Contacts of the helix formed by residues 270 - 282 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B TRP* 1.3 73.2 - - - +
271B HIS* 1.3 50.7 + - - -
274B GLY* 2.7 32.1 + - - -
291B VAL* 4.1 5.3 - - - +
294B GLY* 3.3 7.4 - - - -
295B MET* 3.5 28.7 - - - -
298B GLU* 2.6 30.6 + - - +
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B GLU* 3.3 21.5 - - - -
197B LYS* 3.5 18.1 + - + -
267B LEU 3.9 3.4 + - - -
268B ASN* 3.0 29.3 + - + +
269B TRP 3.1 12.1 + - - -
270B GLY* 1.3 76.9 - - - +
272B SER* 1.3 61.0 + - - +
273B ILE 3.3 0.2 - - - -
274B GLY* 3.5 4.9 - - - +
275B HIS* 2.7 66.5 + + + +
287B HIS* 3.3 6.3 + + - -
291B VAL* 3.6 15.1 - - + +
601B ZN 2.3 31.5 - - - -
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASN* 3.7 8.7 + - - +
271B HIS* 1.3 76.8 - - - +
273B ILE* 1.3 60.3 + - - -
275B HIS* 4.3 2.3 - - - +
276B ALA 3.8 6.4 + - - -
298B GLU* 2.8 17.5 + - - -
352B MET* 3.6 23.5 - - - +
364B LYS 3.4 18.2 + - - -
365B ILE* 3.3 33.2 - - - +
366B VAL* 4.4 1.9 + - - +
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B SER* 1.3 75.7 - - - +
274B GLY* 1.3 66.0 + - - +
276B ALA* 3.1 9.7 + - + +
277B ILE* 3.0 36.0 + - + +
294B GLY* 4.3 5.6 - - - -
297B LYS* 3.4 42.6 - - + +
298B GLU* 2.9 32.8 + - + +
301B LEU* 5.3 4.9 - - + -
348B LEU* 5.7 0.9 - - + -
352B MET* 4.5 16.8 - - + -
365B ILE* 5.1 1.8 - - + -
387B ILE* 5.0 4.9 - - + -
390B VAL* 4.5 6.1 - - + -
391B LEU* 4.2 26.7 - - + -
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLY 2.7 24.2 + - - -
271B HIS* 3.8 2.0 - - - -
272B SER 3.4 0.2 - - - -
273B ILE* 1.3 78.9 - - - +
275B HIS* 1.3 58.4 + - - +
277B ILE* 3.1 5.7 + - - +
278B GLU* 2.8 30.0 + - - +
290B CYS* 3.7 25.1 - - - +
291B VAL* 4.3 3.8 - - - -
294B GLY* 3.8 2.0 - - - -
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Residues in contact with HIS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASN* 4.8 6.3 - - - -
271B HIS* 2.7 54.4 + + + +
272B SER* 4.3 2.9 - - - +
274B GLY* 1.3 72.8 - - - +
276B ALA* 1.3 53.4 + - - +
278B GLU* 3.7 20.2 - - - +
279B ALA* 2.8 35.5 + - - +
287B HIS* 3.8 14.5 - + - -
291B VAL* 5.3 0.2 - - + -
355B ASP* 5.4 9.9 + - + -
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B SER 3.8 1.6 + - - -
273B ILE* 3.1 13.9 + - + +
275B HIS* 1.3 78.1 - - - +
277B ILE* 1.3 64.5 + - - +
279B ALA 3.7 1.6 + - - -
280B ILE* 3.5 6.6 - - - +
348B LEU* 3.5 36.5 - - + +
351B ASN* 3.3 34.2 + - + -
352B MET* 3.5 20.2 - - + +
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Residues in contact with ILE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ILE* 3.0 32.6 + - + +
274B GLY* 3.4 8.3 - - - +
276B ALA* 1.3 76.7 - - - +
278B GLU* 1.3 57.6 + - - +
280B ILE* 2.9 21.8 + - - +
281B LEU* 3.0 38.1 + - + -
290B CYS* 3.9 20.9 - - + +
293B ILE* 5.0 9.4 - - + -
294B GLY 5.2 0.4 - - - +
297B LYS* 5.4 3.6 - - + +
329B LEU* 3.6 37.2 - - + -
343B CYS* 4.8 1.8 - - - -
348B LEU* 4.0 23.1 - - + -
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B GLY 2.8 16.8 + - - +
275B HIS* 3.7 16.0 - - - +
277B ILE* 1.3 75.0 - - - +
279B ALA* 1.3 66.8 + - - +
281B LEU 4.4 0.7 - - - +
282B THR* 2.8 46.9 + - + +
285B ILE 4.8 2.2 - - - +
286B LEU* 4.1 0.3 - - - -
287B HIS* 3.1 52.7 + - - +
290B CYS* 3.4 21.9 - - + -
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B HIS 2.8 20.0 + - - +
276B ALA 3.9 6.7 - - - +
277B ILE 3.3 0.2 + - - -
278B GLU* 1.3 74.6 - - - +
280B ILE* 1.3 61.0 + - - +
282B THR* 3.9 11.8 - - - +
351B ASN* 4.0 21.8 - - + +
354B LEU* 6.0 3.4 - - + -
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Residues in contact with ILE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ALA 3.5 2.7 - - - +
277B ILE 2.9 7.9 + - - +
279B ALA* 1.3 81.7 - - - +
281B LEU* 1.3 62.6 + - + +
282B THR 3.5 3.6 + - - +
341B LYS* 3.4 33.6 + - + -
342B HIS 4.5 10.1 - - - +
343B CYS* 3.4 28.5 - - + -
347B GLN* 3.6 29.4 - - + -
348B LEU* 3.3 33.0 - - + -
351B ASN* 3.2 17.9 - - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B ILE* 3.0 33.3 + - + +
280B ILE* 1.3 78.2 - - + +
282B THR* 1.3 67.1 + - - +
284B GLN* 3.1 12.9 + - - +
285B ILE* 3.1 46.6 + - + -
290B CYS* 4.6 2.9 - - - -
293B ILE* 6.5 0.2 - - + -
329B LEU* 4.1 10.8 - - + -
334B ILE* 4.0 17.9 - - + -
338B THR* 3.8 17.9 - - + +
341B LYS* 4.3 16.8 - - + +
343B CYS* 3.5 21.8 - - - -
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLU* 5.4 4.3 + - - -
278B GLU* 2.8 44.2 + - + +
279B ALA* 3.9 14.1 - - - +
280B ILE 3.8 7.3 - - - +
281B LEU* 1.3 81.5 - - - +
283B PRO* 1.3 75.9 - - + +
284B GLN* 3.3 4.1 - - - +
285B ILE 3.6 10.6 + - - -
341B LYS* 4.6 2.9 + - - -
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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