Contacts of the helix formed by residues 276 - 285 (chain D) in PDB entry 1ZBU
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 LYS 276 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261D ARG* 3.3 25.7 - - - +
273D SER* 3.4 17.9 + - - +
274D GLN 3.6 2.4 + - - -
275D THR* 1.3 88.9 - - - +
277D LEU* 1.3 62.2 + - - +
278D THR* 4.7 9.0 - - + -
279D ILE* 3.5 29.9 - - + +
280D MSE 2.9 19.0 - - - +
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Residues in contact with LEU 277 (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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230D ASP* 4.1 13.2 - - - +
261D ARG* 3.7 6.4 - - - +
276D LYS* 1.3 75.9 - - - +
278D THR* 1.3 70.6 + - + +
279D ILE 3.1 2.0 + - - -
280D MSE 3.2 21.0 + - + +
281D LEU* 3.3 34.4 + - + +
288D TYR* 3.6 23.3 - - + -
298D ASP* 3.8 30.7 - - - +
301D ASN* 4.0 13.5 - - + +
302D ILE* 4.0 26.2 - - + -
305D ILE* 4.9 3.4 - - + -
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Residues in contact with THR 278 (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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326B GLN* 4.1 20.5 + - - +
276D LYS* 4.7 7.4 - - + -
277D LEU* 1.3 82.4 - - + +
279D ILE* 1.3 76.4 + - + +
281D LEU* 3.8 2.1 + - - +
282D GLU* 3.5 20.4 + - - +
288D TYR* 4.2 20.3 - - + -
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Residues in contact with ILE 279 (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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273D SER 4.7 5.2 - - - +
274D GLN* 3.4 44.6 - - + +
276D LYS* 3.5 43.1 - - + +
277D LEU 3.1 0.8 - - - -
278D THR* 1.3 83.5 + - + +
280D MSE 1.3 67.6 + - - +
281D LEU 3.1 0.2 + - - -
282D GLU* 3.3 4.4 + - - +
283D LYS* 2.8 44.2 + - + +
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Residues in contact with MSE 280 (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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230D ASP* 4.0 18.6 - - - +
260D ILE* 4.6 13.9 - - + +
261D ARG* 4.8 5.2 - - - +
264D TYR* 3.6 52.2 + - + -
274D GLN 4.5 0.2 - - - +
275D THR* 3.3 25.8 - - - +
276D LYS 2.9 42.6 + - - +
277D LEU* 3.2 12.6 + - + +
279D ILE* 1.3 77.9 - - - +
281D LEU* 1.3 62.3 + - - +
284D LEU* 3.1 32.2 + - - +
302D ILE* 5.8 1.6 - - + -
305D ILE* 3.7 30.3 - - + -
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Residues in contact with LEU 281 (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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277D LEU* 3.3 19.8 + - + +
278D THR 4.2 3.1 - - - +
279D ILE 3.2 0.4 - - - -
280D MSE 1.3 76.4 - - - +
282D GLU* 1.3 66.3 + - - +
284D LEU* 3.2 5.0 + - - +
285D GLY 3.1 4.7 + - - -
286D MSE 3.0 49.9 + - + +
287D ASP 4.6 4.3 - - - +
288D TYR* 3.7 34.3 - - + -
301D ASN* 3.8 28.7 - - + +
304D ARG* 4.0 18.2 - - - +
305D ILE* 3.7 26.5 - - + -
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Residues in contact with GLU 282 (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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233B TRP* 5.3 0.5 + - - -
236B SER* 4.1 27.0 + - - +
237B LYS* 5.7 1.7 - - - -
240B ASN* 5.3 0.9 - - - +
322B MSE 5.3 1.4 - - - +
325B GLY 4.3 11.5 - - - +
326B GLN* 3.1 36.4 + - - +
327B LEU* 3.1 26.5 + - - +
278D THR 3.5 10.2 + - - +
279D ILE* 3.3 5.0 + - - +
281D LEU* 1.3 77.0 - - - +
283D LYS* 1.3 63.5 - - + +
285D GLY* 2.8 20.8 + - - -
286D MSE 4.0 8.7 + - - -
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Residues in contact with LYS 283 (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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145B PRO* 5.1 12.8 + - - -
146B GLU* 5.3 10.5 + - - -
233B TRP* 4.1 4.3 + - - -
237B LYS* 3.6 32.0 + - - +
264D TYR* 3.6 19.3 - - - +
270D VAL* 6.0 7.6 - - + -
274D GLN* 5.0 11.0 + - - +
279D ILE* 2.8 36.2 + - + +
282D GLU* 1.3 78.1 - - + +
284D LEU* 1.3 61.2 + - - +
285D GLY 3.4 0.5 + - - -
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Residues in contact with LEU 284 (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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233B TRP* 4.0 8.9 + - - -
272B ARG* 4.9 0.2 + - - -
264D TYR* 3.7 22.7 - - + +
268D TYR* 3.3 35.2 - - + +
280D MSE 3.1 22.8 + - - +
281D LEU 3.7 4.0 - - - +
282D GLU 3.2 0.2 - - - -
283D LYS* 1.3 76.1 - - - +
285D GLY* 1.3 58.1 + - - +
286D MSE 4.1 11.2 - - - -
305D ILE* 4.1 20.9 - - + +
308D ARG* 2.8 60.9 + - + +
309D MSE 5.2 0.2 - - + -
312D ASP* 3.7 10.5 - - - +
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Residues in contact with GLY 285 (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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232B SER* 3.2 26.2 + - - -
233B TRP* 4.0 11.7 - - - -
236B SER* 5.5 0.7 - - - -
259B ASN* 5.8 0.7 + - - -
320B GLU* 5.0 1.4 - - - +
327B LEU* 3.7 9.6 - - - +
281D LEU 3.1 0.2 + - - -
282D GLU 2.8 16.3 + - - -
283D LYS 3.2 0.6 - - - -
284D LEU* 1.3 78.8 - - - +
286D MSE 1.3 62.6 + - - +
287D ASP* 5.2 0.5 - - - +
308D ARG* 4.8 1.7 + - - -
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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