Contacts of the helix formed by residues 273 - 281 (chain B) in PDB entry 3JXI
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 LEU 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B HIS* 4.2 1.6 - - - -
250B VAL 5.1 0.4 - - - +
251B HIS* 3.3 46.2 - - + +
252B ALA 3.8 0.4 - - - -
253B GLN* 3.8 16.6 - - + +
270B PHE* 4.1 0.2 - - - -
271B GLY 2.7 19.4 + - - +
272B GLU* 1.3 74.9 - - - +
274B PRO* 1.3 66.3 - - + +
275B LEU* 4.3 6.7 - - + +
276B SER* 3.2 15.8 + - - +
277B LEU* 2.9 28.6 + - - +
302B ARG* 3.7 42.2 - - + +
303B GLN* 4.2 13.5 - - - +
304B ASP* 4.2 1.6 - - + +
308B ASN 4.8 1.6 - - - +
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Residues in contact with PRO 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 5.8 0.2 - - - +
228B LEU* 4.0 20.6 - - + -
229B HIS* 4.0 13.7 - - + +
232B ILE* 3.4 30.7 - - + +
249B ASP 4.3 0.4 - - - +
250B VAL* 3.2 31.4 - - - +
251B HIS* 4.2 0.2 - - - -
252B ALA* 3.2 23.8 - - + +
273B LEU* 1.3 85.8 - - + +
275B LEU* 1.3 59.4 + - - +
277B LEU* 3.5 3.8 + - + +
278B ALA* 3.1 20.8 + - - +
290B LEU* 3.8 8.7 - - + +
298B ALA* 5.9 0.2 - - + -
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL 4.8 1.2 + - - -
273B LEU* 3.3 5.0 - - + +
274B PRO* 1.3 76.0 - - - +
276B SER* 1.3 62.7 + - - +
278B ALA* 3.4 1.0 + - - +
279B ALA* 3.0 27.0 + - - +
287B VAL* 4.0 29.6 - - + +
290B LEU* 3.9 11.8 - - + +
291B THR* 3.7 30.3 - - + -
298B ALA* 4.1 15.9 - - + +
299B ASP 4.3 6.5 - - - +
300B LEU* 3.9 31.0 - - - +
310B VAL* 4.4 15.9 - - + -
335B LEU* 4.3 11.7 - - + -
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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
----------------------------------------------------------
270B PHE 3.2 19.3 - - - -
271B GLY* 3.9 17.5 + - - -
273B LEU* 3.2 20.2 + - - +
275B LEU* 1.3 79.5 - - - +
277B LEU* 1.3 56.3 + - - +
279B ALA* 3.6 0.5 - - - +
280B CYS* 2.9 34.9 + - - -
308B ASN 5.2 0.2 + - - -
309B THR 4.4 1.2 - - - -
310B VAL* 3.6 31.5 + - - +
313B ALA* 4.2 7.4 - - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B HIS* 3.4 46.7 - - + +
232B ILE* 3.8 17.9 - - + -
233B GLU* 4.1 14.8 - - + +
268B PHE* 4.8 2.9 - - + -
270B PHE* 3.6 45.3 + - + -
273B LEU 2.9 10.4 + - - +
274B PRO* 3.6 8.1 - - + +
276B SER* 1.3 76.0 - - - +
278B ALA* 1.3 51.6 + - - +
280B CYS* 3.3 0.7 + - - +
281B THR* 2.8 58.5 + - + +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 3.8 6.7 - - + +
274B PRO 3.1 11.8 + - - +
275B LEU 3.8 4.3 - - - +
277B LEU* 1.3 75.7 - - - +
279B ALA* 1.3 60.0 + - - +
281B THR* 3.6 6.4 + - - -
282B ASN 3.5 2.8 + - - -
283B GLN* 2.8 33.6 + - - +
286B ILE* 3.2 42.4 - - + -
287B VAL* 3.9 10.5 - - + -
290B LEU* 4.3 2.5 - - + -
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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 LEU 3.0 10.6 + - - +
276B SER 3.6 1.8 - - - +
278B ALA* 1.3 75.7 - - - +
280B CYS* 1.3 62.3 + - - +
282B ASN 3.2 10.2 + - - -
287B VAL* 3.8 10.7 - - + +
310B VAL* 3.4 33.0 - - + -
314B LEU* 3.8 8.1 - - + +
327B PHE* 3.7 8.5 - - - -
331B MET* 3.6 31.7 - - + +
335B LEU* 4.1 3.8 - - + -
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Residues in contact with CYS 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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268B PHE* 4.6 7.2 - - + -
270B PHE* 3.7 24.0 - - + -
276B SER 2.9 22.1 + - - +
277B LEU 4.0 2.7 - - - +
279B ALA* 1.3 78.7 - - - +
281B THR* 1.3 57.9 + - - +
282B ASN 3.3 0.9 - - - -
313B ALA* 3.6 35.2 - - - -
314B LEU* 4.0 5.8 - - - -
317B ILE* 3.3 42.5 - - + +
327B PHE* 3.3 9.8 - - - -
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Residues in contact with THR 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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232B ILE* 4.6 0.3 - - - +
233B GLU* 5.4 10.5 - - + +
235B ARG* 2.8 33.5 + - - -
268B PHE* 4.5 14.6 - - + -
277B LEU* 2.8 41.9 + - + +
278B ALA* 3.6 2.6 + - - -
279B ALA 3.3 0.2 - - - -
280B CYS* 1.3 78.1 - - - +
282B ASN* 1.3 67.4 + - - +
283B GLN* 2.9 29.6 + - - +
327B PHE* 5.1 0.4 - - - -
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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