Contacts of the helix formed by residues 273 - 287 (chain B) in PDB entry 3H11
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 THR 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B LYS* 4.3 16.2 - - - +
271B ASP 5.8 0.2 - - - +
272B CYS* 1.3 78.9 - - - +
274B VAL* 1.3 64.1 + - - +
275B GLU* 2.6 33.6 + - + +
276B GLN* 3.0 32.1 + - - +
277B ILE* 3.0 10.3 + - - +
310B GLY* 4.0 0.9 - - - -
311B THR* 3.7 16.6 - - - +
312B ASP* 3.2 33.7 - - + +
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B THR* 1.3 74.5 - - - +
275B GLU* 1.3 63.0 + - - +
277B ILE* 3.3 8.2 + - + +
278B TYR* 3.0 56.5 + - + -
309B TYR 4.4 0.2 - - - -
310B GLY* 3.3 15.5 - - - +
312B ASP* 3.6 3.2 + - - -
314B GLN* 2.9 51.8 - - + +
315B GLU 3.5 17.0 - - - +
316B ALA* 3.6 10.1 - - + +
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B THR* 2.6 32.3 + - - +
274B VAL* 1.3 78.6 - - - +
276B GLN* 1.3 73.9 + - - +
278B TYR* 3.4 7.9 + - - +
279B GLU* 3.1 29.1 + - - +
312B ASP* 4.6 6.0 + - - +
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ASP 3.6 8.1 + - - +
272B CYS* 3.4 18.8 - - + -
273B THR* 3.0 43.4 + - - +
275B GLU* 1.3 88.0 + - - +
277B ILE* 1.3 59.3 + - - +
279B GLU* 3.0 22.7 + - + +
280B ILE* 2.8 37.3 + - + +
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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
----------------------------------------------------------
224B ILE* 4.0 32.3 - - + -
226B ASN* 4.1 13.2 - - - +
272B CYS* 3.6 23.6 - - + +
273B THR 3.0 14.0 + - - +
274B VAL* 3.6 14.1 - - + +
276B GLN* 1.3 75.1 - - - +
278B TYR* 1.3 65.4 + - + +
280B ILE* 3.2 2.6 + - - +
281B LEU* 2.9 29.1 + - + +
299B ILE* 5.1 3.6 - - + -
308B ILE* 3.7 25.6 - - + -
310B GLY* 4.5 2.9 - - - -
316B ALA* 5.5 0.9 - - + -
321B LEU* 4.3 28.3 - - + -
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Residues in contact with TYR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 3.0 49.0 + - + -
275B GLU* 3.7 9.4 - - - +
276B GLN 3.2 0.2 - - - -
277B ILE* 1.3 78.0 - - + +
279B GLU* 1.3 56.4 + - - +
281B LEU* 3.8 5.4 - - - +
282B LYS* 2.9 29.7 + - - +
315B GLU 4.8 1.6 + - - -
316B ALA* 3.8 9.5 - - + +
317B PRO* 3.7 16.6 - - - +
320B GLU* 3.5 27.1 - - + +
321B LEU* 4.0 12.6 - - + -
324B GLN* 3.8 25.9 - - - +
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLU* 3.1 18.0 + - - +
276B GLN* 3.0 42.7 + - + +
278B TYR* 1.3 72.8 - - - +
280B ILE* 1.3 68.9 + - + +
282B LYS* 3.6 7.1 - - - +
283B ILE* 3.0 33.0 + - + +
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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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222B LEU* 3.5 36.8 - - + -
224B ILE* 4.5 9.0 - - + -
269B HIS* 3.4 43.1 - - + +
272B CYS* 3.8 18.6 - - - -
276B GLN* 2.8 22.7 + - + +
277B ILE* 3.7 3.8 - - - +
279B GLU* 1.3 79.6 - - + +
281B LEU* 1.3 63.6 + - - +
283B ILE* 2.9 23.8 + - + +
284B TYR* 3.1 18.5 + - + -
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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
----------------------------------------------------------
222B LEU* 3.9 23.6 - - + -
224B ILE* 4.8 3.4 - - + -
277B ILE* 2.9 25.8 + - + +
278B TYR 3.9 2.5 - - - +
280B ILE* 1.3 76.1 - - - +
282B LYS* 1.3 57.2 + - - +
284B TYR* 3.2 3.3 + - - +
285B GLN* 2.9 28.6 + - - +
297B CYS* 4.0 19.3 - - + -
299B ILE* 5.4 1.1 - - + -
321B LEU* 3.4 56.3 - - + +
324B GLN* 3.6 16.8 - - - +
325B PHE* 3.6 23.8 - - + -
340B PHE* 5.4 0.9 - - + -
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Residues in contact with LYS 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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278B TYR 2.9 19.3 + - - +
279B GLU* 3.6 8.7 - - - +
280B ILE 3.1 0.2 - - - -
281B LEU* 1.3 76.5 - - - +
283B ILE* 1.3 64.0 + - + +
285B GLN* 2.7 33.8 + - - +
286B LEU* 3.1 49.0 + - + +
324B GLN* 3.8 9.4 + - - +
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLU* 3.0 23.7 + - + +
280B ILE* 2.9 13.7 + - + +
282B LYS* 1.3 79.6 - - + +
284B TYR* 1.3 67.4 + - + +
286B LEU* 3.4 8.3 + - + +
287B MET* 2.8 47.8 + - + +
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Residues in contact with TYR 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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220B TYR* 3.9 27.4 - + + -
222B LEU* 3.8 26.9 - - + -
267B LYS* 3.2 35.9 - - + +
269B HIS* 4.8 6.1 + - - -
280B ILE* 3.1 24.4 + - + +
281B LEU* 3.2 7.2 + - - +
283B ILE* 1.3 83.1 - - + +
285B GLN* 1.3 66.7 + - - +
287B MET* 3.3 31.2 + - - -
289B HIS* 2.8 29.6 + + - -
295B PHE* 3.9 36.3 - + + -
325B PHE* 4.0 4.8 - - + -
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Residues in contact with GLN 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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281B LEU 2.9 16.6 + - - +
282B LYS* 2.7 44.0 + - - +
283B ILE 3.3 0.2 - - - -
284B TYR* 1.3 79.0 - - - +
286B LEU* 1.3 64.9 + - + +
287B MET 3.7 1.0 + - - +
324B GLN* 2.9 46.3 + - - +
325B PHE* 3.7 14.7 - - + -
329B LYS* 3.6 37.3 - - - +
330B CYS* 3.5 20.8 - - + +
331B PRO* 5.6 0.5 - - - +
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Residues in contact with LEU 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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282B LYS* 3.1 46.0 + - + +
283B ILE* 3.4 7.6 + - + +
285B GLN* 1.3 82.8 - - - +
287B MET* 1.3 65.8 + - - +
329B LYS 5.8 1.3 - - - +
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Residues in contact with MET 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 3.6 28.0 - - + +
267B LYS* 6.4 0.2 - - - -
283B ILE* 2.8 37.7 + - + +
284B TYR* 3.3 45.2 + - - +
285B GLN 4.2 2.8 - - - +
286B LEU* 1.3 83.6 - - - +
288B ASP* 1.3 67.8 + - + +
289B HIS* 3.4 21.9 + - + +
330B CYS* 5.0 0.2 - - - -
332B SER* 3.6 5.7 + - - -
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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