Contacts of the helix formed by residues 290 - 306 (chain B) in PDB entry 1JPP
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 ASN 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B PHE* 4.6 20.2 - - + -
288B LYS* 3.8 4.0 - - + +
289B THR* 1.3 76.4 + - - +
291B VAL* 1.3 57.0 + - - +
292B LYS* 3.0 15.2 + - - +
293B PHE* 2.8 58.2 + - + +
294B LEU* 3.0 15.3 + - - +
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B THR 3.3 9.6 + - - +
290B ASN* 1.3 72.2 + - - +
292B LYS* 1.3 70.6 + - + +
294B LEU* 3.7 13.1 + - + +
295B ALA* 3.2 22.2 + - - +
331B TYR* 4.5 28.5 - - + -
333B TYR* 4.0 34.1 - - + -
336B LEU* 4.1 17.2 - - + +
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ASN* 3.0 10.6 + - - +
291B VAL* 1.3 87.8 - - + +
293B PHE* 1.3 64.9 + - - +
295B ALA* 3.4 8.1 + - - +
296B ILE* 3.4 27.4 + - + +
333B TYR* 4.2 29.5 + - + +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 6.1 0.2 - - + -
252B LEU* 4.0 17.7 - - + -
253B PHE* 3.1 37.5 - + + -
256B ILE* 4.3 24.2 - - + -
285B LEU* 3.8 36.3 - - + -
288B LYS* 3.7 38.1 - - + -
290B ASN* 2.8 25.4 + - + +
292B LYS* 1.3 74.9 - - - +
294B LEU* 1.3 69.4 + - + +
296B ILE* 3.3 10.8 + - + +
297B THR* 2.9 37.0 + - - -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU 4.0 20.0 - - - +
286B LEU* 4.3 20.6 - - + +
288B LYS* 4.2 21.8 - - + +
289B THR 4.8 0.9 - - - -
290B ASN 3.0 17.9 + - - +
291B VAL* 3.8 12.8 - - - +
293B PHE* 1.3 84.4 - - + +
295B ALA* 1.3 64.5 + - - +
297B THR* 2.8 8.5 + - - +
298B THR* 2.8 30.4 + - + +
327B ILE* 4.7 8.7 - - + -
331B TYR* 4.2 17.3 - - + -
336B LEU* 3.6 28.5 - - + -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL 3.2 12.2 + - - +
292B LYS* 3.5 13.7 - - - +
294B LEU* 1.3 78.1 - - - +
296B ILE* 1.3 63.6 + - + +
298B THR* 3.1 18.3 + - - -
299B ASP* 3.3 13.9 + - - +
333B TYR* 4.8 8.1 - - + -
335B LYS* 4.6 16.2 - - + +
336B LEU* 3.7 19.4 - - + +
339B THR* 4.1 7.5 + - + +
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 4.0 26.9 - - + +
257B THR* 3.8 24.2 - - + -
260B HIS* 3.8 30.1 - - + +
292B LYS* 3.4 14.8 + - + +
293B PHE* 3.3 9.5 + - + +
294B LEU 3.2 0.8 - - - -
295B ALA* 1.3 76.2 - - + +
297B THR* 1.3 64.1 + - - +
299B ASP* 3.5 7.0 + - - +
300B CYS* 3.4 17.7 + - - +
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Residues in contact with THR 297 (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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256B ILE* 4.3 13.5 - - + +
282B MET* 3.7 41.8 - - + +
285B LEU* 4.8 8.5 - - + -
286B LEU* 4.5 11.7 - - + -
293B PHE* 2.9 33.6 + - - -
294B LEU* 2.8 12.0 + - - -
296B ILE* 1.3 78.2 - - - +
298B THR* 1.3 61.7 + - - -
300B CYS* 3.1 17.1 + - - +
301B LEU* 3.3 13.1 + - + +
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Residues in contact with THR 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 4.1 22.4 - - + -
294B LEU* 2.8 22.4 + - - +
295B ALA* 3.1 7.8 + - - -
297B THR* 1.3 72.7 - - - +
299B ASP* 1.3 62.2 + - - +
301B LEU* 3.2 20.5 + - + +
302B GLN* 3.3 9.2 + - - +
324B LEU* 4.6 12.8 - - + -
327B ILE* 4.8 4.0 - - + -
336B LEU* 4.6 2.9 - - + +
339B THR* 2.9 27.8 + - - -
340B THR* 4.0 17.7 + - - +
343B VAL* 3.4 18.0 - - - +
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Residues in contact with ASP 299 (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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260B HIS* 2.9 28.6 + - - +
264B LEU* 5.3 1.4 - - - +
295B ALA 3.3 14.7 + - - +
296B ILE* 3.8 5.4 - - - +
297B THR 3.2 0.8 - - - -
298B THR* 1.3 81.7 + - - +
300B CYS* 1.3 61.1 + - - +
302B GLN* 3.5 18.4 + - - +
303B ILE* 3.3 31.2 + - - +
338B TRP* 5.7 1.9 - - - -
339B THR* 4.7 18.4 - - + +
342B ARG* 4.4 10.4 + - - -
