Contacts of the helix formed by residues 256 - 275 (chain D) in PDB entry 3H90
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 PRO 256 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B ASP 4.3 6.3 - - - +
254B SER* 3.8 16.6 - - - +
255B LEU 3.4 6.7 - - - +
256B PRO* 4.0 3.8 - - + -
254D SER 3.4 5.1 - - - +
255D LEU* 1.3 87.9 - - + +
257D LEU* 1.3 67.7 + - - +
258D VAL* 4.4 6.3 - - + +
259D GLN* 3.1 39.3 + - + +
260D ALA* 3.0 18.0 + - - +
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Residues in contact with LEU 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B MET* 4.0 19.7 - - + +
252B GLU 4.1 7.0 - - - +
253B ASP 3.7 7.5 + - - +
255B LEU* 2.6 19.3 + - + +
257B LEU* 5.0 6.3 - - + +
260B ALA* 3.9 19.7 - - + -
284B GLN* 3.6 34.8 - - + +
285B ASP 3.9 22.9 - - - +
286B PRO* 3.9 13.0 - - + -
255D LEU 3.7 0.8 + - - -
256D PRO* 1.3 70.6 - - - +
258D VAL* 1.3 55.6 + - - +
260D ALA* 2.8 11.3 + - + -
261D HIS* 2.7 36.2 + - + +
284D GLN* 4.2 10.5 - - - +
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ASP* 3.3 41.9 + - + +
254B SER* 6.0 0.2 - - - -
286B PRO* 3.9 17.4 - - + +
287B CYS 6.1 0.4 - - - +
256D PRO* 3.2 6.6 - - + -
257D LEU* 1.3 78.0 - - - +
259D GLN* 1.3 76.5 + - + +
261D HIS* 3.8 3.1 + - - +
262D MET* 3.4 25.8 + - + +
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Residues in contact with GLN 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D LEU* 4.1 17.6 - - + +
256D PRO* 3.1 36.9 + - + +
258D VAL* 1.3 88.2 - - + +
260D ALA* 1.3 66.0 + - - +
261D HIS 3.3 0.4 - - - -
262D MET* 3.3 14.7 + - - +
263D VAL* 3.3 17.3 + - - +
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Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 3.9 27.1 - - + -
251D MET* 3.3 32.6 - - - +
255D LEU* 3.9 12.9 - - + +
256D PRO 3.0 11.1 + - - +
257D LEU* 2.8 9.7 + - - +
259D GLN* 1.3 74.3 - - - +
261D HIS* 1.3 63.6 + - - +
263D VAL 3.4 1.6 + - - -
264D ALA* 3.0 17.7 + - - +
284D GLN* 3.9 7.4 - - - +
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Residues in contact with HIS 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B HIS* 3.5 17.0 - + - -
284B GLN 3.7 8.7 - - - -
285B ASP* 2.6 11.1 + - - -
286B PRO* 3.6 27.8 - - + +
288B SER* 4.3 11.3 + - - -
292B ZN 2.1 34.9 - - - -
257D LEU* 2.7 20.4 + - + +
258D VAL 4.0 3.5 + - - +
260D ALA* 1.3 73.2 - - - +
262D MET* 1.3 62.8 + - + +
264D ALA* 3.2 3.0 - - + +
265D ASP* 2.9 46.2 + - - +
284D GLN* 3.4 11.4 - - - +
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Residues in contact with MET 262 (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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258D VAL* 3.4 16.5 + - + +
259D GLN* 3.3 14.3 + - - +
260D ALA 3.1 0.4 - - - -
261D HIS* 1.3 82.4 - - + +
263D VAL* 1.3 60.0 + - - +
265D ASP* 3.1 26.3 + - + +
266D GLN* 2.8 48.5 + - + +
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Residues in contact with VAL 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D TRP* 4.5 2.2 - - + -
227D GLY* 3.8 31.9 - - - +
228D VAL* 4.1 20.4 - - + +
251D MET* 3.5 23.1 - - + -
255D LEU* 4.5 7.4 - - + -
259D GLN 3.3 16.2 - - - +
260D ALA* 3.5 10.3 - - - +
262D MET* 1.3 71.7 - - - +
264D ALA* 1.3 67.0 + - - +
266D GLN* 3.4 17.6 - - - +
267D VAL* 2.9 25.6 + - + +
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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
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283B HIS* 4.9 3.6 - - + -
249D LEU* 4.1 12.3 - - - -
251D MET* 3.9 5.8 - - + +
260D ALA 3.0 15.0 + - - +
261D HIS* 3.2 17.3 - - + +
263D VAL* 1.3 77.6 - - - +
265D ASP* 1.3 56.6 + - - +
267D VAL* 3.3 3.6 + - - +
268D GLU* 2.8 27.8 + - - +
282D ILE* 3.9 20.1 - - + +
284D GLN* 3.8 18.8 - - - +
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Residues in contact with ASP 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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283B HIS* 6.3 0.7 - - - -
292B ZN 4.0 2.3 - - - -
261D HIS* 2.9 45.1 + - - +
262D MET* 3.6 21.5 - - + +
264D ALA* 1.3 74.9 - - - +
266D GLN* 1.3 69.6 + - - +
268D GLU* 3.5 24.2 - - - +
269D GLN* 2.9 31.6 + - - +
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Residues in contact with GLN 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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225D TRP* 3.0 42.3 + - + +
