Contacts of the helix formed by residues 290 - 306 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PHE* 4.6 20.0 - - + -
288A LYS* 3.8 3.6 - - + +
289A THR* 1.3 75.4 + - - +
291A VAL* 1.3 53.4 + - - +
292A LYS* 2.9 15.2 + - - +
293A PHE* 2.8 64.0 + - + +
294A LEU* 3.0 14.5 + - - +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A THR 3.3 8.4 + - - +
290A ASN* 1.3 71.4 + - - +
292A LYS* 1.3 69.8 + - + +
294A LEU* 3.7 12.8 + - + +
295A ALA* 3.2 21.7 + - - +
331A TYR* 4.5 27.8 - - + -
333A TYR* 4.0 33.8 - - + -
336A LEU* 4.2 17.1 - - + +
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASN* 2.9 11.0 + - - +
291A VAL* 1.3 87.9 - - + +
293A PHE* 1.3 66.6 + - - +
295A ALA* 3.5 14.2 + - - +
296A ILE* 3.5 19.8 + - + +
333A TYR* 4.3 28.2 + - + +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A LEU* 4.1 17.3 - - + -
253A PHE* 3.1 37.2 - + + -
256A ILE* 4.2 23.3 - - + -
285A LEU* 3.7 36.8 - - + -
288A LYS* 3.7 38.4 - - + -
290A ASN* 2.8 28.1 + - + +
292A LYS* 1.3 76.5 - - - +
294A LEU* 1.3 68.0 + - + +
296A ILE* 3.2 10.7 + - + +
297A THR* 3.0 34.6 + - - -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LEU 4.1 19.7 - - - +
286A LEU* 4.3 20.6 - - + +
288A LYS* 4.3 19.1 - - + +
289A THR 4.8 0.9 - - - -
290A ASN 3.0 15.9 + - - +
291A VAL* 3.8 13.5 - - - +
293A PHE* 1.3 85.2 - - + +
295A ALA* 1.3 62.6 + - - +
297A THR* 3.0 6.4 + - - +
298A THR* 2.9 29.5 + - + +
327A ILE* 4.7 10.5 - - + -
331A TYR* 4.1 19.5 - - + -
336A LEU* 3.6 27.8 - - + -
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A VAL 3.2 12.2 + - - +
292A LYS* 3.5 12.8 - - - +
293A PHE 3.3 0.2 - - - -
294A LEU* 1.3 78.8 - - - +
296A ILE* 1.3 62.4 + - + +
298A THR* 3.2 17.3 + - - -
299A ASP* 3.4 14.0 + - - +
333A TYR* 4.8 9.0 - - + -
335A LYS* 4.7 16.2 - - + +
336A LEU* 3.7 18.8 - - + +
339A THR* 4.1 7.1 + - + +
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 4.0 26.2 - - + +
257A THR* 3.7 25.8 - - + -
260A HIS* 3.8 31.8 - - + +
292A LYS* 3.5 14.6 + - + +
293A PHE* 3.2 9.3 + - + +
294A LEU 3.2 0.4 - - - -
295A ALA* 1.3 78.5 - - + +
297A THR* 1.3 62.7 + - - +
299A ASP* 3.5 6.6 + - - +
300A CYS* 3.4 16.5 + - - +
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Residues in contact with THR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 4.1 15.8 - - + +
282A MET* 3.6 42.0 - - + +
285A LEU* 4.8 7.6 - - + -
286A LEU* 4.4 11.2 - - + -
293A PHE* 3.0 32.9 + - - -
294A LEU* 3.0 11.8 + - - -
296A ILE* 1.3 75.5 - - - +
298A THR* 1.3 60.5 + - - +
300A CYS* 3.0 24.5 + - - +
301A LEU* 3.3 9.1 + - + +
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU* 4.1 21.5 - - + -
294A LEU* 2.9 20.8 + - - +
295A ALA* 3.2 7.3 + - - -
297A THR* 1.3 71.0 - - - +
299A ASP* 1.3 61.9 + - - +
301A LEU* 3.2 18.6 + - + +
302A GLN* 3.3 9.4 + - - +
324A LEU* 4.5 12.8 - - + -
327A ILE* 4.7 7.0 - - + -
336A LEU* 4.6 0.8 - - + +
339A THR* 2.8 28.7 + - - -
340A THR* 4.0 17.9 + - - +
343A VAL* 3.3 21.8 - - - +
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Residues in contact with ASP 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A HIS* 3.1 26.8 + - - +
264A LEU* 5.2 1.6 - - - +
295A ALA 3.4 14.5 + - - +
296A ILE* 3.8 6.1 - - - +
297A THR 3.2 0.6 - - - -
298A THR* 1.3 81.7 + - - +
