Contacts of the helix formed by residues 263 - 269 (chain D) in PDB entry 4XH9
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 TYR 263 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189D LEU* 4.9 1.5 - - + +
193D LEU* 4.0 12.8 - - - +
221D ASP 5.1 0.4 - - - -
222D LEU 4.3 8.7 + - - -
225D TYR* 3.8 36.7 + + + +
228D LEU* 4.7 2.0 - - + -
229D HIS* 2.5 45.1 + + - -
260D LEU* 3.1 32.2 + - + +
261D ASN 3.1 0.6 + - - -
262D ALA* 1.3 75.9 - - + +
264D ARG* 1.3 63.1 + - - +
265D GLY 3.2 3.0 + - - -
266D TYR* 3.3 10.3 + - + +
267D CYS* 3.0 28.5 + - - -
311D PRO* 3.7 35.0 - - + -
315D LEU* 3.9 26.5 - - + -
353D ILE* 4.5 2.0 - - + -
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Residues in contact with ARG 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D ASN* 3.1 38.3 + - - +
262D ALA 3.2 1.5 - - - +
263D TYR* 1.3 77.4 - - - +
265D GLY* 1.3 65.6 + - - +
267D CYS* 4.3 0.5 - - - +
268D SER* 3.2 24.9 + - - -
352D ASP* 2.8 38.3 + - - +
353D ILE* 4.0 27.5 - - + +
356D LYS* 3.7 48.6 - - + +
359D GLU* 5.9 0.2 + - - -
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Residues in contact with GLY 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ASP* 4.8 3.8 - - - -
262D ALA 4.1 4.3 + - - -
263D TYR 3.2 0.4 - - - -
264D ARG* 1.3 83.3 - - - +
266D TYR* 1.3 64.2 + - - +
268D SER* 2.7 22.9 + - - -
269D ASN* 3.0 11.5 + - - +
356D LYS* 4.5 5.6 - - - -
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Residues in contact with TYR 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D ILE 4.4 6.3 + - - -
219D PHE 3.3 25.4 - - - -
220D GLY* 4.9 1.6 - - - -
221D ASP* 3.4 27.1 + - - +
222D LEU* 3.4 33.5 - - + +
225D TYR* 5.4 0.2 - - + -
263D TYR* 3.3 16.6 + + + +
265D GLY* 1.3 74.6 - - - +
267D CYS* 1.3 65.0 + - - +
269D ASN* 2.9 38.2 + - - +
270D GLN* 3.4 16.9 + - + +
308D LEU* 2.5 48.3 + - - +
311D PRO* 3.7 28.3 - - + -
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Residues in contact with CYS 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D TYR* 3.0 22.2 + - - +
264D ARG 4.3 1.1 - - - +
266D TYR* 1.3 87.3 - - - +
268D SER* 1.3 60.2 + - - +
269D ASN 3.5 0.3 + - - -
270D GLN* 3.5 22.4 + - - +
271D LEU 4.8 0.9 + - - -
311D PRO* 4.6 0.9 - - - -
312D ARG* 4.3 24.0 - - + -
315D LEU* 3.9 26.2 - - - -
353D ILE* 3.8 23.8 - - + +
357D LYS* 3.8 15.1 - - - +
69E LEU* 4.9 6.1 - - + -
72E LEU* 4.7 2.8 - - + +
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Residues in contact with SER 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D ARG 3.2 15.0 + - - -
265D GLY* 2.7 17.7 + - - -
266D TYR 3.2 0.2 - - - -
267D CYS* 1.3 75.5 - - - +
269D ASN* 1.3 57.6 + - - +
270D GLN 3.4 2.0 + - - -
271D LEU* 4.7 8.4 + - - +
272D ALA* 5.3 0.9 + - - +
353D ILE 5.8 0.2 + - - -
356D LYS* 3.0 32.2 + - - -
357D LYS* 4.2 13.5 - - - +
360D SER* 3.2 35.3 + - - -
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Residues in contact with ASN 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D HIS* 3.0 47.8 + - - +
218D ILE 5.0 0.3 - - - +
265D GLY 3.0 13.1 + - - +
266D TYR* 2.9 21.7 + - + +
268D SER* 1.3 77.0 - - - +
270D GLN* 1.3 58.1 + - - +
271D LEU 3.7 0.7 - - - +
272D ALA* 3.9 12.1 - - - +
273D ALA* 3.8 10.4 + - - +
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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