Contacts of the helix formed by residues 263 - 274 (chain A) in PDB entry 3M0V
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 ASN 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A ASN 3.5 1.8 + - - -
262A THR* 1.3 73.8 - - - +
264A ILE* 1.3 60.9 + - - +
265A GLU* 2.9 28.3 - - - +
266A MET* 2.9 27.0 + - + +
267A ILE* 3.6 14.0 + - - +
192C PHE* 4.2 1.2 - - - -
222C MET* 4.9 1.2 - - - +
228C TYR* 2.9 44.9 + - - -
229C SER* 3.7 13.4 - - - -
233C GLN* 5.2 7.0 + - + +
286D LYS* 3.7 8.2 - - - +
287D TYR* 3.7 13.8 + - - +
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Residues in contact with ILE 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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253A VAL* 4.3 8.7 - - + -
255A LEU* 3.3 48.7 - - + +
258A HIS* 3.6 36.6 - - + +
262A THR* 3.2 17.6 + - + +
263A ASN* 1.3 68.4 + - - +
265A GLU* 1.3 73.7 + - - +
266A MET 3.1 2.0 - - - -
267A ILE* 3.1 16.0 + - + +
268A VAL* 3.1 14.3 + - + +
301A ARG* 4.1 31.4 - - - +
305A VAL* 4.8 4.9 - - + -
286D LYS* 5.0 0.2 - - - +
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Residues in contact with GLU 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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263A ASN* 2.9 20.9 - - - +
264A ILE* 1.3 81.0 + - - +
266A MET* 1.3 56.3 + - - +
268A VAL* 3.4 9.0 + - - +
269A ALA* 3.1 20.4 + - - +
301A ARG* 4.2 19.4 - - - +
304A LEU* 3.5 43.6 - - + +
305A VAL* 4.3 8.0 - - - +
308A GLU* 3.5 18.4 - - + +
192C PHE* 3.7 8.3 - - + -
228C TYR* 2.4 38.6 + - - +
286D LYS* 4.9 5.4 + - - -
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Residues in contact with MET 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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263A ASN* 2.9 27.1 + - + +
264A ILE 3.1 0.2 - - - -
265A GLU* 1.3 74.4 - - - +
267A ILE* 1.3 61.5 + - - +
269A ALA* 3.1 2.3 + - - +
270A ARG* 2.8 56.5 + - + +
192C PHE* 3.7 38.4 - - + -
229C SER* 3.9 14.1 - - - +
230C THR 3.2 31.2 - - - +
231C VAL* 4.5 1.3 - - - -
233C GLN* 3.4 34.1 - - - +
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Residues in contact with ILE 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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235A TRP* 3.5 56.3 - - + +
253A VAL* 4.6 9.2 - - + -
258A HIS* 3.7 30.7 - - + +
262A THR* 3.8 21.5 - - + -
263A ASN 3.8 8.5 - - - +
264A ILE* 3.1 9.8 + - + +
266A MET* 1.3 77.6 - - - +
268A VAL* 1.3 64.7 + - - +
270A ARG* 3.3 7.8 + - - +
271A LEU* 2.9 34.8 + - + +
233C GLN* 4.6 6.1 - - - +
234C ASP* 4.9 1.3 - - - +
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Residues in contact with VAL 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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253A VAL* 4.6 13.5 - - + -
264A ILE* 3.1 16.9 + - + +
265A GLU* 3.5 13.2 - - - +
267A ILE* 1.3 77.8 - - - +
269A ALA* 1.3 62.5 + - - +
271A LEU* 3.4 2.1 + - - +
272A ILE* 3.1 46.0 + - + +
277A LEU* 3.9 9.8 - - + +
280A PHE* 3.3 43.1 - - + -
305A VAL* 4.4 8.7 - - + +
308A GLU* 4.3 10.5 - - + -
309A LEU* 4.0 6.5 - - + -
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Residues in contact with ALA 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 GLU 3.1 11.1 + - - +
266A MET 3.1 6.9 + - - +
268A VAL* 1.3 79.3 - - - +
270A ARG* 1.3 63.7 + - - +
272A ILE* 3.3 9.8 + - - +
273A GLN* 3.0 23.6 + - - +
308A GLU* 3.4 25.1 - - - +
315A ARG* 5.8 1.3 - - - +
192C PHE* 3.8 22.2 - - + -
193C THR* 4.0 15.1 + - - +
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Residues in contact with ARG 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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235A TRP* 3.6 27.1 - - + -
266A MET* 2.8 49.3 + - + +
267A ILE 3.6 3.6 - - - +
269A ALA* 1.3 72.7 - - - +
271A LEU* 1.3 64.8 + - - +
273A GLN* 3.2 17.1 + - - +
274A PHE* 3.3 21.1 + - - +
192C PHE* 3.4 35.0 + - - +
193C THR* 4.5 0.8 - - - +
196C PHE* 3.6 40.3 - - - +
231C VAL* 2.8 30.3 + - - +
233C GLN* 4.7 0.2 - - - +
237C THR* 3.0 29.8 + - - +
240C LEU* 4.5 4.3 - - + -
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Residues in contact with LEU 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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220A HIS* 5.3 0.4 - - + -
235A TRP* 3.9 28.0 - - + +
239A TYR* 4.6 9.6 - - + -
251A CYS* 4.0 35.4 - - + -
253A VAL* 3.7 30.5 - - + -
267A ILE* 2.9 28.1 + - + +
268A VAL 3.9 3.6 - - - +
270A ARG* 1.3 75.4 - - - +
272A ILE* 1.3 62.7 + - - +
274A PHE* 3.2 4.3 + - - +
275A GLY 3.0 4.2 + - - -
276A LYS* 2.8 36.5 + - + +
277A LEU* 3.9 18.8 - - + +
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Residues in contact with ILE 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 VAL* 3.1 29.8 + - + +
269A ALA* 3.6 8.1 - - - +
270A ARG 3.3 0.2 - - - -
271A LEU* 1.3 76.1 - - - +
273A GLN* 1.3 64.5 + - - +
275A GLY* 3.0 14.1 + - - +
277A LEU* 3.3 26.2 - - + +
308A GLU* 4.2 7.6 - - + +
309A LEU* 4.2 4.5 - - + -
312A ALA* 4.0 22.2 - - + -
315A ARG* 4.4 9.9 - - - +
317A VAL* 4.2 25.1 - - + +
320A PHE* 3.3 36.8 - - + -
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Residues in contact with GLN 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 ALA 3.0 12.0 + - - +
270A ARG* 3.2 15.2 + - - +
272A ILE* 1.3 79.6 - - - +
274A PHE* 1.3 82.7 + - + +
275A GLY 3.6 0.3 + - - -
315A ARG* 5.0 4.7 - - - +
193C THR* 3.9 31.5 - - + +
196C PHE* 3.2 31.4 - - - +
197C GLU* 4.0 19.7 + - - +
200C LEU* 4.1 8.9 - - - +
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Residues in contact with PHE 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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239A TYR* 3.9 32.8 - - + +
243A GLN* 5.1 1.4 - - - +
270A ARG* 3.3 17.7 + - - +
271A LEU* 3.2 4.2 + - - +
272A ILE 3.1 0.6 - - - -
273A GLN* 1.3 108.8 - - + +
275A GLY* 1.3 63.2 + - - +
276A LYS* 3.3 14.5 + - - +
196C PHE* 3.8 12.6 - + - -
200C LEU* 4.8 5.2 - - + -
240C LEU* 3.5 41.7 - - + -
244C THR* 4.4 15.9 - - - -
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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