Contacts of the helix formed by residues 260 - 267 (chain A) in PDB entry 1XTG
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 PHE 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A ILE* 3.8 20.2 - - + -
241A ARG* 3.0 30.0 + - + +
242A VAL* 3.4 29.6 - - - -
243A PHE* 3.7 16.4 - + + -
259A SER* 1.3 70.1 - - - +
261A GLU* 1.3 60.6 + - - +
263A LEU* 3.2 13.5 + - + +
264A ARG* 2.8 32.1 + - - +
273A PHE 5.2 2.7 - - - -
274A ILE* 3.6 24.4 - - + +
278A GLN* 3.3 43.5 - - - -
282A PHE* 3.8 24.0 - + - -
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Residues in contact with GLU 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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227A HIS* 3.1 30.5 + - + +
230A HIS* 3.2 17.5 + - - +
231A ARG* 5.6 1.7 - - - +
236A ALA* 3.3 14.6 - - + -
237A ILE* 3.1 40.5 + - - +
238A ASN 5.7 0.4 + - - -
239A PRO* 6.1 0.4 - - + -
259A SER* 3.6 10.0 - - - +
260A PHE* 1.3 79.0 - - - +
262A GLU* 1.3 57.5 + - - +
264A ARG* 2.7 35.8 + - - +
265A THR* 2.9 32.8 + - - -
196B ASN* 4.1 16.1 + - - +
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Residues in contact with GLU 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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223A HIS* 3.1 9.0 + - - -
227A HIS* 3.0 5.5 + - - -
258A VAL* 5.0 4.7 - - + -
259A SER* 3.1 25.9 + - - +
261A GLU* 1.3 77.2 - - - +
263A LEU* 1.3 66.4 + - - +
265A THR* 3.1 1.4 + - - -
266A PHE* 2.9 54.9 + - + -
426A ZN 2.2 35.5 - - - -
196B ASN* 4.7 7.9 - - + -
198B ARG* 2.9 30.5 - - - +
199B ALA* 5.1 2.2 - - - -
200B THR* 4.3 7.6 - - - +
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Residues in contact with LEU 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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243A PHE* 3.8 27.8 - - + -
258A VAL* 3.8 12.3 - - + -
259A SER 3.1 10.4 + - - +
260A PHE* 3.6 13.9 - - + +
262A GLU* 1.3 80.0 - - - +
264A ARG* 1.3 63.8 + - - +
266A PHE* 3.4 7.6 + - + +
267A GLY 3.3 15.9 + - - -
270A ASP* 3.7 22.2 - - + +
271A ALA* 3.4 14.3 + - - -
273A PHE* 3.9 20.6 - - + -
274A ILE* 4.1 19.7 - - + -
366A PHE* 3.7 31.0 - - + -
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Residues in contact with ARG 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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230A HIS* 3.3 34.9 + - + -
235A ILE* 2.9 27.3 + - - +
237A ILE* 3.3 30.5 - - + +
260A PHE 2.8 17.8 + - - +
261A GLU* 2.7 32.1 + - - +
263A LEU* 1.3 76.8 - - - +
265A THR* 1.3 60.5 + - - +
267A GLY* 3.3 13.9 + - - -
271A ALA* 4.5 7.6 - - - +
274A ILE* 4.2 8.0 - - + +
282A PHE* 4.9 0.6 - - - +
286A TYR* 4.2 3.2 - - - -
342A TYR* 3.0 27.5 + - - -
346A THR* 3.4 44.6 - - - +
349A TYR 5.2 0.2 - - - +
350A THR* 4.0 2.6 - - - +
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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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223A HIS* 3.7 35.9 - - + +
226A ILE* 3.6 26.5 - - + -
227A HIS* 3.2 23.8 + - + +
230A HIS* 3.4 17.6 - - - -
261A GLU* 2.9 17.5 + - - -
262A GLU* 3.1 5.6 + - - -
264A ARG* 1.3 77.9 - - - +
266A PHE* 1.3 57.4 + - - +
349A TYR 5.3 0.2 - - - -
350A THR* 3.5 5.6 - - - +
351A GLU* 3.0 23.7 + - - +
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Residues in contact with PHE 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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223A HIS* 3.7 9.6 - + - -
258A VAL* 5.9 1.8 - - + -
262A GLU* 2.9 53.0 + - + +
263A LEU* 3.8 10.5 - - + +
264A ARG 3.3 0.2 - - - -
265A THR* 1.3 76.5 - - - +
267A GLY* 1.3 68.9 + - - +
270A ASP* 3.8 22.2 - - + +
351A GLU* 3.5 34.0 + - + +
352A ASP* 3.0 28.2 + - - +
363A ARG* 4.7 14.1 - - - -
366A PHE* 3.7 29.8 - + + -
198B ARG 5.7 0.2 - - - -
199B ALA* 5.5 7.2 - - + -
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Residues in contact with GLY 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 LEU 3.3 6.5 + - - -
264A ARG 3.3 5.7 + - - -
266A PHE* 1.3 86.3 - - - +
268A GLY* 1.3 68.9 + - - +
269A HIS 3.4 1.4 + - - -
270A ASP* 3.5 3.6 + - - +
271A ALA* 3.2 27.5 + - - -
350A THR* 3.7 21.1 - - - -
352A ASP* 4.2 0.2 - - - -
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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