Contacts of the helix formed by residues 260 - 274 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D GLU* 3.0 17.1 + - - +
259D LEU* 1.3 83.1 - - - +
261D TYR* 1.3 66.0 + - - -
262D VAL 3.1 1.4 + - - -
263D HIS* 3.1 3.6 + - - -
264D ALA* 3.1 19.3 + - - +
362D CYS* 3.6 15.7 + - - +
366D ASN* 3.6 14.8 - - - -
367D PRO* 5.5 0.7 - - - -
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Residues in contact with TYR 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D GLU* 3.3 0.4 + - - -
260D GLY* 1.3 69.2 - - - -
262D VAL* 1.3 65.6 + - - +
264D ALA* 3.7 6.7 - - + -
265D MET* 3.0 37.4 + - + +
288D VAL* 3.8 14.1 - - + -
291D TYR* 3.8 25.4 - + - -
358D LEU* 3.6 21.1 - - + +
363D ALA* 3.6 28.7 - - + -
366D ASN* 2.7 41.4 + - + +
368D ARG 3.5 14.4 + - - -
369D GLN* 3.6 7.3 + - - -
370D GLY* 2.9 22.6 + - - -
375D VAL* 3.9 22.9 - - + -
378D LEU* 4.4 6.5 - - + -
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Residues in contact with VAL 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D THR* 3.5 14.6 - - + -
201D GLU* 2.9 33.2 + - + +
261D TYR* 1.3 72.8 - - - +
263D HIS* 1.3 58.5 + - - +
265D MET* 3.8 2.1 - - - +
266D ALA* 2.8 28.9 + - - +
281D ASN* 3.3 36.8 - - - +
284D LEU* 4.0 6.6 - - + +
285D LEU* 4.0 21.3 - - + +
288D VAL* 3.4 32.5 - - + -
289D LEU* 5.5 2.0 - - + -
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Residues in contact with HIS 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D ASP* 3.3 3.0 + - - -
197D THR* 3.3 18.6 - - + +
198D HIS* 3.2 19.3 + + - -
201D GLU* 2.6 28.2 + - - +
259D LEU* 3.5 17.4 - - + +
260D GLY 3.1 3.3 + - - +
262D VAL* 1.3 73.9 - - - +
264D ALA* 1.3 65.6 + - - +
265D MET 3.0 1.8 - - - -
266D ALA* 4.1 0.9 - - - -
267D HIS* 2.9 32.6 + - + -
277D HIS* 3.5 19.7 + + - -
281D ASN* 3.1 22.6 + - - +
362D CYS* 4.0 17.0 - - - -
501D FE2 2.1 32.1 - - - -
1385D NAD 3.8 7.0 - - - -
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Residues in contact with ALA 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D GLY 3.1 15.3 + - - +
261D TYR* 3.9 11.4 - - + +
262D VAL 3.4 0.2 - - - -
263D HIS* 1.3 77.2 - - - +
265D MET* 1.3 58.1 + - + +
268D GLN* 3.0 31.4 + - - +
357D ALA* 3.4 27.8 - - + +
360D ASP* 3.8 13.5 - - + -
362D CYS* 4.0 1.2 - - - +
363D ALA* 3.9 22.7 - - + +
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Residues in contact with MET 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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261D TYR* 3.0 26.6 + - + +
264D ALA* 1.3 75.9 - - + +
266D ALA* 1.3 65.3 + - - +
267D HIS 3.2 1.6 - - - -
268D GLN* 3.0 16.1 + - - +
269D LEU* 3.3 10.4 + - - +
284D LEU* 3.5 19.1 - - + -
288D VAL* 4.0 20.6 - - + -
357D ALA* 4.1 9.9 - - + -
375D VAL* 3.8 9.6 - - + +
378D LEU* 3.6 21.8 - - + -
379D PHE* 3.3 78.4 - - + +
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Residues in contact with ALA 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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262D VAL 2.8 21.7 + - - +
263D HIS* 4.0 2.2 - - - +
265D MET* 1.3 72.8 - - - +
267D HIS* 1.3 63.4 + - + +
269D LEU* 3.3 5.1 + - - +
270D GLY* 3.0 21.1 + - - -
277D HIS* 4.9 6.2 + - - +
280D CYS* 3.9 15.4 - - + +
281D ASN* 3.3 44.4 - - - +
284D LEU* 3.8 5.7 - - + +
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Residues in contact with HIS 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ILE* 5.0 10.7 - - + +
159D VAL* 6.1 0.2 - - - -
160D LYS* 3.7 36.0 + - + +
263D HIS* 2.9 19.9 + + + +
266D ALA* 1.3 78.8 - - - +
