Contacts of the helix formed by residues 345 - 361 (chain D) in PDB entry 2ONL
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 345 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341D VAL 3.3 3.6 + - - -
342D LEU* 3.6 7.5 - - - +
343D LYS 3.1 0.6 + - - -
344D GLU* 1.3 82.7 - - + +
346D LYS* 1.3 58.0 + - - +
347D GLU* 2.7 29.0 + - - +
348D ARG* 2.3 79.9 + - + +
349D TRP* 3.4 5.9 + - - +
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Residues in contact with LYS 346 (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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148D SER* 5.4 2.7 - - - -
151D GLN* 2.6 48.8 + - - +
342D LEU 3.8 5.0 + - - -
343D LYS* 4.2 11.9 + - - +
344D GLU 4.1 1.2 + - - -
345D ASP* 1.3 71.8 - - - +
347D GLU* 1.3 57.7 + - - +
349D TRP* 4.2 17.3 - - + -
350D GLU* 3.8 17.5 + - + +
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Residues in contact with GLU 347 (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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60B GLN* 4.4 19.3 + - - +
345D ASP* 2.7 17.0 + - - +
346D LYS* 1.3 81.2 - - - +
348D ARG* 1.3 59.9 + - - +
349D TRP 3.3 0.2 - - - -
350D GLU* 3.6 13.3 + - - +
351D ASP* 3.3 18.0 + - - +
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Residues in contact with ARG 348 (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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259D GLY 5.1 1.0 + - - -
260D TYR* 4.1 23.7 + - - -
341D VAL* 3.5 36.9 + - - +
342D LEU* 5.8 1.0 - - - +
344D GLU* 3.3 30.1 + - - +
345D ASP* 2.3 54.9 + - - +
347D GLU* 1.3 66.2 - - - +
349D TRP* 1.3 59.3 + - - +
351D ASP* 2.9 9.9 + - + +
352D VAL* 2.6 44.2 + - + +
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Residues in contact with TRP 349 (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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145D GLU* 4.7 7.5 + - - -
147D PHE* 3.1 56.1 - + + +
148D SER* 5.5 4.5 + - - +
151D GLN* 4.4 16.9 + - - -
189D PRO* 4.5 12.3 - - + -
255D ILE* 3.6 19.5 - - + -
342D LEU* 4.8 24.4 - - + +
345D ASP 3.4 12.1 + - - +
346D LYS* 4.2 17.3 - - + +
347D GLU 3.3 0.2 - - - -
348D ARG* 1.3 84.6 - - + +
350D GLU* 1.3 56.6 + - - +
352D VAL* 3.1 33.6 + - + -
353D LYS* 2.9 47.5 + - + +
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Residues in contact with GLU 350 (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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33B GLY 5.0 1.7 - - - +
34B ALA* 4.6 2.6 - - - +
346D LYS* 3.8 12.5 + - + +
347D GLU* 3.6 16.7 + - - +
348D ARG 3.2 0.4 - - - -
349D TRP* 1.3 78.9 - - - +
351D ASP* 1.3 59.6 + - - +
353D LYS* 3.3 28.7 + - - +
354D GLU* 2.9 43.6 + - - +
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Residues in contact with ASP 351 (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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347D GLU 3.3 11.2 + - - +
348D ARG* 2.9 16.1 + - + +
350D GLU* 1.3 79.3 - - - +
352D VAL* 1.3 58.7 + - - +
353D LYS 3.2 0.7 - - - -
354D GLU* 3.1 31.8 - - - +
355D GLU* 3.0 35.7 - - - +
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Residues in contact with VAL 352 (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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255D ILE* 4.1 11.0 - - + -
261D PRO* 3.3 36.8 - - + -
263D PHE* 4.7 4.1 - - + -
348D ARG* 2.6 25.5 + - + +
349D TRP* 3.1 40.6 + - + +
351D ASP* 1.3 71.9 - - - +
353D LYS* 1.3 65.7 + - - +
355D GLU* 3.6 15.8 + - - +
356D MET* 3.2 24.8 + - + +
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Residues in contact with LYS 353 (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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145D GLU* 4.9 7.2 - - - +
188D LYS* 4.6 2.8 + - - -
189D PRO* 5.5 0.9 - - + -
190D GLU* 3.4 36.9 - - + +
349D TRP* 2.9 40.9 + - + +
350D GLU* 3.3 35.5 + - - +
352D VAL* 1.3 76.6 - - - +