226D PRO* 5.4 3.3 - - - +
227D GLY 5.4 0.9 + - - -
262D MET* 2.8 41.0 + - + +
263D VAL* 3.4 15.2 - - - +
265D ASP* 1.3 76.3 - - - +
267D VAL* 1.3 57.8 + - - +
269D GLN* 3.2 7.5 + - - +
270D ALA* 3.0 23.9 + - - +
273D ARG* 4.9 0.5 + - - -
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Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ILE 5.3 0.2 - - - +
222D VAL* 3.9 29.4 - - + -
225D TRP* 3.9 15.7 - - + -
228D VAL* 3.6 28.7 - - + -
249D LEU* 3.9 14.8 - - + -
263D VAL* 2.9 22.1 + - + +
264D ALA 3.5 6.3 - - - +
266D GLN* 1.3 68.1 - - - +
268D GLU* 1.3 67.6 + - - +
270D ALA* 3.1 10.1 + - + +
271D ILE* 3.1 44.5 + - + +
282D ILE* 4.7 4.5 - - + -
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Residues in contact with GLU 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B HIS* 5.9 3.1 + - - -
264D ALA 2.8 19.6 + - - +
265D ASP* 3.1 25.9 + - - +
267D VAL* 1.3 74.0 - - - +
269D GLN* 1.3 57.4 + - - +
271D ILE* 3.4 7.2 + - - +
272D LEU* 3.1 43.6 + - + +
280D VAL* 3.2 43.2 + - + +
281D ILE* 6.0 0.4 - - - -
282D ILE* 4.4 8.3 - - + +
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Residues in contact with GLN 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 ASP* 2.9 22.1 + - - +
266D GLN* 3.5 6.1 - - - +
268D GLU* 1.3 77.9 - - - +
270D ALA* 1.3 58.9 + - - +
272D LEU* 3.6 14.4 - - + +
273D ARG* 2.9 59.0 + - - +
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Residues in contact with ALA 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ILE* 3.6 24.1 - - + +
225D TRP* 3.8 28.3 - - + -
266D GLN 3.0 13.6 + - - +
267D VAL* 3.1 10.3 + - - +
269D GLN* 1.3 76.8 - - - +
271D ILE* 1.3 60.8 + - - +
273D ARG* 3.5 15.3 - - - +
274D ARG* 3.4 20.1 + - - +
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Residues in contact with ILE 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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218D ILE* 4.2 19.5 - - + -
221D ILE* 4.4 15.9 - - + -
222D VAL* 3.8 13.7 - - + -
245D ILE* 3.8 24.0 - - + -
247D ILE* 5.5 1.3 - - + -
267D VAL* 3.1 45.8 + - + +
268D GLU* 3.6 8.5 - - - +
270D ALA* 1.3 73.7 - - - +
272D LEU* 1.3 57.0 + - + +
274D ARG* 3.1 3.8 + - - +
275D PHE* 2.8 42.1 + - + +
278D SER* 5.1 0.9 - - - -
280D VAL* 3.7 24.2 - - + -
282D ILE* 4.8 9.0 - - + -
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Residues in contact with LEU 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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268D GLU* 3.1 37.4 + - + +
269D GLN* 3.3 15.9 + - + +
271D ILE* 1.3 76.6 - - - +
273D ARG* 1.3 64.8 + - - +
275D PHE 3.8 4.0 - - - +
276D PRO* 3.2 23.0 - - - +
277D GLY 5.6 2.9 - - - +
278D SER* 3.5 33.2 - - - +
280D VAL* 3.9 24.5 - - + +
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Residues in contact with ARG 273 (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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225D TRP* 5.0 9.9 - - - -
266D GLN 4.9 1.6 + - - -
269D GLN* 2.9 56.9 + - - +
270D ALA* 3.5 18.9 - - - +
271D ILE 3.1 0.2 - - - -
272D LEU* 1.3 80.6 - - - +
274D ARG* 1.3 60.8 + - - +
275D PHE 3.4 0.2 + - - -
276D PRO* 3.5 10.9 - - - +
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Residues in contact with ARG 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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213D GLU* 5.4 0.6 + - - +
214D GLU* 5.8 0.6 - - - +
217D GLU* 2.6 41.2 + - + -
221D ILE* 3.6 26.5 - - + -
270D ALA 3.4 3.9 + - - +
271D ILE 3.1 4.9 + - - +
273D ARG* 1.3 78.3 - - - +
275D PHE* 1.3 86.7 + - + +
276D PRO* 3.7 4.7 - - - +
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Residues in contact with PHE 275 (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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214D GLU* 3.7 41.1 - - + -
217D GLU* 3.5 20.6 - - + -
218D ILE* 3.6 32.5 - - + -
221D ILE* 4.5 2.0 - - + -
243D ARG* 3.5 31.2 - - - +
245D ILE* 5.1 1.6 - - + -
271D ILE* 2.8 26.4 + - + +
272D LEU* 3.4 8.9 - - - +
274D ARG* 1.3 106.8 - - + +
276D PRO* 1.3 68.4 - - - +
278D SER* 3.2 31.0 + - - +
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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
------------------------------------------------------------
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