268D GLN* 1.3 63.1 + - - +
271D GLY* 2.8 26.7 + - - -
277D HIS* 3.6 29.3 - + - -
360D ASP* 3.1 29.5 + - - +
362D CYS* 3.8 15.9 - - - -
1385D NAD 3.0 39.0 + - - -
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Residues in contact with GLN 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D HIS 5.5 1.1 - - - +
159D VAL* 4.5 12.8 - - - +
160D LYS 5.8 0.2 + - - -
264D ALA 3.0 25.6 + - - +
265D MET* 3.0 7.4 + - - +
267D HIS* 1.3 78.4 - - - +
269D LEU* 1.3 58.0 + - - +
271D GLY* 4.8 0.7 - - - -
272D TYR* 2.7 39.8 + - - +
352D LEU* 6.0 0.4 - - + +
353D LEU* 3.4 43.5 - - + +
356D HIS* 3.2 37.8 + - + +
357D ALA* 3.6 3.3 - - + +
360D ASP* 3.3 20.4 + - - +
379D PHE* 4.8 0.4 - - + -
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Residues in contact with LEU 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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265D MET 3.3 7.7 + - - +
266D ALA* 3.7 7.0 - - - +
268D GLN* 1.3 77.2 - - - +
270D GLY* 1.3 58.8 + - - +
273D TYR* 2.9 63.2 + - + +
274D ASN 3.6 0.2 + - - -
275D LEU* 4.0 4.0 + - + +
280D CYS* 3.9 25.1 - - + -
284D LEU* 4.1 20.9 - - + -
340D LEU* 3.5 29.8 - - + -
343D LEU* 5.1 1.6 - - + -
345D ALA* 4.2 12.6 - - + -
353D LEU* 3.9 16.2 - - + -
379D PHE* 4.1 11.7 - - + -
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Residues in contact with GLY 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ASN* 3.9 9.6 + - - -
160D LYS* 4.7 6.3 - - - -
266D ALA 3.0 14.8 + - - -
267D HIS 4.0 0.4 - - - -
269D LEU* 1.3 76.3 - - - +
271D GLY* 1.3 58.1 + - - +
272D TYR 3.1 1.6 - - - -
274D ASN* 2.7 31.9 + - - +
275D LEU* 3.6 25.4 - - - -
277D HIS* 6.1 1.3 - - - -
280D CYS* 4.4 1.5 - - - -
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Residues in contact with GLY 271 (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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71D ASN* 5.7 1.3 - - - -
153D THR* 5.2 10.7 - - - +
158D HIS* 2.7 36.8 - - - +
159D VAL* 5.4 1.8 - - - -
160D LYS* 4.2 15.7 - - - +
267D HIS 2.8 22.6 + - - -
268D GLN* 3.5 2.5 - - - -
270D GLY* 1.3 72.4 - - - +
272D TYR* 1.3 55.5 + - - +
274D ASN* 4.5 6.9 - - - +
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Residues in contact with TYR 272 (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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158D HIS* 4.4 34.1 + + + +
268D GLN* 2.7 21.0 + - + +
269D LEU 4.4 0.7 - - - +
271D GLY* 1.3 76.8 - - - +
273D TYR* 1.3 82.8 + + - +
274D ASN* 3.5 7.5 + - - -
349D ASP* 3.1 39.9 + - + -
352D LEU* 4.1 36.7 - - + +
353D LEU* 3.9 15.0 - - + -
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Residues in contact with TYR 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D LEU* 2.9 44.8 + - + +
272D TYR* 1.3 99.1 - + - +
274D ASN* 1.3 74.9 + - - +
275D LEU* 3.4 23.1 + - + +
343D LEU 5.7 0.2 - - - +
344D GLY 3.9 13.7 - - - +
345D ALA* 3.5 18.4 - - + -
346D LYS* 2.8 35.0 + - + -
349D ASP* 2.8 28.7 + - + +
353D LEU* 4.1 7.6 - - + +
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Residues in contact with ASN 274 (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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70D PRO* 5.9 1.6 - - - +
71D ASN* 4.1 15.3 + - - +
153D THR* 5.8 3.6 - - - +
270D GLY 2.7 22.9 + - - +
271D GLY* 4.5 8.0 - - - +
272D TYR 4.4 6.9 + - - -
273D TYR* 1.3 84.0 + - - +
275D LEU* 1.3 61.5 + - - +
276D PRO* 4.5 1.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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