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Residues in contact with CYS 300 (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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256B ILE* 4.6 13.2 - - + -
259B LEU* 4.8 2.0 - - - -
260B HIS* 3.7 38.1 - - - -
263B LEU* 3.7 25.4 - - + +
282B MET* 3.9 18.6 - - - -
296B ILE 3.4 8.2 + - - +
297B THR* 3.1 12.0 + - - +
299B ASP* 1.3 76.7 - - - +
301B LEU* 1.3 64.6 + - - +
303B ILE* 3.7 5.1 + - - +
304B LEU* 3.5 29.7 + - - +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 4.3 20.5 - - + +
282B MET* 4.2 21.8 - - + -
283B VAL* 4.1 23.6 - - + -
286B LEU* 4.5 27.1 - - + -
297B THR* 3.8 9.0 - - + +
298B THR* 3.2 23.6 + - + +
300B CYS* 1.3 77.0 - - - +
302B GLN* 1.3 60.1 + - - +
304B LEU* 3.5 5.3 + - - +
305B ALA* 3.0 32.6 + - - +
315B ILE* 4.4 16.7 - - + +
324B LEU* 5.1 5.8 - - + -
343B VAL* 4.3 14.4 - - + -
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Residues in contact with GLN 302 (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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298B THR 3.3 9.1 + - - +
299B ASP* 3.7 21.8 + - - +
301B LEU* 1.3 79.8 - - - +
303B ILE* 1.3 80.1 + - - +
305B ALA* 3.4 5.0 + - - +
306B TYR* 3.2 29.8 + - + +
339B THR 5.5 0.2 - - - +
342B ARG* 3.4 64.0 + - + +
343B VAL* 4.1 14.1 - - + +
346B VAL* 4.4 12.6 - - + +
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Residues in contact with ILE 303 (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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260B HIS* 5.1 3.6 - - + +
263B LEU* 4.4 32.3 - - + +
264B LEU* 3.8 32.8 - - + -
270B LYS* 3.4 38.5 + - + +
299B ASP* 3.3 25.5 + - - +
300B CYS* 3.9 6.5 - - - +
301B LEU 3.3 0.4 - - - -
302B GLN* 1.3 89.5 - - - +
304B LEU* 1.3 62.6 + - + +
306B TYR* 3.7 11.1 + - - +
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Residues in contact with LEU 304 (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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263B LEU* 4.1 26.7 - - + -
270B LYS* 4.2 15.0 - - + +
273B VAL* 4.2 20.6 - - + -
274B ARG* 2.6 56.3 + - + +
278B GLY 5.7 0.2 - - - -
279B LEU* 4.5 24.5 - - + -
282B MET* 4.3 16.2 - - + -
300B CYS 3.5 18.6 + - - +
301B LEU* 3.5 4.4 + - - +
302B GLN 3.3 0.2 - - - -
303B ILE* 1.3 80.2 - - - +
305B ALA* 1.3 61.0 + - - +
306B TYR 3.4 1.1 + - - +
308B ASN* 4.1 2.4 - - - +
311B SER* 3.6 11.3 + - - +
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Residues in contact with ALA 305 (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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279B LEU* 6.0 0.6 - - + +
301B LEU 3.0 18.7 + - - +
302B GLN* 3.4 4.5 + - - +
303B ILE 3.4 0.2 - - - -
304B LEU* 1.3 76.0 - - - +
306B TYR* 1.3 63.6 + - - +
307B GLY 3.4 0.5 + - - -
308B ASN 3.7 6.8 - - - +
311B SER* 4.3 9.6 - - - -
312B LYS* 3.3 32.0 - - + -
315B ILE* 4.2 20.6 - - + -
343B VAL* 6.3 2.2 - - + -
346B VAL* 4.2 12.6 - - + -
347B LEU* 5.5 3.4 - - + -
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Residues in contact with TYR 306 (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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270B LYS* 4.8 9.4 + - - +
274B ARG* 5.0 1.4 + - - -
302B GLN* 3.2 21.3 + - - +
303B ILE* 4.0 10.6 - - - +
304B LEU 3.4 3.8 - - - +
305B ALA* 1.3 75.0 - - - +
307B GLY* 1.3 73.2 + - - +
308B ASN* 4.2 2.6 - - - +
346B VAL* 4.4 25.1 - - + -
1034D GLU* 4.7 21.2 + - - +
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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
------------------------------------------------------------
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