Contacts of the helix formed by residues 262 - 276 (chain A) in PDB entry 1QO0
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 THR 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ILE* 3.6 18.0 - - + +
261A ASP* 1.3 82.1 - - - +
263A PRO* 1.3 71.2 - - + +
264A ALA* 3.8 3.8 + - - +
265A SER* 3.1 22.9 + - - -
266A ARG* 2.9 30.9 + - - +
323A PRO 4.1 4.9 + - - -
341A ARG* 5.4 4.0 - - - +
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Residues in contact with PRO 263 (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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262A THR* 1.3 90.2 - - - +
264A ALA* 1.3 56.6 + - - +
266A ARG* 3.4 6.8 + - + +
267A ALA* 2.9 28.8 + - - +
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Residues in contact with ALA 264 (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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262A THR* 3.3 3.9 + - - +
263A PRO* 1.3 76.9 - - - +
265A SER* 1.3 66.0 + - - +
267A ALA* 3.5 5.8 + - - +
268A PHE* 3.1 22.0 + - - +
321A ASP* 5.2 7.4 - - + +
322A ALA 3.8 24.2 - - - +
323A PRO* 3.9 10.3 - - + +
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Residues in contact with SER 265 (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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256A TYR* 3.0 25.4 + - - -
260A ILE* 2.9 38.9 + - - +
262A THR* 3.1 21.0 + - - -
264A ALA* 1.3 77.5 - - - +
266A ARG* 1.3 60.4 + - - +
268A PHE* 3.3 1.0 + - - +
269A VAL* 3.0 28.9 + - - +
323A PRO* 3.8 14.3 + - - -
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Residues in contact with ARG 266 (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 SER 3.1 20.8 + - - -
259A SER* 3.8 5.7 + - - +
260A ILE 2.6 37.9 + - - -
261A ASP* 3.9 20.8 - - - +
262A THR 2.9 21.7 + - - +
263A PRO* 4.0 5.6 - - + +
265A SER* 1.3 75.3 + - - +
267A ALA* 1.3 67.3 + - - +
269A VAL* 3.4 25.7 + - - +
270A GLN* 3.0 40.0 + - - +
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Residues in contact with ALA 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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263A PRO 2.9 17.9 + - - +
264A ALA* 3.9 7.2 - - - +
265A SER 3.3 0.2 - - - -
266A ARG* 1.3 79.0 - - - +
268A PHE* 1.3 56.5 + - - +
270A GLN* 3.4 6.7 + - - +
271A ALA* 2.9 28.8 + - - +
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Residues in contact with PHE 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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30A GLY* 5.3 1.1 - - - -
33A LEU* 4.2 7.2 - - + -
256A TYR* 3.6 23.3 - + - -
264A ALA 3.1 6.8 + - - +
265A SER 3.6 6.5 - - - +
266A ARG 3.2 0.2 - - - -
267A ALA* 1.3 77.6 - - - +
269A VAL* 1.3 56.4 + - - +
271A ALA* 3.1 4.8 + - - -
272A CYS* 2.8 49.5 + - - -
276A PHE* 5.2 0.2 - + - -
282A ILE* 3.9 22.2 - - + -
283A THR 4.6 0.2 - - - -
286A ALA* 4.0 7.9 - - + -
287A GLU* 3.5 37.5 - - + -
290A TYR* 3.7 37.5 - + + -
323A PRO* 3.6 30.7 - - + -
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Residues in contact with VAL 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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256A TYR* 3.5 15.7 - - - +
258A SER* 3.6 27.1 - - - +
265A SER 3.0 18.1 + - - +
266A ARG* 3.8 26.2 - - - +
268A PHE* 1.3 73.5 - - + +
270A GLN* 1.3 61.8 + - + +
272A CYS* 3.1 2.9 + - - +
273A HIS* 2.8 56.8 + - + +
282A ILE* 4.0 13.2 - - + +
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Residues in contact with GLN 270 (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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266A ARG* 3.0 28.3 + - + +
267A ALA* 3.8 5.7 - - - +
269A VAL* 1.3 77.5 - - + +
271A ALA* 1.3 66.3 + - - +
273A HIS* 4.0 7.5 - - - +
274A GLY* 3.0 20.3 + - - -
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Residues in contact with ALA 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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33A LEU* 3.7 30.1 - - + +
37A GLN* 6.1 1.3 - - - +
267A ALA 2.9 17.5 + - - +
268A PHE* 3.7 5.2 - - - +
270A GLN* 1.3 77.0 - - - +
272A CYS* 1.3 64.1 + - - +
274A GLY* 3.2 1.6 + - - -
275A PHE* 3.1 24.3 + - - +
290A TYR* 6.0 2.5 - - + +
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Residues in contact with CYS 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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33A LEU* 3.8 4.3 - - - -
268A PHE* 2.8 55.8 + - - +
269A VAL 3.1 0.2 + - - -
271A ALA* 1.3 76.8 - - - +
273A HIS* 1.3 57.4 + - - +
276A PHE* 2.7 68.6 + - + +
282A ILE* 3.3 31.2 - - + -
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Residues in contact with HIS 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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269A VAL* 2.8 43.4 + - + +
270A GLN* 4.0 7.1 - - - +
272A CYS* 1.3 71.8 - - - +
274A GLY* 1.3 60.9 + - - +
275A PHE 3.4 0.2 + - - -
276A PHE* 4.3 8.2 - - - +
282A ILE* 4.0 19.1 - - + +
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Residues in contact with GLY 274 (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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270A GLN 3.0 15.0 + - - -
271A ALA* 3.7 2.9 - - - -
273A HIS* 1.3 77.0 - - - +
275A PHE* 1.3 58.5 + - - +
276A PHE 5.1 0.4 - - - -
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Residues in contact with PHE 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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29A TYR* 3.9 22.1 - + - -
32A LEU* 3.6 31.9 - - + -
33A LEU* 3.6 41.3 - - + -
36A GLU* 3.8 36.8 - - + -
271A ALA 3.1 13.8 + - - +
272A CYS 3.0 2.0 + - - +
274A GLY* 1.3 78.7 - - - +
276A PHE* 1.3 72.6 + + + +
277A PRO* 3.6 4.2 - - - +
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Residues in contact with PHE 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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26A SER* 4.2 7.9 - - - -
29A TYR* 3.6 38.6 - - + -
30A GLY* 3.8 12.8 - - - -
33A LEU* 4.5 5.4 - - + -
272A CYS* 2.7 57.2 + - + +
273A HIS* 4.3 8.2 - - - +
274A GLY 5.1 0.2 - - - -
275A PHE* 1.3 82.4 - + - +
277A PRO* 1.3 75.2 - - + +
280A ALA* 3.3 26.2 - - + +
281A THR 4.2 5.4 - - - -
282A ILE* 4.1 24.2 - - + -
286A ALA* 4.0 9.9 - - + -
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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