Contacts of the helix formed by residues 297 - 313 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256K LEU* 4.1 18.4 - - + -
260K SER* 6.1 0.4 - - - +
289K LEU* 3.3 37.7 - - + +
290K MET* 4.1 20.6 - - + +
295K LEU* 2.7 49.6 + - + +
296K TYR* 1.3 69.6 - - - +
298K GLU* 1.3 64.7 + - - +
299K LYS 3.3 0.7 - - - -
300K TYR* 2.9 22.7 + - + +
301K VAL* 3.2 9.4 + - - -
304K LEU* 4.1 24.9 - - + -
344K PHE* 5.0 5.8 - - + -
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Residues in contact with GLU 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296K TYR 3.2 4.6 + - - +
297K LEU* 1.3 74.1 - - - +
299K LYS* 1.3 91.8 + - + +
301K VAL* 2.8 46.2 + - + +
302K HIS 4.0 0.2 + - - -
344K PHE* 4.5 17.7 - - + -
347K THR* 4.5 17.0 - - - +
348K THR* 5.3 7.5 - - + +
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Residues in contact with LYS 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J ASN* 4.6 13.2 - - - +
296K TYR* 4.2 5.8 + - + +
297K LEU 3.1 1.0 + - - -
298K GLU* 1.3 105.8 + - + +
300K TYR* 1.3 85.6 + - + +
301K VAL 3.7 0.3 + - - -
302K HIS* 4.0 12.8 + - - +
303K GLU* 4.5 1.7 + - - +
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Residues in contact with TYR 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J ASN* 4.0 24.0 + - - -
253K TYR* 6.4 0.7 - + - -
256K LEU* 3.9 34.1 - - + -
257K PRO* 4.0 30.0 - - + +
260K SER* 4.4 24.7 - - - +
296K TYR 4.5 4.9 - - - -
297K LEU* 2.9 21.4 + - + +
299K LYS* 1.3 95.7 - - + +
301K VAL* 1.3 52.7 + - - +
302K HIS 3.3 1.3 - - - -
303K GLU* 3.1 14.8 + - + +
304K LEU* 2.8 40.7 + - + +
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Residues in contact with VAL 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290K MET* 4.3 9.6 - - + +
297K LEU 3.2 5.9 + - - +
298K GLU* 2.8 28.8 + - + +
300K TYR* 1.3 74.1 - - - +
302K HIS* 1.3 63.6 + - + +
304K LEU* 3.1 6.0 + - - +
305K ILE* 2.8 56.6 + - + +
340K ILE* 4.2 5.2 - - + -
344K PHE* 3.8 38.4 - - + -
348K THR* 4.8 17.9 - - + -
351K ILE* 5.0 3.8 - - + -
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Residues in contact with HIS 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298K GLU 5.4 0.2 - - - +
299K LYS 4.0 9.5 + - - +
300K TYR 3.3 0.8 - - - -
301K VAL* 1.3 83.6 - - + +
303K GLU* 1.3 53.1 + - - +
305K ILE* 4.8 2.5 - - - -
306K PRO* 2.8 31.0 - - - +
350K ASN* 3.8 18.9 + - + -
351K ILE* 4.3 13.9 - - + -
354K ARG* 3.6 32.1 + - - -
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Residues in contact with GLU 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346J THR* 6.2 0.2 - - - +
260K SER* 4.9 6.5 - - - +
264K SER* 3.5 32.9 + - - +
299K LYS 4.5 1.4 + - - +
300K TYR* 3.1 23.3 + - + +
302K HIS* 1.3 76.2 - - - +
304K LEU* 1.3 66.3 + - + +
306K PRO* 3.4 7.8 - - - +
307K ALA* 3.3 26.9 + - - +
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Residues in contact with LEU 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260K SER* 4.3 19.3 - - - +
263K ILE* 5.3 2.5 - - + -
264K SER* 4.4 12.6 - - - +
286K VAL* 3.5 42.4 - - + +
289K LEU* 5.4 5.6 - - + -
290K MET* 3.4 31.0 - - + -
297K LEU* 4.1 17.9 - - + -
300K TYR* 2.8 25.5 + - + +
301K VAL 3.9 1.8 - - - +
303K GLU* 1.3 72.4 - - + +
305K ILE* 1.3 61.1 + - - +
307K ALA* 3.6 6.4 + - + +
308K VAL* 3.0 37.1 + - + +
340K ILE* 5.0 2.2 - - + -
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Residues in contact with ILE 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301K VAL* 2.8 35.0 + - + +
302K HIS* 4.9 0.2 - - - -
304K LEU* 1.3 72.4 - - - +