354D GLU* 1.3 65.4 + - - +
356D MET* 3.3 7.8 + - - +
357D THR* 3.1 22.8 + - - -
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Residues in contact with GLU 354 (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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33B GLY* 3.8 7.9 - - - -
34B ALA* 2.4 52.3 + - - +
350D GLU* 2.9 40.1 + - - +
351D ASP* 3.1 32.8 - - - +
353D LYS* 1.3 76.5 - - - +
355D GLU* 1.3 49.4 + - - +
357D THR* 2.8 13.3 + - - -
358D SER* 2.7 37.1 + - - +
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Residues in contact with GLU 355 (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 PRO* 5.2 0.3 - - - +
263D PHE* 3.9 21.8 - - + +
351D ASP* 3.0 38.4 + - - +
352D VAL* 3.6 21.9 - - - +
354D GLU* 1.3 76.0 - - - +
356D MET* 1.3 53.4 + - - +
358D SER* 3.1 8.1 + - - -
359D ALA* 2.7 36.9 + - - +
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Residues in contact with MET 356 (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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187D VAL 4.2 4.3 - - - +
188D LYS* 4.4 11.4 - - + +
189D PRO* 3.8 27.1 - - - -
247D TRP* 4.5 12.8 - - + -
248D SER* 4.1 13.0 - - - +
251D VAL* 3.8 24.9 - - + -
252D ILE* 3.6 27.8 - - + -
255D ILE* 6.0 4.5 - - - -
263D PHE* 4.3 18.8 - - + -
352D VAL* 3.2 14.8 + - + +
353D LYS* 3.6 9.6 - - - +
354D GLU 3.1 0.6 - - - -
355D GLU* 1.3 75.6 - - - +
357D THR* 1.3 60.0 + - - +
359D ALA* 3.9 4.4 - - - +
360D LEU* 3.0 39.2 + - + +
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Residues in contact with THR 357 (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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31B GLY* 6.0 0.7 - - - -
32B SER 3.5 30.3 - - - +
33B GLY* 5.2 0.4 - - - -
188D LYS* 3.7 22.3 + - - +
190D GLU* 4.4 2.6 + - - -
353D LYS 3.1 12.8 + - - -
354D GLU* 2.8 13.2 + - - -
356D MET* 1.3 77.1 - - - +
358D SER* 1.3 60.1 + - - +
360D LEU* 4.2 2.6 - - - +
361D ALA* 3.5 21.5 + - + +
364D ARG* 5.2 0.9 + - - -
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Residues in contact with SER 358 (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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32B SER 4.9 5.9 + - - -
33B GLY* 5.3 4.2 - - - -
354D GLU* 2.7 13.2 + - - +
355D GLU* 3.4 12.1 - - - -
357D THR* 1.3 76.7 - - - +
359D ALA* 1.3 63.3 + - - +
361D ALA* 3.3 6.6 + - - +
362D THR* 2.8 31.5 + - - +
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Residues in contact with ALA 359 (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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247D TRP* 4.1 24.9 - - + -
263D PHE* 5.5 4.5 - - + -
355D GLU 2.7 20.5 + - - +
356D MET* 3.9 5.4 - - - +
358D SER* 1.3 71.8 - - - +
360D LEU* 1.3 55.4 + - - +
362D THR* 2.3 43.1 + - - +
363D MET* 3.3 11.1 - - + +
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Residues in contact with LEU 360 (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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185D ARG 3.2 27.6 - - - +
186D ASP* 3.3 28.9 - - - +
187D VAL 4.2 7.6 - - - +
188D LYS* 4.7 8.5 - - - -
244D CYS* 5.4 3.4 - - + +
247D TRP* 3.5 33.9 - - + -
248D SER* 4.8 4.3 - - - +
356D MET* 3.0 22.1 + - + +
357D THR* 4.2 4.9 - - - +
359D ALA* 1.3 77.7 - - - +
361D ALA* 1.3 57.1 + - - +
362D THR 2.8 6.2 + - - -
363D MET* 3.1 18.6 + - + +
364D ARG* 3.4 27.6 + - + +
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Residues in contact with ALA 361 (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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112B ASP* 5.6 1.9 - - - +
115B ASN* 5.6 3.1 + - - -
357D THR* 3.5 16.2 + - + +
358D SER* 3.3 6.3 + - - +
359D ALA 3.3 0.8 - - - -
360D LEU* 1.3 76.1 - - - +
362D THR* 1.3 60.9 + - + +
363D MET 3.7 0.2 - - - -
364D ARG* 3.7 26.1 + - - +
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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