Contacts of the helix formed by residues 281 - 293 (chain B) in PDB entry 5JJA
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 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B LEU* 4.0 27.1 - - + -
244B LYS* 4.2 29.6 - - + -
247B LEU* 3.6 29.6 - - + -
248B LEU* 4.9 15.0 - - + -
274B PHE* 4.1 8.7 - - + +
275B LEU* 3.7 9.9 - - + -
278B ASP* 3.7 21.3 - - + +
279B SER 3.1 1.2 - - - -
280B THR* 1.3 81.0 - - - +
282B THR* 1.3 63.3 + - - +
283B GLU 3.3 1.9 + - - -
284B PRO* 3.4 11.1 - - + +
285B VAL* 3.2 22.3 + - - +
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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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275B LEU* 3.7 23.4 - - + +
279B SER* 2.7 28.9 + - - -
280B THR 3.2 1.6 - - - -
281B LEU* 1.3 77.1 - - - +
283B GLU* 1.3 60.5 + - - +
285B VAL* 3.6 0.7 - - - +
286B VAL* 2.9 40.0 + - + +
311B ILE* 5.2 0.2 - - + -
315B ILE* 3.7 35.8 - - + +
319B GLU* 3.8 22.7 - - + +
323B ILE* 4.8 1.8 - - + -
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Residues in contact with GLU 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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280B THR 4.5 1.9 + - - +
282B THR* 1.3 80.4 - - - +
284B PRO* 1.3 74.7 - - + +
286B VAL* 4.1 0.2 - - - +
287B MET* 3.0 38.9 + - + +
319B GLU* 4.3 9.6 + - - +
322B LYS* 4.0 30.9 + - + +
323B ILE* 3.9 24.2 - - + +
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Residues in contact with PRO 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 LEU* 4.0 27.1 - - + -
252B LEU* 4.1 3.3 - - + +
280B THR 4.4 5.6 - - - +
281B LEU* 3.4 23.6 - - + +
283B GLU* 1.3 95.4 - - + +
285B VAL* 1.3 54.4 + - - +
287B MET* 3.9 4.1 - - + +
288B ALA* 3.0 31.4 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 3.8 30.5 - - + -
248B LEU* 5.0 1.6 - - + -
252B LEU* 4.1 22.3 - - + +
271B VAL* 3.6 27.4 - - + -
275B LEU* 4.1 17.7 - - + -
281B LEU 3.2 18.5 + - - +
282B THR 3.6 3.6 - - - +
283B GLU 3.2 0.6 - - - -
284B PRO* 1.3 77.4 - - - +
286B VAL* 1.3 59.1 + - + +
288B ALA* 3.3 2.8 + - - +
289B LEU* 3.0 27.9 + - + +
311B ILE* 4.1 15.5 - - + -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 2.9 36.2 + - + +
283B GLU 4.1 2.0 - - - +
285B VAL* 1.3 77.7 - - + +
287B MET* 1.3 59.4 + - - +
289B LEU* 3.2 7.5 + - - +
290B LEU* 3.0 42.9 + - + +
308B LEU* 4.7 8.7 - - + -
311B ILE* 4.1 24.7 - - + -
315B ILE* 5.2 0.7 - - + -
323B ILE* 3.9 35.9 - - + -
327B LEU* 4.7 10.3 - - + -
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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
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283B GLU* 3.0 34.7 + - + +
284B PRO* 4.1 4.0 - - + +
286B VAL* 1.3 73.4 - - - +
288B ALA* 1.3 57.1 - - - +
290B LEU* 3.4 15.0 + - + +
291B LYS* 2.9 28.5 + - - +
323B ILE* 3.8 20.0 - - + -
326B PRO* 4.0 31.0 - - + -
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Residues in contact with ALA 288 (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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252B LEU* 3.8 31.4 - - + -
255B HIS* 6.2 0.2 - - - -
284B PRO 3.0 20.3 + - - +
285B VAL 3.5 4.3 - - - +
286B VAL 3.3 0.2 - - - -
287B MET* 1.3 73.8 - - - +
289B LEU* 1.3 59.4 + - - +
291B LYS* 3.1 14.6 + - - +
292B TYR* 3.0 44.6 + - + -
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Residues in contact with LEU 289 (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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252B LEU* 5.6 0.8 - - + +
255B HIS* 3.7 18.6 - - + +
285B VAL* 3.0 13.9 + - + +
286B VAL* 3.2 9.8 + - - +
288B ALA* 1.3 76.6 - - - +
290B LEU* 1.3 58.5 + - + +
292B TYR* 3.4 5.1 + - - +
293B TRP* 3.0 38.2 + - + +
304B PHE* 3.7 26.0 - - + +
307B GLU* 3.4 32.5 - - + +
308B LEU* 4.1 27.6 - - + +
311B ILE* 4.0 26.0 - - + -
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Residues in contact with LEU 290 (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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286B VAL* 3.0 34.4 + - + +
287B MET* 3.7 14.6 - - + +
289B LEU* 1.3 76.2 - - + +
291B LYS* 1.3 63.2 + - - +
293B TRP* 3.4 22.8 - - + +
295B LYS* 3.2 15.8 + - - -
308B LEU* 5.1 7.2 - - + -
326B PRO* 3.8 37.9 - - + +
327B LEU* 3.8 10.5 - - + +
330B GLN* 3.9 35.9 + - + +
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Residues in contact with LYS 291 (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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287B MET 2.9 15.0 + - - +
288B ALA* 3.1 13.1 + - - +
290B LEU* 1.3 77.7 - - - +
292B TYR* 1.3 95.9 + - + +
295B LYS* 3.1 24.4 + - - +
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Residues in contact with TYR 292 (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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252B LEU* 3.4 30.3 - - + -
253B PRO* 3.8 22.5 - - + +
255B HIS* 3.8 28.6 - + + +
256B LYS* 3.7 32.1 - - + +
288B ALA* 3.0 34.5 + - + +
289B LEU 3.7 3.1 - - - +
291B LYS* 1.3 106.4 + - + +
293B TRP* 1.3 66.7 + - - +
294B PRO* 3.4 2.6 - - - +
304B PHE* 3.7 14.5 - - + -
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Residues in contact with TRP 293 (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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289B LEU* 3.0 26.5 + - + -
290B LEU* 3.4 29.2 - - + +
291B LYS 3.3 1.2 - - - -
292B TYR* 1.3 77.3 - - - +
294B PRO* 1.3 95.3 - - + +
295B LYS* 2.8 23.6 + - - +
301B GLU* 2.8 27.5 + - - +
304B PHE* 3.6 51.6 - + + -
305B LEU* 3.8 14.6 - - + -
308B LEU* 3.9 29.4 - - + -
330B GLN* 3.3 32.1 + - + +
334B CYS* 3.8 18.4 - - - -
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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