Contacts of the helix formed by residues 260 - 273 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A GLU* 2.8 19.8 + - - +
259A LEU* 1.3 84.0 - - - +
261A TYR* 1.3 59.0 + - - -
263A HIS 3.3 1.7 + - - -
264A ALA* 2.9 25.1 + - - +
362A CYS* 3.3 18.6 + - - +
366A ASN* 3.6 12.8 - - - -
367A PRO* 5.7 0.7 - - - -
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Residues in contact with TYR 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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201A GLU* 3.0 0.6 + - - -
260A GLY* 1.3 67.9 - - - -
262A VAL* 1.3 66.8 + - - +
264A ALA* 3.7 6.5 - - + -
265A MET* 2.9 39.5 + - + +
288A VAL* 3.8 13.0 - - + -
291A TYR* 3.6 33.4 - + - -
358A LEU* 3.6 18.8 - - + +
363A ALA* 3.6 32.1 - - + -
366A ASN* 2.8 41.3 + - + +
368A ARG 3.5 8.1 + - - -
369A GLN* 3.5 7.4 + - - -
370A GLY 2.8 24.7 + - - -
375A VAL* 4.4 13.0 - - + -
378A LEU* 4.2 11.0 - - + -
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Residues in contact with VAL 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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197A THR* 3.6 9.0 - - + -
201A GLU* 2.7 35.5 + - + +
261A TYR* 1.3 72.5 - - - +
263A HIS* 1.3 56.8 + - - +
265A MET* 4.9 0.4 - - - -
266A ALA* 2.8 30.3 + - - +
281A ASN* 3.4 39.7 - - - +
284A LEU* 3.8 7.4 - - + +
285A LEU* 3.8 24.7 - - + +
288A VAL* 3.5 32.3 - - + -
289A LEU* 5.5 1.8 - - + +
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Residues in contact with HIS 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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194A ASP* 3.3 2.7 + - - -
197A THR* 3.3 20.1 - - + +
198A HIS* 3.3 17.2 + + - -
201A GLU* 2.7 24.7 + - - +
259A LEU* 3.4 24.9 - - + +
260A GLY 3.3 2.9 + - - +
262A VAL* 1.3 78.6 - - - +
264A ALA* 1.3 65.4 + - - +
266A ALA* 4.0 1.3 - - - -
267A HIS* 2.8 36.7 + - - +
277A HIS* 3.6 17.7 - + - -
281A ASN* 3.0 27.3 + - - +
362A CYS* 4.2 9.6 - - - -
501A FE2 2.1 31.0 - - - -
1385A NAD 4.7 2.2 - + - -
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Residues in contact with ALA 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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260A GLY 2.9 17.8 + - - +
261A TYR* 3.9 11.0 - - + -
263A HIS* 1.3 77.9 - - - +
265A MET* 1.3 60.5 + - + +
267A HIS* 3.8 0.9 + - - +
268A GLN* 3.1 29.1 + - - +
357A ALA* 3.7 24.4 - - + +
360A ASP* 3.6 15.3 - - + +
362A CYS* 4.0 1.0 - - - +
363A ALA* 3.8 22.4 - - + +
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Residues in contact with MET 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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261A TYR* 2.9 33.5 + - + +
264A ALA* 1.3 75.7 - - + +
266A ALA* 1.3 64.5 + - - +
268A GLN* 3.0 20.6 + - - +
269A LEU* 3.5 5.7 + - - +
284A LEU* 3.8 19.3 - - + -
288A VAL* 4.1 12.8 - - + -
357A ALA* 4.0 12.3 - - + -
375A VAL* 4.3 6.7 - - + +
378A LEU* 3.8 31.4 - - + +
379A PHE* 3.5 71.4 - - + +
382A ALA* 5.6 0.4 - - + -
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Residues in contact with ALA 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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262A VAL 2.8 22.9 + - - +
263A HIS* 3.1 3.3 + - - +
265A MET* 1.3 68.5 - - - +
267A HIS* 1.3 59.0 + - + +
268A GLN 3.0 6.0 + - - -
269A LEU* 3.1 3.3 + - - +
270A GLY* 2.9 28.8 + - - -
277A HIS* 5.2 1.7 - - + +
280A CYS* 4.0 16.5 - - + +
