues in contact with LYS 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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265A ASN* 3.5 17.3 + - + +
267A LEU* 1.3 79.8 - - - +
269A TYR* 1.3 84.1 + - + +
271A GLU* 3.4 10.4 + - - +
272A GLU* 3.0 51.4 + - + +
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Residues in contact with TYR 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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258A THR* 5.3 0.2 - - - +
260A ALA* 3.7 39.5 - - + -
261A MET* 3.6 21.5 - - + +
264A GLU 5.9 0.7 - - - -
265A ASN 4.3 7.0 - - - -
266A GLY* 2.9 12.5 + - - +
268A LYS* 1.3 104.2 + - + +
270A ILE* 1.3 67.2 + - - +
271A GLU 3.2 0.4 - - - -
272A GLU* 3.3 24.0 + - - +
273A ALA* 2.9 23.6 + - - +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A MET* 3.8 24.7 - - + +
266A GLY 3.0 18.2 + - - +
267A LEU* 3.3 16.6 + - + +
269A TYR* 1.3 75.7 - - - +
271A GLU* 1.3 63.8 + - - +
273A ALA* 3.0 4.9 + - - +
274A ILE* 2.9 33.1 + - + +
325A ILE* 4.5 11.2 - - + -
329A VAL* 3.7 20.2 - - + -
335A GLY 3.8 8.3 - - - +
336A TYR 3.7 27.6 - - - +
337A PHE* 3.6 31.0 - - + -
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Residues in contact with GLU 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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267A LEU* 2.9 48.2 + - + +
268A LYS* 3.6 8.0 - - - +
270A ILE* 1.3 79.0 - - - +
272A GLU* 1.3 61.4 + - - +
274A ILE* 3.8 8.4 - - + +
275A GLU* 3.1 23.4 + - - +
325A ILE* 4.9 11.6 - - + +
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Residues in contact with GLU 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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268A LYS* 3.0 46.3 + - + +
269A TYR* 3.6 27.7 - - + +
270A ILE 3.2 0.4 - - - -
271A GLU* 1.3 77.5 - - - +
273A ALA* 1.3 61.6 + - - +
275A GLU* 3.4 9.3 - - - +
276A LYS* 3.3 43.5 + - - +
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Residues in contact with ALA 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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261A MET* 3.6 20.6 - - + -
269A TYR 2.9 13.8 + - - +
270A ILE 3.0 7.6 + - - +
272A GLU* 1.3 74.3 - - - +
274A ILE* 1.3 65.5 + - - +
276A LYS* 3.2 11.2 + - - +
277A LEU* 3.1 27.1 + - - +
337A PHE* 3.7 17.7 - - + -
359A CYS* 4.0 18.6 - - + +
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 2.9 37.4 + - + +
271A GLU* 3.8 9.2 - - + +
273A ALA* 1.3 71.9 - - - +
275A GLU* 1.3 67.0 + - - +
277A LEU* 3.2 9.4 + - - +
278A SER* 2.9 22.8 + - - -
312A PHE* 3.9 12.9 - - + -
314A ALA* 4.0 25.8 - - + -
323A ILE* 3.9 27.8 - - + -
325A ILE* 4.0 19.7 - - + -
337A PHE* 4.4 9.9 - - + -
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Residues in contact with GLU 275 (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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271A GLU 3.1 13.7 + - - +
272A GLU* 3.4 14.4 - - - +
274A ILE* 1.3 78.2 - - - +
276A LYS* 1.3 64.7 + - + +
278A SER* 2.6 28.4 + - - -
279A LYS* 2.9 39.5 + - - +
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Residues in contact with LYS 276 (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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272A GLU* 3.3 31.0 + - - +
273A ALA* 3.2 7.6 + - - +
275A GLU* 1.3 80.7 - - + +
277A LEU* 1.3 63.2 + - - +
279A LYS* 3.3 18.6 + - - +
280A ARG* 3.6 8.5 + - - +
358A THR* 3.8 31.2 - - + +
359A CYS* 3.5 17.6 + - - +
362A ASN* 2.9 35.6 + - - +
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Residues in contact with LEU 277 (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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273A ALA 3.1 16.5 + - - +
274A ILE* 3.2 11.6 + - - +
276A LYS* 1.3 71.5 - - - +
278A SER* 1.3 63.7 + - - +
279A LYS 3.0 2.9 - - - -
280A ARG* 3.0 13.8 + - - -
281A HIS* 3.3 9.7 + - - -
284A HIS* 3.4 38.4 - - + +
312A PHE* 3.8 17.9 - - + -
323A ILE* 4.5 9.2 - - + -
337A PHE* 3.6 37.2 - - + -
341A ARG* 4.2 12.0 + - - +
355A LEU* 4.1 8.5 - - + -
358A THR* 3.6 6.3 - - + -
359A CYS* 3.5 19.1 - - - -
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 2.9 9.3 + - - -
275A GLU* 2.6 31.1 + - - -
277A LEU* 1.3 74.4 - - - +
279A LYS* 1.3 63.3 + - - +
280A ARG 3.3 0.4 + - - -
281A HIS* 4.2 9.9 + - - +
312A PHE* 3.4 39.6 - - - +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLU* 2.9 40.9 + - - +
276A LYS* 3.3 9.8 + - - +
277A LEU 3.0 0.6 - - - -
278A SER* 1.3 83.1 - - - +
280A ARG* 1.3 62.8 + - + +
281A HIS 3.6 1.1 - - - -
364A THR* 6.1 7.0 - - + -
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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