300A CYS* 1.3 61.4 + - - +
301A LEU 3.3 0.2 - - - -
302A GLN* 3.6 17.2 + - - -
303A ILE* 3.3 28.9 + - - +
338A TRP* 5.6 2.6 - - - -
339A THR* 4.5 19.5 - - + +
342A ARG* 4.5 10.0 + - - -
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Residues in contact with CYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ILE* 4.6 11.0 - - - -
259A LEU* 4.9 1.6 - - - -
260A HIS* 3.8 35.9 - - - -
263A LEU* 3.7 26.1 - - + +
282A MET* 3.9 22.2 - - - -
296A ILE 3.4 6.7 + - - +
297A THR* 3.0 13.1 + - - +
299A ASP* 1.3 79.2 - - - +
301A LEU* 1.3 63.4 + - - +
303A ILE* 3.6 5.2 + - - +
304A LEU* 3.5 29.2 + - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LEU* 4.4 14.5 - - + +
282A MET* 4.2 20.0 - - + +
283A VAL* 4.1 24.0 - - + -
286A LEU* 4.5 26.2 - - + -
297A THR* 3.8 9.0 - - + +
298A THR* 3.2 25.2 + - + +
300A CYS* 1.3 79.0 - - - +
302A GLN* 1.3 56.4 + - - +
304A LEU* 3.5 5.0 + - - +
305A ALA* 3.0 33.1 + - - +
315A ILE* 4.4 22.7 - - + +
324A LEU* 5.1 5.8 - - + -
343A VAL* 4.2 14.1 - - + -
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Residues in contact with GLN 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A THR 3.3 9.1 + - - +
299A ASP* 3.9 20.8 + - - +
300A CYS 3.3 0.2 - - - -
301A LEU* 1.3 78.8 - - - +
303A ILE* 1.3 72.9 + - - +
305A ALA* 4.2 4.2 - - - +
306A TYR* 3.4 27.4 + - - +
339A THR 5.5 0.2 - - - +
342A ARG* 3.4 63.1 + - + +
343A VAL* 4.0 13.6 - - + +
346A VAL* 4.3 14.0 - - + +
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A HIS* 5.2 3.6 - - + +
263A LEU* 4.4 28.5 - - + +
264A LEU* 3.7 33.4 - - + -
270A LYS* 3.9 36.4 + - + +
274A ARG* 4.8 1.7 + - - -
299A ASP* 3.3 26.4 + - - +
300A CYS* 4.0 6.7 - - - +
301A LEU 3.3 0.6 - - - -
302A GLN* 1.3 88.3 - - - +
304A LEU* 1.3 62.0 + - + +
305A ALA 3.7 0.2 + - - -
306A TYR* 3.8 14.4 + - - +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 4.0 30.3 - - + -
270A LYS* 4.1 25.8 - - + +
273A VAL* 4.3 20.0 - - + -
274A ARG* 2.7 44.1 + - + +
278A GLY 5.6 0.4 - - - +
279A LEU* 4.5 25.8 - - + -
282A MET* 4.6 12.3 - - + -
300A CYS 3.5 19.5 + - - +
301A LEU* 3.5 4.4 + - - +
302A GLN 3.4 0.2 - - - -
303A ILE* 1.3 78.6 - - - +
305A ALA* 1.3 58.8 + - - +
306A TYR 3.4 0.7 + - - +
308A ASN* 3.9 2.3 - - - +
311A SER* 3.5 10.8 + - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LEU* 5.9 0.6 - - + +
301A LEU 3.0 19.6 + - - +
302A GLN* 3.7 4.7 + - - +
303A ILE 3.4 0.2 - - - -
304A LEU* 1.3 75.8 - - - +
306A TYR* 1.3 61.6 + - - +
307A GLY 3.4 0.7 + - - -
308A ASN 3.6 6.6 - - - +
311A SER* 4.1 9.6 - - - -
312A LYS* 3.1 37.1 - - + -
315A ILE* 4.1 20.9 - - + -
343A VAL* 6.4 1.6 - - + -
346A VAL* 4.3 10.5 - - + -
347A LEU* 5.1 3.6 - - + -
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Residues in contact with TYR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ARG* 5.1 2.4 + - - -
302A GLN* 3.4 22.3 + - - +
303A ILE* 3.8 11.5 + - - +
304A LEU 3.4 2.6 - - - +
305A ALA* 1.3 74.1 - - - +
307A GLY* 1.3 71.1 + - - +
308A ASN* 3.5 3.6 + - - +
346A VAL* 4.3 24.7 - - + -
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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
------------------------------------------------------------
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