Contacts of the helix formed by residues 297 - 313 (chain J) in PDB entry 5FUR
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 297 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256J LEU* 3.7 32.8 - - + -
289J LEU* 3.2 39.0 - - + +
290J MET* 3.7 26.7 - - + +
295J LEU* 3.0 30.1 + - + +
296J TYR* 1.3 69.8 - - - +
298J GLU* 1.3 63.8 + - - +
299J LYS 3.4 0.9 - - - -
300J TYR* 3.0 16.2 + - + -
301J VAL* 3.1 10.0 + - - -
304J LEU* 3.6 30.1 - - + -
344J PHE* 4.7 4.9 - - + -
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Residues in contact with GLU 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296J TYR* 3.0 6.1 + - + +
297J LEU* 1.3 74.1 - - - +
299J LYS* 1.3 93.1 + - + +
301J VAL* 2.8 37.8 + - + +
344J PHE* 3.7 33.1 - - + -
347J THR* 4.0 22.5 - - - +
348J THR* 5.2 7.1 - - + +
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Residues in contact with LYS 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296J TYR 4.2 5.0 + - - +
297J LEU 3.4 0.6 - - - -
298J GLU* 1.3 107.6 + - + +
300J TYR* 1.3 85.1 + - + +
301J VAL 3.6 0.3 + - - -
302J HIS* 3.9 14.0 + - - +
303J GLU 4.8 0.5 + - - -
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Residues in contact with TYR 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253J TYR* 5.7 4.7 - + - -
256J LEU* 3.7 28.3 - - + -
257J PRO* 3.5 45.4 - - + +
260J SER* 4.7 10.5 - - - +
296J TYR 4.6 4.0 - - - -
297J LEU* 3.0 20.0 + - + +
299J LYS* 1.3 98.6 - - + +
301J VAL* 1.3 62.5 + - - +
302J HIS 3.2 2.0 - - - -
303J GLU* 3.0 12.6 + - + +
304J LEU* 2.9 30.4 + - + +
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Residues in contact with VAL 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290J MET* 4.5 10.1 - - + -
297J LEU 3.1 6.6 + - - +
298J GLU* 2.8 30.9 + - + +
300J TYR* 1.3 69.0 - - - +
302J HIS* 1.3 62.5 + - + +
304J LEU* 3.2 4.4 + - - +
305J ILE* 3.0 43.5 + - + +
340J ILE* 3.3 34.1 - - + -
344J PHE* 3.9 29.8 - - + -
348J THR* 4.8 7.9 - - + -
351J ILE* 4.6 13.2 - - + -
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Residues in contact with HIS 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299J LYS 3.9 10.6 + - - +
300J TYR 3.2 1.2 - - - -
301J VAL* 1.3 80.9 - - + +
303J GLU* 1.3 56.7 + - - +
305J ILE* 4.9 1.1 - - - -
306J PRO* 3.3 19.4 - - - +
350J ASN* 3.4 24.9 + - + -
351J ILE* 3.7 21.8 - - + -
354J ARG* 3.3 27.8 + - - +
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Residues in contact with GLU 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260J SER* 4.1 15.5 - - - +
261J THR* 6.2 3.4 - - + -
264J SER* 3.0 34.0 + - - +
299J LYS 4.8 0.4 + - - -
300J TYR* 3.0 17.8 + - + +
302J HIS* 1.3 77.5 - - - +
304J LEU* 1.3 63.9 + - - +
305J ILE 3.3 2.0 - - - -
306J PRO* 3.2 16.3 - - - +
307J ALA* 3.3 15.2 + - - +
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Residues in contact with LEU 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260J SER* 3.4 30.7 - - - +
263J ILE* 5.5 1.3 - - + -
264J SER* 4.6 9.0 - - - +
286J VAL* 3.5 41.1 - - + +
289J LEU* 5.3 4.3 - - + -
290J MET* 3.6 20.4 - - + -
297J LEU* 3.6 31.4 - - + -
300J TYR* 2.9 17.4 + - + +
301J VAL* 4.1 2.5 - - - +
303J GLU* 1.3 77.1 - - - +
305J ILE* 1.3 56.8 + - - +
307J ALA* 3.6 5.1 + - + +
308J VAL* 3.0 37.6 + - + +
340J ILE* 5.0 4.5 - - + -
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Residues in contact with ILE 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301J VAL* 3.0 24.9 + - + +
304J LEU* 1.3 76.3 - - - +
306J PRO* 1.3 65.3 - - + +
308J VAL* 3.2 5.3 + - - +
309J MET* 2.8 51.6 + - + +
337J VAL* 5.0 4.5 - - + -
