Contacts of the helix formed by residues 270 - 282 (chain A) in PDB entry 1NUA
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 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A TRP* 1.3 73.9 - - - +
271A HIS* 1.3 50.9 + - - +
274A GLY* 2.8 31.4 + - - -
291A VAL* 4.0 6.1 - - - +
294A GLY* 3.3 8.5 - - - -
295A MET* 3.5 27.6 - - - -
298A GLU* 2.6 31.1 + - - -
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLU* 3.3 18.4 + - - -
197A LYS* 3.5 17.3 - - + -
267A LEU 3.9 3.0 + - - -
268A ASN* 3.1 29.8 + - + +
269A TRP 3.1 11.5 + - - -
270A GLY* 1.3 76.3 - - - +
272A SER* 1.3 61.2 + - - +
273A ILE 3.3 0.7 - - - -
274A GLY* 3.5 4.5 - - - +
275A HIS* 2.7 66.0 + + + +
287A HIS* 3.4 6.6 + + - -
291A VAL* 3.6 16.3 - - + +
600A ZN 2.3 35.7 - - - -
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASN* 3.7 10.1 + - - +
271A HIS* 1.3 80.7 - - - +
273A ILE* 1.3 61.7 + - - +
275A HIS* 4.2 2.3 - - - +
276A ALA 3.7 7.1 + - - -
298A GLU* 2.9 12.0 + - - -
352A MET* 3.6 21.0 - - - +
364A LYS 3.2 20.5 + - - -
365A ILE* 3.3 29.3 - - - +
366A VAL* 4.5 2.3 + - - +
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A SER* 1.3 76.7 - - - +
274A GLY* 1.3 67.0 + - - +
276A ALA* 3.1 7.6 + - + +
277A ILE* 2.9 36.0 + - + +
294A GLY* 4.3 5.6 - - - -
297A LYS* 3.5 39.0 - - + +
298A GLU* 3.1 28.8 + - + +
301A LEU* 5.6 3.6 - - + -
348A LEU* 5.0 3.4 - - + -
352A MET* 4.3 19.1 - - + -
365A ILE* 5.1 3.1 - - + -
387A ILE* 5.0 3.6 - - + -
390A VAL* 4.2 7.4 - - + -
391A LEU* 4.2 26.2 - - + -
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Residues in contact with GLY 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLY 2.8 24.0 + - - -
271A HIS* 3.8 2.0 - - - -
272A SER 3.3 0.2 - - - -
273A ILE* 1.3 78.7 - - - +
275A HIS* 1.3 58.2 + - - +
277A ILE* 3.1 5.3 + - - +
278A GLU* 2.8 30.0 + - - +
290A CYS* 3.7 24.4 - - - +
291A VAL* 4.3 4.3 - - - -
294A GLY* 3.8 2.4 - - - -
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Residues in contact with HIS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASN* 4.7 6.7 - - - -
271A HIS* 2.7 53.7 + + + +
272A SER* 4.2 2.4 - - - +
274A GLY* 1.3 72.6 - - - -
276A ALA* 1.3 58.2 + - - +
278A GLU* 3.7 20.5 - - - +
279A ALA* 2.8 32.2 + - - +
287A HIS* 3.8 13.6 - + - -
351A ASN 5.7 1.8 - - - +
355A ASP* 5.3 11.1 + - - +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A SER 3.7 2.0 + - - +
273A ILE* 3.1 11.7 + - + +
275A HIS* 1.3 79.0 - - - +
277A ILE* 1.3 63.6 + - - +
279A ALA 3.7 2.8 + - - -
280A ILE* 3.4 19.9 - - - +
348A LEU* 3.6 36.6 - - + +
351A ASN* 3.6 21.7 + - + -
352A MET* 3.6 20.2 - - + +
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ILE* 2.9 30.9 + - + +
274A GLY* 3.4 9.2 - - - +
276A ALA* 1.3 76.4 - - - +
278A GLU* 1.3 58.4 + - - +
280A ILE* 2.9 22.4 + - - +
281A LEU* 3.0 38.0 + - + -
290A CYS* 3.9 20.6 - - + +
293A ILE* 5.0 7.0 - - + -
294A GLY 5.2 0.7 - - - +
297A LYS* 4.8 5.8 - - - +
329A LEU* 3.7 36.1 - - + -
343A CYS* 4.6 2.9 - - - -
348A LEU* 3.4 24.9 - - + -
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A GLY 2.8 16.3 + - - +
275A HIS* 3.8 17.0 - - - +
277A ILE* 1.3 74.6 - - - +
279A ALA* 1.3 65.5 + - - +
281A LEU 4.4 0.4 - - - +
282A THR* 2.8 45.6 + - + +
285A ILE 4.8 2.4 - - - +
286A LEU 4.1 0.2 - - - -
287A HIS* 3.1 50.7 + - - +
290A CYS* 3.4 23.3 - - + -
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A HIS 2.8 20.5 + - - +
276A ALA 3.9 6.3 - - - +
277A ILE 3.3 0.4 - - - -
278A GLU* 1.3 73.2 - - - +
280A ILE* 1.3 59.9 + - - +
282A THR* 3.9 11.8 - - - +
351A ASN* 4.3 20.9 - - + +
354A LEU* 6.0 3.8 - - + -
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ALA 3.4 9.4 - - - +
277A ILE 2.9 8.6 + - - +
279A ALA* 1.3 80.4 - - - +
281A LEU* 1.3 63.5 + - + +
282A THR 3.5 2.4 + - - +
341A LYS* 3.0 34.4 + - + -
342A HIS 4.8 4.7 - - - +
343A CYS* 3.6 44.2 - - + +
347A GLN* 3.3 32.8 - - + +
348A LEU* 4.2 7.6 - - + -
351A ASN* 3.3 20.9 - - - +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ILE* 3.0 34.4 + - + +
280A ILE* 1.3 76.9 - - + +
282A THR* 1.3 67.5 + - - +
284A GLN* 3.1 11.1 + - - +
285A ILE* 3.0 47.8 + - + -
290A CYS* 4.6 3.1 - - - -
293A ILE* 6.5 0.4 - - + -
329A LEU* 4.5 7.6 - - + -
334A ILE* 4.2 16.4 - - + -
338A THR* 4.1 5.4 - - + +
341A LYS* 3.7 35.1 + - + +
343A CYS* 3.6 24.2 - - - -
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 5.3 3.1 + - - -
278A GLU* 2.8 43.3 + - + +
279A ALA* 3.9 14.5 - - - +
280A ILE 3.8 2.6 - - - +
281A LEU* 1.3 80.1 - - - +
283A PRO* 1.3 73.5 - - + +
284A GLN* 3.3 0.7 - - - -
285A ILE 3.7 10.4 + - - -
341A LYS* 3.2 12.3 + - - -
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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