Contacts of the helix formed by residues 306 - 318 (chain D) in PDB entry 1O97
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 ASP 306 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247C ILE* 5.0 1.6 - - + +
289D THR* 3.5 7.5 - - + +
305D ALA* 1.3 72.7 - - - +
307D ILE* 1.3 66.7 + - - +
308D PHE* 3.1 20.0 + - - +
309D ASP* 3.0 46.9 + - + +
310D ILE* 3.1 23.8 + - - +
1319D FAD 2.9 28.0 + - - -
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Residues in contact with ILE 307 (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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211D GLY 3.7 30.7 - - - +
212D ILE* 3.7 21.5 - - + -
221D PHE* 4.0 15.3 - - + -
266D MET* 4.1 11.4 - - + +
267D GLY* 3.7 15.0 - - - +
287D VAL* 3.4 36.1 - - + +
306D ASP* 1.3 73.1 - - - +
308D PHE* 1.3 69.8 + - + +
310D ILE* 4.0 1.8 - - - +
311D GLU* 2.9 29.8 + - - +
1319D FAD 3.0 30.4 + - + +
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Residues in contact with PHE 308 (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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211D GLY 3.7 13.9 - - - -
212D ILE* 3.3 28.5 - - - -
213D GLY* 5.2 0.4 - - - -
214D GLU* 4.9 1.1 - - - -
217D ASN* 3.6 19.3 - - - -
220D GLN* 3.5 22.2 - - - +
221D PHE* 4.0 19.5 - + - -
306D ASP* 3.1 18.1 + - - +
307D ILE* 1.3 80.1 - - + +
309D ASP* 1.3 62.0 + - - +
311D GLU* 3.1 11.1 - - - +
312D GLU* 3.0 29.9 + - - +
1319D FAD 3.8 18.4 - - - -
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Residues in contact with ASP 309 (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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247C ILE* 3.6 27.0 - - + +
306D ASP* 3.0 30.9 + - + +
308D PHE* 1.3 76.2 - - - +
310D ILE* 1.3 64.7 + - - +
312D GLU* 3.3 21.3 - - - +
313D GLU* 3.1 23.9 + - - +
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Residues in contact with ILE 310 (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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247C ILE* 3.7 28.0 - - + +
250C GLN* 3.9 29.8 - - + +
251C ALA* 4.4 5.4 - - + +
254C ILE* 4.0 15.9 - - + -
266D MET* 5.7 4.9 - - - -
287D VAL* 4.0 20.2 - - + -
303D ILE* 4.1 7.6 - - + -
305D ALA* 3.8 12.6 - - + -
306D ASP 3.1 16.7 + - - +
307D ILE 4.0 4.0 - - - +
309D ASP* 1.3 75.6 - - - +
311D GLU* 1.3 56.0 + - - +
313D GLU* 3.3 1.6 + - - +
314D LEU* 2.7 54.0 + - + +
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Residues in contact with GLU 311 (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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220D GLN* 3.0 56.8 + - - +
221D PHE* 3.8 22.2 - - + -
224D LEU* 3.9 27.9 - - + +
266D MET* 5.7 0.7 - - - -
307D ILE 2.9 19.5 + - - +
308D PHE 3.1 12.6 - - - +
309D ASP 3.3 0.2 - - - -
310D ILE* 1.3 77.7 - - - +
312D GLU* 1.3 71.7 + - - +
314D LEU* 3.6 2.5 - - - +
315D LYS* 3.0 28.2 + - - +
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Residues in contact with GLU 312 (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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308D PHE 3.0 17.4 + - - +
309D ASP* 3.3 28.5 - - - +
311D GLU* 1.3 86.8 + - - +
313D GLU* 1.3 65.7 + - + +
315D LYS* 3.2 6.2 + - - +
316D ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 313 (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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247C ILE* 3.5 15.5 - - + +
248C SER* 3.8 28.6 + - - -
251C ALA* 3.5 20.4 - - + -
309D ASP 3.1 16.9 + - - +
310D ILE 3.8 1.8 - - - +
312D GLU* 1.3 76.3 - - + +
314D LEU* 1.3 66.1 + - - +
316D ALA* 3.1 12.7 + - - +
317D GLN* 2.8 47.0 + - - +
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Residues in contact with LEU 314 (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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251C ALA* 3.5 35.4 - - + +
254C ILE* 3.9 29.6 - - + -
255C ILE* 4.8 6.1 - - + +
258C ILE* 5.5 2.9 - - + -
206D MET* 4.3 10.8 - - + -
224D LEU* 3.7 29.4 - - + -
264D VAL* 6.0 1.1 - - + -
266D MET* 5.5 3.8 - - - -
310D ILE* 2.7 34.9 + - + +
311D GLU 3.6 4.9 - - - +
312D GLU 3.4 0.2 - - - -
313D GLU* 1.3 73.6 - - - +
315D LYS* 1.3 56.0 + - - +
317D GLN* 3.4 5.0 + - + +
318D LEU* 2.9 43.1 + - + +
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Residues in contact with LYS 315 (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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223D GLU 6.1 0.4 - - - +
224D LEU* 4.0 16.5 - - + +
227D GLU* 6.1 4.8 - - + +
311D GLU* 3.0 23.3 + - - +
312D GLU* 3.7 6.3 - - - +
313D GLU 3.2 0.2 - - - -
314D LEU* 1.3 76.6 - - - +
316D ALA* 1.3 62.0 + - - +
318D LEU* 3.6 17.8 + - - +
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Residues in contact with ALA 316 (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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312D GLU 3.0 13.5 + - - +
313D GLU* 3.1 18.8 + - - +
315D LYS* 1.3 75.3 - - - +
317D GLN* 1.3 64.2 + - + +
318D LEU 3.3 5.0 + - - -
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Residues in contact with GLN 317 (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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248C SER* 2.8 27.2 - - - +
251C ALA* 3.8 9.1 + - - +
252C ALA* 3.3 33.0 + - - +
255C ILE* 4.6 11.7 - - + +
313D GLU* 2.8 40.2 + - - +
314D LEU* 3.9 4.9 - - + +
316D ALA* 1.3 74.5 - - - +
318D LEU* 1.3 62.4 + - + +
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Residues in contact with LEU 318 (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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255C ILE* 4.8 17.5 - - + -
258C ILE* 5.3 13.2 - - + -
224D LEU* 4.6 11.4 - - + -
227D GLU* 4.3 16.2 - - + +
228D ALA* 4.0 37.5 - - + +
314D LEU* 2.9 32.4 + - + +
315D LYS* 3.9 14.6 - - - +
316D ALA 3.2 5.0 - - - -
317D GLN* 1.3 83.7 - - + +
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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