340J ILE* 3.6 32.3 - - + -
351J ILE* 3.6 43.7 - - + -
354J ARG* 4.1 11.0 - - - +
355J ILE* 4.0 21.5 - - + -
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Residues in contact with PRO 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302J HIS 3.3 23.8 - - - +
303J GLU* 3.2 24.0 - - - +
305J ILE* 1.3 87.4 - - + +
307J ALA* 1.3 59.2 + - - +
309J MET* 4.0 14.3 - - + +
310J THR* 2.8 29.6 + - - -
354J ARG* 3.6 25.4 - - - +
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Residues in contact with ALA 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J SER* 4.0 21.3 - - - +
267J VAL* 4.3 19.2 - - + +
283J MET* 4.9 3.6 - - + -
303J GLU* 3.3 20.4 + - - +
304J LEU* 3.9 8.5 - - + +
305J ILE 3.3 0.6 - - - -
306J PRO* 1.3 75.8 - - - +
308J VAL* 1.3 64.9 + - + +
310J THR* 3.2 8.3 + - - -
311J CYS* 3.1 24.7 + - - -
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Residues in contact with VAL 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283J MET* 4.2 15.7 - - + -
286J VAL* 4.4 8.7 - - + -
304J LEU* 3.0 21.9 + - - +
305J ILE 3.9 2.7 - - - +
307J ALA* 1.3 76.2 - - + +
309J MET* 1.3 55.8 + - - +
311J CYS* 3.0 6.1 + - - +
312J ILE* 2.9 26.0 + - - +
333J ALA* 2.9 39.7 - - + +
336J LEU* 3.4 31.0 - - + -
337J VAL* 3.6 17.0 - - + +
340J ILE* 5.0 2.2 - - + -
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Residues in contact with MET 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305J ILE* 2.8 33.1 + - + +
306J PRO* 4.0 15.3 - - + +
308J VAL* 1.3 69.2 - - - +
310J THR* 1.3 63.3 + - - +
312J ILE* 3.2 8.7 + - - +
313J VAL* 3.0 31.7 + - + +
337J VAL* 4.1 12.1 - - + -
354J ARG* 4.5 17.0 - - + +
355J ILE* 3.9 33.2 - - - -
358J THR* 4.3 27.8 - - + +
359J PHE* 4.1 18.2 - - + -
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Residues in contact with THR 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267J VAL* 5.6 4.0 - - + -
268J ARG* 6.5 1.3 - - - -
271J VAL* 4.9 15.5 - - + -
306J PRO 2.8 20.0 + - - -
307J ALA* 3.2 11.3 + - - -
309J MET* 1.3 73.0 - - - +
311J CYS* 1.3 59.0 + - - +
313J VAL* 5.4 0.9 - - - -
314J SER* 2.8 45.7 + - - +
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Residues in contact with CYS 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267J VAL* 3.8 26.5 - - - -
271J VAL* 4.4 13.5 - - - -
279J LEU* 4.4 7.4 - - - -
283J MET* 3.6 25.8 - - - -
307J ALA 3.1 8.1 + - - +
308J VAL 3.0 9.8 + - - +
310J THR* 1.3 77.4 - - - +
312J ILE* 1.3 62.0 + - - +
314J SER* 4.0 1.5 + - - -
317J LEU* 3.0 30.0 - - + +
329J LEU* 4.8 9.0 - - + -
330J ARG* 3.7 3.1 + - - +
333J ALA* 3.7 18.2 - - + -
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Residues in contact with ILE 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308J VAL 2.9 19.2 + - - +
309J MET* 3.2 7.6 + - - +
311J CYS* 1.3 71.2 - - - +
313J VAL* 1.3 57.4 + - + +
330J ARG* 2.7 40.1 + - - +
333J ALA 3.6 3.8 - - - +
334J ALA* 3.4 39.7 - - + +
337J VAL* 3.6 21.3 - - + -
359J PHE* 3.4 41.3 - - + -
371J THR 4.7 0.2 - - - +
375J GLY* 3.5 33.2 - - - +
379J GLY* 5.3 0.2 - - - -
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Residues in contact with VAL 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309J MET* 3.0 15.6 + - + +
310J THR* 5.4 0.9 - - - -
312J ILE* 1.3 77.6 - - + +
314J SER* 1.3 66.9 + - - +
315J ARG* 3.4 2.3 + - + +
330J ARG* 3.3 5.4 - - - +
358J THR* 5.0 11.0 - - + -
359J PHE* 3.9 28.3 - - + -
362J SER* 3.4 29.2 - - - +
372J THR* 3.3 28.4 - - - +
376J SER* 4.6 5.4 - - - -
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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