Contacts of the helix formed by residues 260 - 270 (chain C) in PDB entry 3OX4
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 GLY 260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C GLU* 2.8 20.1 + - - +
259C LEU* 1.3 83.1 - - - +
261C TYR* 1.3 64.5 + - - -
262C VAL 3.3 0.5 + - - -
263C HIS 3.4 1.7 + - - -
264C ALA* 3.1 19.9 + - - +
362C CYS* 3.4 17.4 + - - +
366C ASN* 3.8 13.7 - - - -
367C PRO* 5.5 1.1 - - - -
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Residues in contact with TYR 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C GLU* 3.1 1.2 + - - -
260C GLY* 1.3 70.9 - - - -
262C VAL* 1.3 66.5 + - - +
264C ALA* 3.6 5.8 - - + +
265C MET* 3.0 36.6 + - + +
288C VAL* 3.6 15.3 - - + -
291C TYR* 3.6 28.3 - + - -
358C LEU* 3.8 20.1 - - + +
363C ALA* 3.9 26.0 - - + -
366C ASN* 2.9 39.0 + - + +
368C ARG 3.3 19.4 + - - -
369C GLN* 3.6 8.5 + - - -
370C GLY* 2.8 27.2 + - - -
375C VAL* 4.8 11.4 - - + -
378C LEU* 4.6 8.1 - - + -
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Residues in contact with VAL 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C THR* 3.5 15.5 - - + -
201C GLU* 2.8 30.0 + - + +
261C TYR* 1.3 73.0 - - - +
263C HIS* 1.3 57.2 + - - +
265C MET* 3.8 3.3 - - - +
266C ALA* 3.0 21.7 + - - +
281C ASN* 3.0 42.1 + - - +
284C LEU* 4.1 6.3 - - + +
285C LEU* 4.1 25.8 - - + +
288C VAL* 3.4 34.5 - - + -
289C LEU* 5.4 1.3 - - + +
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Residues in contact with HIS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ASP* 3.7 0.9 - - - -
197C THR* 3.2 26.2 - - + +
198C HIS* 3.3 16.0 - + - -
201C GLU* 2.7 24.5 + - - +
259C LEU* 3.4 27.3 - - + +
260C GLY 3.4 3.6 + - - +
262C VAL* 1.3 75.5 - - - +
264C ALA* 1.3 66.3 + - - +
265C MET 3.0 2.0 - - - -
266C ALA* 4.2 1.1 - - - -
267C HIS* 3.0 35.3 + - - +
277C HIS* 3.0 22.7 - + - -
281C ASN* 2.8 15.6 + - - +
360C ASP* 4.2 1.3 - - - -
362C CYS* 4.1 8.1 - - - -
501C FE2 2.1 32.4 - - - -
1385C NAD 4.4 1.1 - - - -
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Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C GLY 3.1 17.4 + - - +
261C TYR* 3.2 14.6 + - + +
263C HIS* 1.3 76.7 - - - +
265C MET* 1.3 60.0 + - + +
268C GLN* 3.5 10.6 + - - +
357C ALA* 3.4 38.4 - - + +
360C ASP* 3.3 24.8 + - + +
363C ALA* 4.0 15.0 - - + +
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Residues in contact with MET 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C TYR* 3.0 21.3 + - + +
262C VAL 3.8 0.2 - - - +
264C ALA* 1.3 77.9 - - + +
266C ALA* 1.3 57.5 + - - +
267C HIS 3.0 1.3 - - - -
268C GLN* 2.6 34.5 + - - +
269C LEU* 3.4 5.8 + - - +
284C LEU* 3.6 19.5 - - + -
288C VAL* 4.1 10.5 - - - -
357C ALA* 4.3 10.5 - - + -
375C VAL* 3.9 10.8 - - + +
378C LEU* 3.5 35.7 - - + -
379C PHE* 3.4 65.1 - - + +
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Residues in contact with ALA 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C LYS* 5.2 0.2 + - - -
262C VAL 3.0 7.6 + - - +
263C HIS* 4.2 2.5 - - - +
265C MET* 1.3 75.4 - - - +
267C HIS* 1.3 58.2 + - - +
269C LEU* 2.9 7.5 + - - +
270C GLY* 2.8 27.5 + - - -
277C HIS* 4.3 7.9 - - + -
280C CYS* 4.0 23.8 - - + +
281C ASN* 2.9 41.7 - - - +
284C LEU* 4.0 6.5 - - + +
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Residues in contact with HIS 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ILE* 5.0 13.1 - - + +
160C LYS* 4.1 34.3 + - + +
263C HIS* 3.0 24.3 + - - +
264C ALA 4.4 0.4 - - - +
266C ALA* 1.3 75.9 - - - +
268C GLN* 1.3 65.0 + - - +
270C GLY 3.8 1.9 - - - +
271C GLY* 3.3 21.0 + - - -
277C HIS* 3.4 32.0 + + - -
360C ASP* 3.4 25.4 + - - +
362C CYS* 4.1 15.7 - - - -
1385C NAD 3.3 33.6 + - - -
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Residues in contact with GLN 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C VAL* 5.2 12.9 - - - +
264C ALA 3.5 21.3 + - - +
265C MET* 2.6 17.7 + - - +
267C HIS* 1.3 78.5 + - - +
269C LEU* 1.3 59.1 + - - +
271C GLY 4.0 0.7 - - - -
272C TYR* 3.4 39.2 + - - +
273C TYR* 4.2 0.3 - - - -
352C LEU 4.8 0.5 - - - +
353C LEU* 3.4 42.2 - - + +
356C HIS* 2.9 44.9 + - - +
357C ALA* 3.9 2.0 - - + +
360C ASP* 4.3 12.3 + - - +
379C PHE* 4.9 0.7 - - + -
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C MET 4.1 8.3 - - - +
266C ALA* 2.9 5.9 + - - +
268C GLN* 1.3 76.5 - - - +
270C GLY* 1.3 57.7 + - - +
271C GLY 3.2 2.5 - - - -
273C TYR* 3.1 40.8 - - + +
275C LEU* 3.1 25.5 + - + +
280C CYS* 4.1 16.2 - - + -
284C LEU* 4.7 7.6 - - + -
340C LEU* 3.5 41.5 - - + -
343C LEU* 5.1 1.8 - - + -
345C ALA* 4.2 10.3 - - + -
353C LEU* 3.3 34.8 - - + -
379C PHE* 4.6 8.3 - - + -
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ASN* 3.3 19.6 + - - +
153C THR* 5.0 0.2 + - - -
160C LYS* 3.1 27.7 - - - -
266C ALA 2.8 15.3 + - - -
269C LEU* 1.3 77.6 - - - +
271C GLY* 1.3 56.5 + - - +
274C ASN* 3.4 7.2 - - - -
275C LEU* 3.2 21.3 - - - -
277C HIS* 5.2 1.8 - - - -
280C CYS* 4.6 2.6 - - - -
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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