Contacts of the helix formed by residues 263 - 275 (chain A) in PDB entry 1Q6X
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 ASP 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LEU 3.2 6.1 + - - +
261A LEU 3.2 0.4 - - - +
262A LYS* 1.3 79.6 - - + +
264A SER* 1.3 67.7 + - - +
265A THR* 2.7 37.8 + - - -
266A ASN* 3.2 19.9 + - - +
267A ARG* 3.1 23.8 + - - +
378A LYS* 3.0 41.2 - - + +
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ASP* 1.3 76.5 + - - +
265A THR* 1.3 62.3 + - - +
267A ARG* 3.4 28.7 + - - +
268A ASP* 3.0 37.2 + - - +
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Residues in contact with THR 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 ASP* 2.7 22.1 + - - -
264A SER* 1.3 75.0 - - - +
266A ASN* 1.3 59.5 + - - +
268A ASP* 3.4 9.2 + - - +
269A SER* 3.2 21.5 + - - -
376A ARG* 3.6 36.8 - - + +
377A TRP* 4.2 6.7 - - - +
378A LYS* 4.6 9.4 - - + +
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Residues in contact with ASN 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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259A VAL 5.2 0.2 + - - -
260A LEU* 3.0 48.0 + - + +
263A ASP* 3.2 8.1 + - - +
265A THR* 1.3 73.3 - - - +
267A ARG* 1.3 60.0 + - - +
269A SER* 3.2 0.9 + - - -
270A LEU* 2.8 37.2 + - + +
377A TRP* 3.2 28.3 - - + +
378A LYS* 2.6 53.7 + - - +
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Residues in contact with ARG 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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260A LEU 4.7 0.6 + - - -
261A LEU* 3.1 50.3 + - + +
262A LYS 3.4 16.8 + - - -
263A ASP 3.1 6.2 + - - +
264A SER* 3.4 40.4 + - - +
266A ASN* 1.3 77.3 - - - +
268A ASP* 1.3 63.4 + - - +
270A LEU* 3.7 2.8 + - - +
271A ASP* 3.2 22.3 + - - +
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Residues in contact with ASP 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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264A SER* 3.0 25.5 + - - +
265A THR* 3.8 9.2 - - - +
266A ASN 3.2 0.2 - - - -
267A ARG* 1.3 77.7 - - - +
269A SER* 1.3 63.3 + - - +
271A ASP* 3.3 7.5 + - - +
272A MET* 3.1 28.6 + - + +
373A ARG* 6.2 1.8 - - - +
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Residues in contact with SER 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 THR 3.2 5.7 + - - -
266A ASN 3.2 3.7 + - - -
268A ASP* 1.3 77.3 - - - +
270A LEU* 1.3 62.8 + - - +
272A MET* 3.3 3.8 + - - +
273A ILE* 3.2 26.9 + - - +
375A LEU* 3.7 19.5 - - - +
376A ARG* 2.7 40.6 + - - +
377A TRP* 3.6 26.0 - - - -
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Residues in contact with LEU 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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172A TYR* 5.3 2.2 - - - +
253A TRP* 4.6 10.1 - - + -
257A ARG* 4.4 21.3 - - + +
260A LEU* 4.4 14.8 - - + -
261A LEU* 3.6 31.9 - - + -
266A ASN 2.8 21.4 + - - +
267A ARG 4.0 3.4 - - - +
269A SER* 1.3 75.7 - - - +
271A ASP* 1.3 57.6 + - - +
273A ILE* 3.3 5.3 + - - +
274A GLU* 2.8 46.4 + - - +
313A TRP* 3.6 34.8 - - + -
377A TRP* 4.1 10.3 - - + -
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Residues in contact with ASP 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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267A ARG 3.2 16.8 + - - +
268A ASP* 3.5 8.1 - - - +
269A SER 3.2 0.2 - - - -
270A LEU* 1.3 78.7 - - - +
272A MET* 1.3 63.4 + - - +
274A GLU* 3.2 13.5 + - - +
275A ARG* 2.7 64.3 + - - +
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Residues in contact with MET 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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193A PRO 5.9 0.2 - - - +
195A HIS* 2.9 40.9 + - + +
197A ILE* 4.4 2.5 - - + -
206A VAL* 3.6 33.7 - - + -
208A ASP* 5.3 1.8 - - - +
268A ASP* 3.1 20.0 + - + +
269A SER 3.6 7.6 - - - +
270A LEU 3.3 0.2 - - - -
271A ASP* 1.3 76.9 - - - +
273A ILE* 1.3 62.9 + - - +
275A ARG* 3.2 28.5 + - - +
276A CYS* 3.4 3.1 + - - +
373A ARG* 3.6 19.7 - - - +
375A LEU* 4.1 23.1 - - + -
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Residues in contact with ILE 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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172A TYR* 4.4 8.4 - - + +
197A ILE* 4.2 13.5 - - + -
204A PHE* 4.8 8.1 - - + -
269A SER 3.2 15.3 + - - +
270A LEU* 3.7 7.4 - - - +
272A MET* 1.3 77.4 - - - +
274A GLU* 1.3 61.8 + - + +
275A ARG 3.1 1.4 + - - -
276A CYS* 3.4 17.2 + - - -
279A LEU* 4.8 12.3 - - + -
313A TRP* 3.6 68.6 - - + +
316A LYS* 4.4 4.9 - - + +
375A LEU* 3.7 21.1 - - + -
377A TRP* 4.1 8.3 - - + -
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Residues in contact with GLU 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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172A TYR* 3.6 47.3 + - + +
174A LEU* 4.1 12.6 - - - +
185A GLN* 4.3 8.7 - - - +
257A ARG* 3.0 31.8 + - - -
270A LEU* 2.8 39.0 + - + +
271A ASP* 3.2 11.5 + - - +
273A ILE* 1.3 75.1 - - + +
275A ARG* 1.3 64.5 + - + +
276A CYS 3.7 1.1 - - - +
316A LYS* 5.2 3.1 + - - -
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Residues in contact with ARG 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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185A GLN* 3.4 37.7 + - + +
186A LYS 6.0 1.6 - - - -
189A ILE* 4.8 22.5 - - - +
192A GLU* 6.2 2.2 - - - +
193A PRO 5.6 2.0 + - - -
195A HIS* 3.6 22.0 + - + -
271A ASP* 2.7 47.3 + - - +
272A MET* 3.2 25.1 + - - +
273A ILE 3.1 0.8 - - - -
274A GLU* 1.3 83.7 - - + +
276A CYS* 1.3 64.6 + - - +
277A ILE* 4.2 0.7 + - - +
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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