Contacts of the helix formed by residues 279 - 286 (chain B) in PDB entry 2IHU
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 PRO 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B ASP* 4.4 6.5 - - - +
277B ASN 4.9 0.7 - - - +
278B PHE* 1.3 101.3 - - + +
280B ALA* 1.3 56.4 + - - +
281B LEU 3.5 2.0 - - - -
282B GLN* 4.1 19.1 - - + -
283B THR* 2.8 32.0 + - - +
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Residues in contact with ALA 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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272B MET* 3.7 25.1 - - + -
273B ASP* 3.0 11.6 + - - +
276B LEU* 4.1 11.2 - - + -
278B PHE* 2.8 18.9 + - + +
279B PRO* 1.3 71.0 - - - +
281B LEU* 1.3 59.0 + - - +
283B THR* 3.2 3.8 + - - -
284B MET* 2.9 29.6 + - - +
364B LEU* 3.7 27.9 - - + +
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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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268B VAL* 3.9 19.3 - - + -
269B THR 4.7 2.0 - - - +
270B GLY* 4.9 11.7 - - - +
272B MET* 3.7 27.6 - - + -
273B ASP* 2.9 26.4 + - - +
280B ALA* 1.3 74.7 - - - +
282B GLN* 1.3 58.8 + - + +
284B MET* 4.3 3.4 - - + -
285B PHE* 2.8 43.0 + - + +
306B MET* 3.7 25.1 - - + +
309B LYS* 3.8 35.7 - - - +
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Residues in contact with GLN 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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273B ASP* 5.1 3.1 + - - +
279B PRO* 3.7 21.8 + - + +
280B ALA 3.3 0.4 - - - -
281B LEU* 1.3 78.5 - - - +
283B THR* 1.3 58.7 + - - +
286B ALA* 2.7 54.7 + - + +
287B PRO* 4.1 0.7 - - - +
309B LYS* 3.8 28.0 - - + +
310B GLY* 3.6 13.8 + - - +
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Residues in contact with THR 283 (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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278B PHE* 3.5 16.7 - - + -
279B PRO* 2.8 28.0 + - - +
280B ALA 3.2 4.2 + - - -
282B GLN* 1.3 75.3 - - - +
284B MET* 1.3 61.5 + - - +
287B PRO* 4.2 4.7 - - - +
359B HIS* 3.8 8.3 - - - -
360B ASP 4.2 6.7 - - - +
361B ILE* 3.6 31.1 - - + +
363B PRO* 4.8 7.8 - - + +
364B LEU* 3.8 26.9 - - + +
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Residues in contact with MET 284 (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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248B ILE* 3.5 29.9 - - + +
265B TYR* 3.2 41.3 - - - +
266B GLY* 5.0 3.1 - - - +
267B ALA 4.7 8.1 - - - +
268B VAL* 5.0 4.5 - - + -
272B MET* 4.4 16.4 - - + -
280B ALA 2.9 14.1 + - - +
281B LEU* 3.7 6.7 - - + +
283B THR* 1.3 78.3 - - - +
285B PHE* 1.3 75.4 + - + +
288B VAL* 3.6 4.0 - - - +
359B HIS* 2.7 25.9 + - - -
361B ILE* 4.3 5.8 - - - -
364B LEU* 3.5 26.4 - - + +
368B ILE* 6.2 0.9 - - + -
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Residues in contact with PHE 285 (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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220B VAL* 4.4 7.0 - - + -
222B VAL* 4.2 15.0 - - + -
248B ILE* 3.7 28.9 - - + -
268B VAL* 3.8 30.3 - - + -
281B LEU* 2.8 26.6 + - + +
284B MET* 1.3 85.4 - - + +
286B ALA* 1.3 61.3 + - - +
287B PRO* 3.4 4.0 - - - -
288B VAL* 3.0 20.5 + - + +
291B VAL* 4.9 2.9 - - + -
302B LEU* 5.2 4.5 - - + -
306B MET* 3.5 24.0 - - + -
307B TRP* 3.6 39.3 - - + +
309B LYS* 4.0 5.4 - - + -
313B LYS* 2.8 23.7 + - - -
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Residues in contact with ALA 286 (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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281B LEU 4.2 0.4 + - - -
282B GLN* 2.7 47.7 + - + +
285B PHE* 1.3 70.9 - - - +
287B PRO* 1.4 60.8 - - + +
309B LYS 3.4 11.0 + - - -
310B GLY* 3.9 7.4 - - - -
311B ILE* 3.1 29.9 + - - +
313B LYS* 3.3 5.9 + - - -
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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