Contacts of the helix formed by residues 289 - 304 (chain A) in PDB entry 3J8B
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 ALA 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A PHE 5.0 0.4 - - - -
287A GLY 3.6 6.9 + - - +
288A ASN* 1.3 71.1 - - - +
290A LEU* 1.3 65.2 + - - +
292A HIS* 3.4 9.8 - - - +
293A ALA* 3.1 23.2 + - - +
325A ALA* 4.9 7.9 - - - +
328A SER 5.7 1.1 - - - +
329A ILE* 4.5 25.2 - - + +
330A PRO* 5.1 4.9 - - + -
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Residues in contact with LEU 290 (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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288A ASN 3.3 0.8 - - - -
289A ALA* 1.3 77.6 - - - +
291A PHE* 1.3 64.7 + - - +
293A ALA* 3.5 4.9 + - - +
294A SER* 3.1 22.9 + - - -
329A ILE* 5.6 2.7 - - - +
365A PRO* 5.3 14.4 - - + +
366A THR 6.4 1.3 - - - -
370A LEU* 6.1 7.2 - - + +
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Residues in contact with PHE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 4.1 12.5 - - + +
288A ASN* 3.4 19.1 + - + +
290A LEU* 1.3 76.4 - - - +
292A HIS* 1.3 65.6 + - - +
294A SER* 3.2 8.0 + - - -
295A THR* 2.9 26.0 + - - -
355A LEU* 6.1 5.4 - - + -
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 4.4 12.8 - - - +
283A PHE* 3.7 22.8 - - + +
284A TRP* 4.5 6.5 - - + +
288A ASN 3.1 15.0 + - - +
289A ALA* 3.4 15.0 - - - +
291A PHE* 1.3 78.0 - - - +
293A ALA* 1.3 61.3 + - - +
295A THR* 3.4 4.9 + - - -
296A LEU* 3.1 21.1 + - - +
325A ALA* 6.0 4.3 - - + -
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Residues in contact with ALA 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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289A ALA 3.1 12.7 + - - +
290A LEU* 4.0 5.2 - - - +
291A PHE 3.3 0.2 - - - -
292A HIS* 1.3 76.1 - - - +
294A SER* 1.3 64.7 + - - +
296A LEU* 3.3 9.5 + - - +
297A HIS* 3.0 23.0 + - - +
322A VAL* 4.7 11.6 - - + +
325A ALA* 4.7 20.6 - - + +
326A THR* 4.9 11.9 - - - -
370A LEU* 5.8 7.0 - - + -
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU 3.1 15.3 + - - -
291A PHE* 3.5 12.1 - - - -
293A ALA* 1.3 76.9 - - - +
295A THR* 1.3 57.3 + - - +
297A HIS* 3.0 9.0 + - - +
298A ARG* 2.9 28.0 + - - +
359A LEU* 5.7 9.9 - - - -
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TYR* 3.9 10.9 - - - +
279A VAL* 3.7 32.1 - - - -
280A SER* 3.8 11.9 - - - -
291A PHE 2.9 16.3 + - - -
292A HIS 3.7 4.9 - - - -
294A SER* 1.3 75.5 - - - +
296A LEU* 1.3 63.2 + - - +
298A ARG* 3.3 8.4 + - - +
299A LEU* 3.0 23.2 + - - +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER* 4.7 9.1 - - - -
292A HIS 3.1 14.2 + - - +
293A ALA* 3.4 12.6 - - - +
295A THR* 1.3 75.6 - - - +
297A HIS* 1.3 57.9 + - - +
299A LEU* 3.2 7.8 + - - +
300A TYR* 2.9 29.0 + - - +
322A VAL* 4.7 20.6 - - + +
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Residues in contact with HIS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA 3.0 13.0 + - - +
294A SER* 3.4 10.5 - - - +
296A LEU* 1.3 73.3 - - - +
298A ARG* 1.3 60.7 + - - +
300A TYR* 3.1 8.1 + - - +
301A HIS* 2.8 32.1 + - - +
322A VAL* 5.7 6.1 - - + -
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TYR* 4.5 10.3 - - + +
294A SER 2.9 12.3 + - - +
295A THR* 3.6 11.0 - - - +
297A HIS* 1.3 77.2 - - - +
299A LEU* 1.3 60.5 + - - +
301A HIS* 3.8 5.7 + - - +
302A LEU* 3.3 23.2 + - - +
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 4.7 10.9 - - + +
276A TYR* 4.0 17.4 - - + +
277A ASN* 4.7 11.4 - - + +
295A THR 3.0 13.0 + - - +
296A LEU* 3.5 10.8 - - - +
298A ARG* 1.3 76.9 - - - +
300A TYR* 1.3 54.8 + - - +
302A LEU* 3.3 4.5 + - - +
303A SER* 2.7 38.0 + - - -
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Residues in contact with TYR 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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296A LEU 2.9 16.3 + - - +
297A HIS* 3.1 8.7 + - - +
299A LEU* 1.3 73.7 - - - +
301A HIS* 1.3 60.8 + - - +
303A SER* 3.7 4.9 - - - +
304A ARG* 2.8 32.4 + - - +
318A MET* 5.5 13.9 - - + -
319A SER* 6.2 2.0 - - - +
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Residues in contact with HIS 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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297A HIS 2.8 16.8 + - - +
298A ARG* 4.1 6.1 - - - +
300A TYR* 1.3 76.8 - - - +
302A LEU* 1.3 59.1 + - - +
304A ARG* 3.9 14.2 + - - +
305A GLU* 4.0 7.8 + - - +
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Residues in contact with LEU 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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269A PRO* 5.7 7.6 - - + +
272A MET* 6.5 0.7 - - + -
273A ALA* 4.7 19.4 - - + +
298A ARG 3.3 17.0 + - - +
299A LEU* 3.3 6.0 + - - +
300A TYR 3.1 0.4 - - - -
301A HIS* 1.3 79.8 - - - +
303A SER* 1.3 61.6 + - - +
304A ARG 3.3 0.4 - - - -
305A GLU* 3.7 7.2 + - - +
306A MET* 3.4 19.2 + - - +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 5.6 4.9 - - - +
299A LEU 2.7 19.1 + - - -
300A TYR* 3.1 5.4 + - - -
302A LEU* 1.3 73.7 - - - +
304A ARG* 1.3 63.3 + - - +
306A MET 2.4 28.9 - - - +
307A ARG 3.9 0.7 + - - +
310A LEU* 4.7 7.3 - - - +
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR 2.8 16.0 + - - +
301A HIS* 3.9 9.6 - - - +
302A LEU 3.3 0.2 - - - -
303A SER* 1.3 79.9 - - - +
305A GLU* 1.3 61.9 + - - +
307A ARG 3.8 7.1 - - - +
308A LYS 5.1 1.9 - - - +
310A LEU* 5.2 2.8 - - - +
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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