306K PRO* 1.3 63.9 - - + +
308K VAL* 3.1 6.1 + - - +
309K MET* 2.8 50.2 + - + +
337K VAL* 5.5 2.0 - - + -
340K ILE* 3.4 38.4 - - + -
351K ILE* 3.3 37.2 - - + -
354K ARG* 3.7 17.9 - - - +
355K ILE* 4.5 10.8 - - + -
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Residues in contact with PRO 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302K HIS* 2.8 30.1 - - - +
303K GLU* 3.4 15.7 - - - +
305K ILE* 1.3 86.2 - - + +
307K ALA* 1.3 54.9 + - - -
309K MET* 4.3 10.8 - - + -
310K THR* 2.6 39.9 + - - +
354K ARG* 3.7 25.8 - - - +
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Residues in contact with ALA 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264K SER* 5.4 4.5 - - - +
267K VAL* 4.2 23.0 - - + +
283K MET* 5.1 5.6 - - + -
303K GLU* 3.3 27.3 + - - +
304K LEU* 3.9 9.0 - - + +
306K PRO* 1.3 75.2 - - - +
308K VAL* 1.3 59.4 + - + +
310K THR* 3.6 5.9 - - - -
311K CYS* 3.0 33.7 + - - -
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Residues in contact with VAL 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283K MET* 4.4 14.1 - - + -
286K VAL* 4.7 6.7 - - + -
304K LEU* 3.0 25.8 + - + +
305K ILE* 3.7 3.6 - - - +
307K ALA* 1.3 78.0 - - + +
309K MET* 1.3 55.2 + - - +
311K CYS* 3.0 11.0 + - - +
312K ILE* 3.0 27.7 + - - +
333K ALA* 3.1 34.8 - - + +
336K LEU* 3.6 27.4 - - + -
337K VAL* 3.5 21.3 - - + +
340K ILE* 4.6 4.9 - - + -
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Residues in contact with MET 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305K ILE* 2.8 37.6 + - + +
306K PRO* 4.1 7.2 - - + +
308K VAL* 1.3 67.8 - - - +
310K THR* 1.3 65.0 + - - +
312K ILE* 3.0 8.7 + - - +
313K VAL* 2.9 29.4 + - + +
337K VAL* 3.9 16.2 - - + -
354K ARG* 3.8 32.8 - - + +
355K ILE* 3.3 38.8 - - + -
358K THR* 5.3 10.1 - - + +
359K PHE* 4.6 13.5 - - + -
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Residues in contact with THR 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271K VAL* 5.5 15.3 - - + -
306K PRO* 2.6 32.0 + - - +
307K ALA* 3.6 7.2 - - - -
309K MET* 1.3 69.9 - - - +
311K CYS* 1.3 57.5 + - - +
314K SER* 2.2 57.5 + - - +
317K LEU* 4.5 0.4 - - - +
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Residues in contact with CYS 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267K VAL* 5.0 5.8 - - - -
271K VAL* 4.4 22.9 - - - -
279K LEU* 5.2 2.2 - - - -
283K MET* 4.4 19.1 - - - -
307K ALA 3.0 16.6 + - - +
308K VAL* 3.0 11.6 + - - +
310K THR* 1.3 77.2 - - - +
312K ILE* 1.3 61.9 + - - +
317K LEU* 2.7 38.1 - - + +
329K LEU* 4.6 13.0 - - + -
330K ARG* 3.2 6.6 + - - +
333K ALA* 3.6 18.8 - - + -
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Residues in contact with ILE 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308K VAL 3.0 10.8 + - - +
309K MET* 3.0 7.4 + - - +
311K CYS* 1.3 74.0 - - - +
313K VAL* 1.3 59.0 + - + +
330K ARG* 2.5 40.5 + - - +
333K ALA 3.5 3.8 - - - +
334K ALA* 3.3 39.5 - - + +
337K VAL* 3.3 36.6 - - + -
359K PHE* 3.5 30.7 - - + -
371K THR 4.3 0.3 - - - +
375K GLY* 3.5 28.1 - - - +
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Residues in contact with VAL 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309K MET* 2.9 12.5 + - + +
312K ILE* 1.3 74.5 - - + +
314K SER* 1.3 65.2 + - - +
315K ARG* 3.4 2.9 + - - +
330K ARG* 3.3 5.6 - - - -
358K THR* 4.6 13.9 - - + -
359K PHE* 3.3 41.1 - - + -
362K SER* 3.6 22.7 - - - +
372K THR* 3.5 30.3 - - + +
376K SER* 4.4 9.4 - - - -
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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