281A ASN* 3.5 30.3 - - - +
284A LEU* 3.5 15.8 - - + +
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Residues in contact with HIS 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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151A ILE* 5.0 8.9 - - + +
160A LYS* 5.2 16.0 + - + +
263A HIS* 2.8 31.8 + + + +
264A ALA 4.0 3.1 - - - +
266A ALA* 1.3 72.5 - - + +
268A GLN* 1.3 62.7 + - - +
270A GLY 5.0 1.8 - - - -
271A GLY* 3.1 26.3 - - - +
272A TYR* 5.4 0.2 - - - -
277A HIS* 3.4 36.0 - + - -
360A ASP* 3.2 27.6 + - - +
362A CYS* 4.0 23.3 - - - -
1385A NAD 4.0 19.4 + - - -
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Residues in contact with GLN 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 ALA 3.1 25.0 + - - +
265A MET 3.2 8.7 - - - +
266A ALA 3.0 0.4 - - - -
267A HIS* 1.3 84.5 + - - +
269A LEU* 1.3 64.5 + - - +
272A TYR* 3.2 41.4 + - + +
273A TYR* 4.1 0.3 - - - -
353A LEU* 3.6 44.0 - - + +
356A HIS* 3.2 37.5 + - - +
357A ALA* 3.8 4.7 - - + +
360A ASP* 3.9 15.4 + - - +
379A PHE* 4.7 0.7 - - + -
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Residues in contact with LEU 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 MET 3.9 8.7 - - - +
266A ALA 3.1 5.0 + - - +
268A GLN* 1.3 76.3 - - - +
270A GLY* 1.3 58.2 - - - +
271A GLY 3.1 0.7 - - - -
273A TYR* 2.9 43.1 + - + +
275A LEU* 4.0 17.1 + - + +
280A CYS* 4.2 11.0 - - + -
284A LEU* 4.0 18.6 - - + -
340A LEU* 3.4 38.8 - - + -
343A LEU* 6.0 0.7 - - + -
345A ALA* 4.6 16.4 - - + -
353A LEU* 3.6 32.3 - - + -
379A PHE* 4.0 8.5 - - + -
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Residues in contact with GLY 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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71A ASN* 4.3 15.1 + - - +
160A LYS* 4.8 1.3 + - - -
266A ALA 2.9 13.3 + - - -
267A HIS* 4.0 3.8 - - - -
269A LEU* 1.3 75.4 - - - +
271A GLY* 1.3 56.9 + - - +
274A ASN* 3.7 5.0 - - - -
275A LEU* 3.1 43.4 + - - +
277A HIS* 5.5 2.4 - - - -
280A CYS* 3.9 4.6 - - - -
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Residues in contact with GLY 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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71A ASN* 5.3 2.9 + - - -
160A LYS* 4.8 20.2 - - - +
267A HIS 3.1 21.6 + - - -
269A LEU 3.1 0.8 - - - -
270A GLY* 1.3 81.3 - - - +
272A TYR* 1.3 64.3 + - - +
273A TYR 3.3 0.7 - - - -
274A ASN* 3.2 18.5 - - - +
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Residues in contact with TYR 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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158A HIS 5.0 11.9 - - - -
268A GLN* 3.2 44.8 + - + +
271A GLY* 1.3 77.0 - - - +
273A TYR* 1.3 78.4 + - + +
274A ASN* 3.4 5.9 + - - +
352A LEU* 5.3 10.1 - - + -
353A LEU* 4.6 9.0 - - + -
356A HIS* 3.0 48.8 + + + +
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Residues in contact with TYR 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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268A GLN 4.1 1.8 - - - -
269A LEU* 2.9 33.5 + - + +
272A TYR* 1.3 88.9 - - + +
274A ASN* 1.3 67.6 + - - +
275A LEU* 2.7 21.2 + - + +
344A GLY 6.0 2.7 - - - -
345A ALA* 5.6 10.8 - - + -
346A LYS* 5.8 0.4 - - + -
349A ASP* 2.8 41.3 + - + +
352A LEU* 5.1 7.0 - - + +
353A LEU* 3.7 29.9 - - + +
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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