Contacts of the helix formed by residues 266 - 279 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260D ALA 3.3 25.4 - - - -
261D MET* 3.4 19.2 - - - -
263D GLU 3.0 8.0 + - - -
264D GLU 3.3 0.8 + - - -
265D ASN* 1.3 73.4 - - - +
267D LEU* 1.3 60.3 + - - +
268D LYS 3.0 0.4 - - - -
269D TYR* 2.8 26.6 + - - +
270D ILE* 3.0 13.3 + - - +
333D LYS 3.1 2.4 + - - -
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Residues in contact with LEU 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D ASN* 4.6 1.1 - - - +
266D GLY* 1.3 77.5 - - - +
268D LYS* 1.3 62.0 + - - +
270D ILE* 3.9 29.8 - - + -
271D GLU* 2.8 46.0 + - - +
325D ILE* 4.4 23.1 - - + -
329D VAL* 4.5 5.8 - - + +
330D GLY* 4.3 12.1 - - - +
333D LYS* 3.0 45.7 + - + +
334D LYS* 3.9 1.0 - - - +
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Residues in contact with LYS 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D ASN* 3.0 19.3 + - + +
267D LEU* 1.3 78.7 - - - +
269D TYR* 1.3 86.8 + - + +
271D GLU* 3.4 10.6 + - - +
272D GLU* 3.2 47.4 + - - +
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Residues in contact with TYR 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D ALA* 3.8 38.1 - - + -
261D MET* 3.7 20.9 - - + +
264D GLU 5.8 1.1 - - - -
265D ASN 4.5 4.9 - - - -
266D GLY* 2.8 12.6 + - - +
268D LYS* 1.3 108.6 + - + +
270D ILE* 1.3 66.1 + - - +
271D GLU 3.3 0.2 - - - -
272D GLU* 3.3 23.0 + - - +
273D ALA* 2.9 24.6 + - - +
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Residues in contact with ILE 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D MET* 3.8 24.6 - - + +
266D GLY 3.0 12.5 + - - +
267D LEU* 3.5 31.9 - - + +
269D TYR* 1.3 75.0 - - - +
271D GLU* 1.3 63.5 + - - +
273D ALA* 3.1 4.9 + - - +
274D ILE* 3.0 36.4 + - + +
325D ILE* 4.5 6.1 - - + -
329D VAL* 3.5 30.3 - - + -
335D GLY 3.7 11.2 - - - +
336D TYR* 3.7 17.9 - - - +
337D PHE* 3.8 26.7 - - + -
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Residues in contact with GLU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D LEU* 2.8 45.6 + - + +
268D LYS* 3.7 9.8 - - - +
270D ILE* 1.3 72.9 - - - +
272D GLU* 1.3 57.9 + - + +
274D ILE* 3.4 9.1 + - + +
275D GLU* 2.9 30.1 + - - +
325D ILE* 5.0 12.6 - - + +
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Residues in contact with GLU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D LYS* 3.2 39.1 + - + +
269D TYR* 3.6 27.2 - - - +
270D ILE 3.3 0.2 - - - -
271D GLU* 1.3 77.8 - - + +
273D ALA* 1.3 63.3 + - - +
275D GLU* 3.4 8.7 + - - +
276D LYS* 3.0 43.4 + - - +
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D MET* 3.6 21.3 - - + -
269D TYR 2.9 16.9 + - - +
270D ILE 3.6 4.3 - - - +
272D GLU* 1.3 75.2 - - - +
274D ILE* 1.3 53.4 + - - +
276D LYS* 3.2 11.9 + - - +
277D LEU* 2.8 38.3 + - - +
337D PHE* 3.7 16.2 - - + -
359D CYS* 3.9 21.0 - - + +
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Residues in contact with ILE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ILE* 3.0 34.2 + - + +
271D GLU* 3.7 11.0 - - + +
273D ALA* 1.3 73.1 - - - +
275D GLU* 1.3 56.0 + - - +
277D LEU* 2.9 9.3 + - - +
278D SER* 2.7 34.5 + - - -
312D PHE* 4.1 14.1 - - + -
314D ALA* 3.7 27.1 - - + -
323D ILE* 4.0 27.4 - - + -
325D ILE* 4.1 20.6 - - + -
337D PHE* 4.4 11.0 - - + -
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D GLU 2.9 18.2 + - - +
272D GLU* 3.6 9.4 - - - +
274D ILE* 1.3 76.6 - - - +
276D LYS* 1.3 63.7 + - + +
278D SER* 2.4 28.7 + - - -
279D LYS* 3.1 37.4 + - - +
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Residues in contact with LYS 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D GLU* 3.0 32.4 + - - +
273D ALA* 3.4 7.5 - - - +
275D GLU* 1.3 77.7 - - + +
277D LEU* 1.3 63.7 + - - +
279D LYS* 3.3 19.3 + - + +
280D ARG* 3.8 6.2 + - - +
358D THR* 3.8 33.1 - - + +
359D CYS* 3.6 18.4 + - - +
362D ASN* 2.8 34.1 + - - +
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D ALA 2.8 19.8 + - - +
274D ILE* 2.9 9.6 + - - +
276D LYS* 1.3 73.3 - - - +
278D SER* 1.3 63.6 + - - +
280D ARG* 3.1 13.2 + - - -
281D HIS* 3.6 8.7 + - - -
284D HIS* 3.3 42.4 - - + +
312D PHE* 3.7 21.3 - - + -
323D ILE* 4.6 10.3 - - + -
337D PHE* 3.5 39.3 - - + -
341D ARG* 3.9 9.2 + - - +
355D LEU* 4.0 10.3 - - + -
358D THR* 4.2 4.0 - - + -
359D CYS* 3.7 13.9 - - - -
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Residues in contact with SER 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ILE* 2.7 12.4 + - - -
275D GLU* 2.4 37.4 + - - -
277D LEU* 1.3 74.7 - - - +
279D LYS* 1.3 63.8 + - - +
280D ARG 3.6 0.5 + - - -
281D HIS* 4.4 5.8 + - - +
312D PHE* 3.5 41.2 - - - +
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Residues in contact with LYS 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D GLU* 3.1 40.4 + - - +
276D LYS* 3.3 10.6 + - - +
277D LEU 3.1 1.0 - - - -
278D SER* 1.3 82.6 - - - +
280D ARG* 1.3 65.1 + - + +
281D HIS 3.7 1.7 + - - -
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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