Contacts of the helix formed by residues 260 - 271 (chain A) in PDB entry 2QFI
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 ALA 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A ILE* 3.6 28.4 - - + +
256A PRO* 4.4 13.7 - - + -
257A LEU 2.7 18.9 + - - +
258A VAL* 3.8 3.8 - - - -
259A GLN* 1.3 67.9 - - - +
261A HIS* 1.3 64.7 + - - +
262A MET* 3.6 9.9 - - - +
263A VAL* 3.2 18.5 - - + +
284A GLN* 4.2 9.5 + - - +
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Residues in contact with HIS 261 (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 VAL* 2.9 21.3 + - + +
259A GLN 2.1 24.4 + - - +
260A ALA* 1.3 64.7 - - - +
262A MET* 1.3 56.6 - - + +
263A VAL* 2.0 23.1 + - - -
264A ALA* 2.5 19.7 + - + +
265A ASP* 3.3 29.0 + - + +
268A GLU* 4.1 4.9 + - - -
284A GLN* 4.2 17.5 - - - +
302A ZN 2.2 37.5 - - - -
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Residues in contact with MET 262 (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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259A GLN* 2.9 45.2 + - + +
260A ALA* 3.6 7.2 - - - +
261A HIS* 1.3 77.9 - - + +
263A VAL* 1.3 68.4 + - + +
265A ASP* 2.8 20.5 - - + +
266A GLN* 1.9 71.0 + - + +
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Residues in contact with VAL 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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225A TRP* 3.8 3.2 - - + -
226A PRO* 4.5 18.8 - - + -
227A GLY* 5.0 9.9 - - - +
246A GLN* 5.0 2.5 - - - +
247A ILE* 3.8 22.9 - - + -
260A ALA* 3.2 25.6 - - + +
261A HIS 2.0 17.2 + - - +
262A MET* 1.3 80.6 - - + +
264A ALA* 1.3 73.8 + - + +
266A GLN* 3.2 24.1 - - - +
267A VAL* 2.9 29.9 + - - +
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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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246A GLN* 4.1 8.5 - - - +
260A ALA 4.8 0.2 - - - +
261A HIS* 2.5 12.5 + - + +
263A VAL* 1.3 79.8 - - + +
265A ASP* 1.3 50.1 + - - +
267A VAL* 2.6 19.0 + - - +
268A GLU* 2.4 38.7 + - + +
282A ILE* 3.8 26.2 - - + -
284A GLN* 3.6 24.2 - - + +
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Residues in contact with ASP 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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261A HIS* 3.3 24.7 + - + +
262A MET* 3.1 27.7 + - - +
264A ALA* 1.3 77.9 - - - +
266A GLN* 1.3 52.5 - - - +
268A GLU* 3.4 17.1 + - - -
269A GLN* 2.7 39.6 + - - +
279A ASP* 3.6 16.3 - - - +
302A ZN 3.5 7.8 - - - -
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Residues in contact with GLN 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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225A TRP* 2.5 53.3 - - + -
226A PRO* 4.3 5.5 - - - +
262A MET* 1.9 61.2 + - + +
263A VAL* 3.2 23.6 - - - +
264A ALA 3.0 0.2 - - - -
265A ASP* 1.3 67.0 - - - +
267A VAL* 1.3 52.2 + - - +
269A GLN* 3.0 8.5 + - - +
270A ALA* 2.3 38.1 + - - +
225B TRP* 5.9 3.5 - - - -
269B GLN* 5.2 0.7 - - - +
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Residues in contact with VAL 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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221A ILE* 5.4 2.6 - - + +
222A VAL* 3.4 34.5 - - + +
225A TRP* 3.4 25.2 - - + -
227A GLY* 5.7 4.5 - - - +
246A GLN* 3.7 20.9 - - - +
263A VAL* 2.9 17.0 + - + +
264A ALA* 2.6 15.6 + - - +
266A GLN* 1.3 71.7 - - - +
268A GLU* 1.3 72.1 + - - +
270A ALA* 2.5 19.5 + - - +
271A ILE* 2.7 24.5 + - + +
282A ILE* 4.5 4.5 - - + -
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Residues in contact with GLU 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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261A HIS* 4.1 8.5 + - - -
264A ALA* 2.4 26.1 + - - +
265A ASP* 3.4 22.6 + - - +
267A VAL* 1.3 79.4 - - - +
269A GLN* 1.3 63.9 + - - +
271A ILE* 2.6 32.9 + - - +
279A ASP* 3.0 33.5 - - - +
280A VAL* 3.8 13.7 - - + +
281A ILE* 3.1 7.3 - - - +
282A ILE* 2.3 58.7 + - + +
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Residues in contact with GLN 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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265A ASP* 2.7 30.1 + - - +
266A GLN* 3.1 5.4 - - - +
268A GLU* 1.3 71.2 - - - +
270A ALA* 1.3 50.4 + - - +
271A ILE 3.2 0.8 - - - +
272A LEU* 2.6 32.7 + - - +
279A ASP* 3.6 6.9 + - - -
269B GLN* 2.7 33.8 + - - +
272B LEU* 5.7 10.1 - - - +
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Residues in contact with ALA 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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221A ILE* 4.6 17.7 - - + +
225A TRP* 3.6 25.8 - - + +
266A GLN 2.3 26.4 + - - +
267A VAL* 2.5 11.7 + - - +
269A GLN* 1.3 63.5 - - - +
271A ILE* 1.4 49.8 + - - +
272A LEU* 2.6 19.7 + - - +
273A ARG* 3.3 10.9 + - - +
266B GLN* 6.0 1.1 - - + -
269B GLN* 3.2 23.0 - - + +
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Residues in contact with ILE 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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218A ILE* 3.4 41.7 - - + -
221A ILE* 4.8 13.8 - - + +
222A VAL* 4.3 14.4 - - + -
242A THR* 5.5 2.0 - - + -
244A PHE* 5.6 2.9 - - + -
267A VAL* 2.7 27.8 + - + +
268A GLU* 2.6 31.0 + - - +
269A GLN* 3.2 1.1 - - - +
270A ALA* 1.4 65.7 - - - +
272A LEU* 1.3 66.1 + - - +
273A ARG* 3.8 1.1 - - - +
274A ARG* 4.4 13.5 - - - +
276A PRO* 5.0 6.9 - - - +
277A GLY 5.7 0.5 + - - -
278A SER 5.6 0.7 - - - +
280A VAL* 4.9 22.9 - - + +
282A ILE* 5.6 4.5 - - + -
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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