Contacts of the helix formed by residues 273 - 284 (chain B) in PDB entry 4I6J
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 GLN 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B ASP* 2.7 24.8 + - - +
271B THR* 4.0 7.4 + - + +
272B ILE* 1.3 73.7 + - - +
274B LYS* 1.3 55.7 + - - +
275B SER* 2.8 25.2 + - - +
276B SER* 2.5 35.4 + - - +
277B TRP 3.5 0.5 + - - -
306B TYR* 3.8 0.9 - - - -
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Residues in contact with LYS 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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272B ILE 3.5 0.2 + - - -
273B GLN* 1.3 72.3 - - - +
275B SER* 1.3 61.9 + - - +
276B SER 3.1 0.3 + - - -
277B TRP* 3.1 3.0 + - - +
278B ASP* 2.8 74.3 + - - +
306B TYR* 3.4 65.2 + - + -
307B GLU* 3.8 21.7 + - - +
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.7 2.6 - - - +
273B GLN* 2.7 26.8 + - - +
274B LYS* 1.3 76.0 - - - +
276B SER* 1.3 61.6 + - - +
278B ASP* 4.2 7.4 - - - +
279B ALA* 3.3 22.7 + - - +
282B ARG* 5.6 0.2 + - - -
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Residues in contact with SER 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASP* 2.6 45.5 + - - +
241B LEU* 3.9 20.0 - - - +
242B LEU* 3.9 16.4 - - - +
245B SER* 4.2 1.9 + - - -
272B ILE* 3.7 9.0 - - - -
273B GLN* 2.5 12.7 + - - +
275B SER* 1.3 71.5 - - - +
277B TRP* 1.3 65.5 + - - -
279B ALA* 3.3 3.8 + - - +
280B PHE* 3.2 22.8 + - - +
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Residues in contact with TRP 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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233B TYR* 6.0 0.2 - + - -
236B LEU* 4.0 24.2 - - + -
241B LEU* 4.1 26.9 - - + -
255B LEU* 4.4 4.5 - - + -
257B ILE* 5.2 0.9 - - + -
272B ILE* 4.1 18.2 - - + +
273B GLN 3.5 1.0 + - - -
274B LYS 3.1 7.2 + - - +
276B SER* 1.3 79.5 - - - +
278B ASP* 1.3 60.7 + - - +
280B PHE* 3.0 50.8 + + - +
281B ILE* 3.3 14.2 + - - +
289B LEU* 3.6 33.4 - - + -
291B MET* 4.1 13.7 - - + -
306B TYR* 3.3 38.3 + + + -
307B GLU 4.9 1.1 - - - +
308B ILE* 3.8 17.8 - - + +
309B PRO* 4.0 16.6 - - + +
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Residues in contact with ASP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LYS* 2.8 63.1 + - - +
275B SER* 4.2 6.2 + - - +
277B TRP* 1.3 73.9 - - - +
279B ALA* 1.3 63.1 + - - +
280B PHE 3.3 0.2 + - - -
281B ILE* 3.8 16.5 - - + +
282B ARG* 3.2 35.0 + - - +
307B GLU* 4.1 7.8 - - - +
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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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242B LEU* 3.9 17.7 - - + -
245B SER* 3.2 20.6 + - - +
275B SER 3.3 16.5 + - - +
276B SER 3.3 6.2 + - - +
277B TRP 3.2 0.4 - - - -
278B ASP* 1.3 78.5 - - - +
280B PHE* 1.3 56.8 + - - +
282B ARG* 3.4 29.0 + - - +
283B HIS* 3.2 22.2 + - - +
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Residues in contact with PHE 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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241B LEU* 3.9 20.4 - - + -
244B LEU* 4.6 10.5 - - + -
245B SER* 2.9 19.4 + - - +
252B LEU* 4.2 18.4 - - + -
255B LEU* 3.4 30.7 - - + -
276B SER 3.2 11.3 + - - +
277B TRP* 3.1 40.8 - + + +
279B ALA* 1.3 74.5 - - - +
281B ILE* 1.3 65.3 + - - +
282B ARG 3.2 0.9 - - - -
283B HIS* 3.4 3.1 + - - +
284B SER* 3.1 25.8 + - - +
287B VAL* 4.0 34.5 - - + -
289B LEU* 4.7 8.7 - - + -
309B PRO* 4.2 6.7 - - + -
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Residues in contact with ILE 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 TRP 3.3 14.4 - - - +
278B ASP* 3.8 19.7 - - - +
280B PHE* 1.3 73.6 - - - +
282B ARG* 1.3 68.0 + - + +
284B SER 3.2 26.6 - - - +
285B PRO* 3.2 16.6 - - + +
287B VAL* 4.6 1.3 - - + -
307B GLU* 5.5 10.5 - - + +
308B ILE 5.2 1.1 - - - -
309B PRO* 3.3 41.7 - - + -
333B ARG* 3.9 23.1 - - - +
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Residues in contact with ARG 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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251B ARG* 5.2 1.9 + - - -
275B SER 5.6 0.2 + - - -
278B ASP* 3.2 24.3 + - - +
279B ALA* 3.4 37.3 + - - +
280B PHE 3.2 0.6 - - - -
281B ILE* 1.3 82.1 - - + +
283B HIS* 1.3 61.5 + - - +
285B PRO* 4.4 8.0 - - - +
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Residues in contact with HIS 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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244B LEU 3.5 22.0 - - - -
245B SER* 3.2 23.4 + - - +
246B SER 3.2 16.2 + - - -
247B GLU* 4.4 7.3 - - - -
249B HIS 3.0 27.8 + - - -
250B VAL 3.2 15.7 + - - -
251B ARG* 2.6 43.5 + - - +
279B ALA 3.2 11.5 + - - +
280B PHE 3.4 2.6 + - - +
282B ARG* 1.3 80.4 - - - +
284B SER* 1.3 57.6 + - - +
285B PRO* 4.0 0.9 - - - -
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU 5.2 0.5 + - - -
251B ARG* 3.0 15.2 - - - +
252B LEU* 2.8 42.0 + - - +
280B PHE* 3.1 13.8 + - - -
281B ILE* 3.2 9.3 - - - +
283B HIS* 1.3 83.9 - - - +
285B PRO* 1.3 64.3 - - - +
286B LYS 3.4 2.2 - - - -
287B VAL* 3.1 31.1 - - - +
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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