Contacts of the helix formed by residues 266 - 279 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B ALA 3.3 25.4 - - - -
261B MET* 3.4 18.1 - - - -
263B GLU 3.0 9.0 + - - -
264B GLU 3.2 0.6 + - - -
265B ASN* 1.3 71.7 - - - +
267B LEU* 1.3 58.4 + - - +
268B LYS 3.1 2.2 - - - -
269B TYR* 2.9 12.8 + - - +
270B ILE* 2.9 29.1 + - - +
333B LYS 3.2 2.6 + - - -
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ASN* 4.7 0.9 - - - +
266B GLY* 1.3 73.8 - - - +
268B LYS* 1.3 67.1 + - - +
270B ILE* 4.0 22.9 - - + -
271B GLU* 2.9 48.0 + - - +
325B ILE* 4.3 26.0 - - + -
329B VAL* 4.5 6.3 - - + +
330B GLY* 4.3 13.0 - - - +
333B LYS* 3.2 47.8 + - + +
334B LYS* 3.9 0.4 - - - +
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASN* 3.1 18.7 + - + +
267B LEU* 1.3 79.0 - - - +
269B TYR* 1.3 83.5 + - + +
271B GLU* 3.4 8.8 + - - +
272B GLU* 3.0 46.9 + - + +
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Residues in contact with TYR 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ALA* 3.5 40.8 - - + -
261B MET* 3.8 21.1 - - + +
264B GLU 5.8 1.3 - - - -
265B ASN 4.5 4.7 - - - -
266B GLY* 2.9 12.3 + - - +
268B LYS* 1.3 97.4 + - + +
270B ILE* 1.3 67.2 + - - +
271B GLU 3.2 0.2 - - - -
272B GLU* 3.4 27.3 + - - +
273B ALA* 3.0 24.1 + - - +
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B MET* 3.7 23.8 - - + +
266B GLY 2.9 17.8 + - - +
267B LEU* 3.6 22.9 - - + +
269B TYR* 1.3 76.6 - - - +
271B GLU* 1.3 62.4 + - - +
273B ALA* 3.0 14.3 + - - +
274B ILE* 3.0 24.5 + - + +
325B ILE* 4.4 5.8 - - + -
329B VAL* 3.7 29.2 - - + -
335B GLY 3.9 9.6 - - - +
336B TYR 3.7 18.2 - - - +
337B PHE* 3.7 30.7 - - + -
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 2.9 46.5 + - + +
268B LYS* 3.7 6.7 - - - +
270B ILE* 1.3 75.9 - - - +
272B GLU* 1.3 64.0 + - - +
274B ILE* 3.4 8.8 + - + +
275B GLU* 3.1 23.3 + - - +
325B ILE* 4.9 12.4 - - + +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LYS* 3.0 41.5 + - + +
269B TYR* 3.6 32.7 - - - +
270B ILE 3.3 0.4 - - - -
271B GLU* 1.3 78.0 - - - +
273B ALA* 1.3 60.9 + - - +
275B GLU* 3.4 8.8 + - - +
276B LYS* 3.2 41.6 + - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B MET* 3.8 20.4 - - + -
269B TYR 3.0 12.5 + - - +
270B ILE 3.0 9.4 + - - +
272B GLU* 1.3 73.5 - - - +
274B ILE* 1.3 62.3 + - - +
276B LYS* 3.2 10.5 + - - +
277B LEU* 2.9 32.0 + - - +
337B PHE* 3.9 15.0 - - + -
359B CYS* 3.8 21.8 - - + +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.0 32.2 + - + +
271B GLU* 3.9 8.7 - - + +
273B ALA* 1.3 72.9 - - - +
275B GLU* 1.3 56.6 + - - +
277B LEU* 3.0 9.4 + - - +
278B SER* 2.7 33.9 + - - -
312B PHE* 3.8 13.9 - - + -
314B ALA* 3.9 25.4 - - + -
323B ILE* 3.8 28.9 - - + -
325B ILE* 3.9 19.5 - - + -
337B PHE* 4.3 12.1 - - + -
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B GLU 3.1 13.3 + - - +
272B GLU* 3.5 12.3 - - - +
273B ALA 3.3 0.2 - - - -
274B ILE* 1.3 77.3 - - - +
276B LYS* 1.3 64.0 + - + +
278B SER* 2.7 29.4 + - - -
279B LYS* 3.1 38.2 + - - +
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B GLU* 3.2 32.3 + - - +
273B ALA* 3.5 9.4 - - - +
275B GLU* 1.3 76.3 - - + +
277B LEU* 1.3 64.2 + - - +
279B LYS* 3.2 20.3 + - - +
280B ARG* 3.6 8.7 + - - +
358B THR* 3.6 32.5 - - + +
359B CYS* 3.6 15.9 + - - +
362B ASN* 2.6 39.8 + - + +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ALA 2.9 16.7 + - - +
274B ILE* 3.0 11.2 + - - +
276B LYS* 1.3 76.1 - - - +
278B SER* 1.3 63.3 + - - +
280B ARG* 3.1 13.3 + - - +
281B HIS* 3.6 8.8 + - - -
284B HIS* 3.3 38.4 - - + +
312B PHE* 3.6 21.6 - - + -
323B ILE* 4.7 10.3 - - + -
337B PHE* 3.5 38.1 - - + -
341B ARG* 4.4 6.6 + - - +
355B LEU* 4.1 8.7 - - + -
358B THR* 3.5 14.6 - - + -
359B CYS* 3.6 11.9 - - - -
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 2.7 12.7 + - - -
275B GLU* 2.7 30.8 + - - -
276B LYS 3.2 0.2 - - - -
277B LEU* 1.3 74.5 - - - +
279B LYS* 1.3 63.9 + - - +
280B ARG 3.7 0.3 + - - -
281B HIS* 4.5 5.7 + - - +
312B PHE* 3.6 40.6 - - - +
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLU* 3.1 41.6 + - + +
276B LYS* 3.2 9.8 + - - +
277B LEU 3.1 0.8 - - - -
278B SER* 1.3 81.6 - - - +
280B ARG* 1.3 64.1 + - + +
281B HIS 3.7 1.8 - - - -
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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