Contacts of the helix formed by residues 378 - 403 (chain R) in PDB entry 6XOX
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 THR 378 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374R HIS 4.5 2.0 - - - -
375R ALA* 5.7 0.9 - - - +
376R ARG 3.6 3.4 - - - +
377R GLY* 1.3 78.2 - - - +
379R LEU* 1.3 60.5 + - - +
380R ARG* 3.3 9.1 + - - +
381R PHE* 3.3 38.8 + - - +
382R ILE* 4.2 4.2 + - - +
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Residues in contact with LEU 379 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373R GLU 4.7 1.8 - - - +
374R HIS* 3.3 34.5 + - + +
376R ARG 3.3 27.4 - - - +
377R GLY* 3.0 7.3 + - - +
378R THR* 1.3 74.0 - - - +
380R ARG* 1.3 58.9 + - - +
381R PHE 3.2 2.0 - - - -
382R ILE* 3.3 17.0 - - + +
383R LYS* 2.9 31.0 + - + +
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Residues in contact with ARG 380 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374R HIS* 2.9 32.5 + - + +
375R ALA* 3.7 32.3 - - - +
378R THR* 4.7 6.5 - - - -
379R LEU* 1.3 78.1 - - - +
381R PHE* 1.3 84.4 + - + +
383R LYS* 3.3 8.5 + - - +
384R LEU* 2.9 29.6 + - - +
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Residues in contact with PHE 381 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R GLN* 6.3 1.1 - - - -
141R LEU* 5.2 18.9 - - + +
144R LEU* 5.3 2.3 - - - +
378R THR* 3.3 27.9 + - - +
379R LEU 3.2 0.4 - - - -
380R ARG* 1.3 105.1 - - + +
382R ILE* 1.3 57.9 + - - +
384R LEU* 3.5 9.7 + - + +
385R PHE* 2.9 27.8 + - - +
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Residues in contact with ILE 382 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378R THR 4.2 3.3 + - - +
379R LEU* 3.3 30.0 - - + +
381R PHE* 1.3 76.3 - - - +
383R LYS* 1.3 60.1 + - - +
385R PHE* 3.3 29.6 - - + +
386R THR* 2.9 36.5 + - + +
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Residues in contact with LYS 383 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366R ILE* 6.5 0.9 - - + -
367R PHE* 4.5 25.2 + - + +
374R HIS* 4.9 15.7 - - + -
379R LEU* 2.9 20.8 + - + +
380R ARG* 3.6 10.1 - - - +
381R PHE 3.2 0.2 - - - -
382R ILE* 1.3 76.4 - - + +
384R LEU* 1.3 69.4 + - - +
386R THR* 3.2 8.7 + - - +
387R GLU* 2.9 40.0 + - + +
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Residues in contact with LEU 384 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R LEU* 4.5 13.2 - - + -
144R LEU* 4.3 12.7 - - + +
380R ARG 2.9 16.6 + - - +
381R PHE* 3.8 10.3 - - + +
383R LYS* 1.3 85.6 - - + +
385R PHE* 1.3 61.9 + - - +
387R GLU* 3.4 24.9 - - + +
388R LEU* 3.0 41.1 + - + +
501R V6G 3.8 22.9 - - + -
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Residues in contact with PHE 385 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143R PHE* 3.8 28.3 - + - -
144R LEU* 3.7 31.1 - - + +
147R ILE* 3.7 30.1 - - + -
381R PHE 2.9 19.1 + - - +
382R ILE* 3.3 31.0 - - + +
383R LYS 3.2 0.2 - - - -
384R LEU* 1.3 76.3 - - - +
386R THR* 1.3 71.0 + - + +
388R LEU 3.8 0.2 - - - -
389R SER* 2.9 35.1 + - - -
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Residues in contact with THR 386 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366R ILE* 5.7 5.0 - - - +
382R ILE* 2.9 25.3 + - + +
383R LYS* 3.2 12.3 + - - +
385R PHE* 1.3 90.9 - - + +
387R GLU* 1.3 60.1 + - - +
389R SER* 4.0 6.7 - - - -
390R PHE* 2.9 47.1 + - + +
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Residues in contact with GLU 387 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367R PHE* 3.3 54.1 - - + -
383R LYS* 2.9 28.6 + - + +
384R LEU* 3.4 21.2 - - + +
386R THR* 1.3 76.3 + - - +
388R LEU* 1.3 79.9 + - - +
390R PHE* 4.1 1.5 - - - +
391R THR* 2.6 41.2 + - - -
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Residues in contact with LEU 388 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144R LEU* 4.2 8.7 - - + -
148R TYR* 3.7 35.0 - - + +
152R TYR* 5.7 0.5 - - - -
384R LEU* 3.0 36.2 + - + +
385R PHE 4.2 1.8 - - - +
387R GLU* 1.3 107.6 - - - +
389R SER* 1.3 57.1 + - - +
391R THR* 3.8 5.9 - - - -
392R SER* 2.9 30.7 + - - -
501R V6G 3.6 35.2 - - + -
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Residues in contact with SER 389 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147R ILE* 4.0 19.8 - - - +
385R PHE* 2.9 26.7 + - - -
386R THR* 3.7 9.0 - - - -
387R GLU 3.2 0.2 - - - -
388R LEU* 1.3 75.6 - - - +
390R PHE* 1.3 68.1 + - - +
392R SER* 2.5 23.6 + - - -
393R PHE* 2.9 30.1 + - - +
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Residues in contact with PHE 390 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363R HIS* 3.5 38.0 + + + -
366R ILE* 6.1 8.5 - - + -
367R PHE* 5.9 1.6 - + - -
386R THR* 2.9 31.7 + - + +
387R GLU* 4.3 1.8 - - - +
389R SER* 1.3 83.0 - - - +
391R THR* 1.3 61.0 + - - +
393R PHE* 3.8 10.0 - + + +
394R GLN* 2.9 32.4 + - - +
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Residues in contact with THR 391 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R TYR* 3.6 24.7 - - - +
187R PHE* 5.5 3.3 - - - -
190R ARG* 3.7 30.7 - - - +
241R TYR* 4.3 5.1 + - - +
363R HIS* 4.0 4.5 + - - -
364R GLU* 3.8 13.4 + - - +
367R PHE* 4.6 1.7 - - - -
387R GLU* 2.6 31.2 + - - -
388R LEU* 3.9 6.5 - - - -
390R PHE* 1.3 77.3 - - - +
392R SER* 1.3 62.2 + - - +
394R GLN* 3.8 18.8 + - - +
395R GLY 4.8 1.2 + - - -
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Residues in contact with SER 392 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147R ILE* 4.5 1.0 + - - +
148R TYR* 3.7 31.3 - - - -
151R GLY* 3.6 21.7 - - - +
152R TYR* 3.6 18.5 + - - -
155R SER* 3.9 10.7 - - - -
388R LEU 2.9 16.6 + - - -
389R SER* 2.5 27.2 + - - -
391R THR* 1.3 80.6 - - - +
393R PHE* 1.3 71.1 + - - -
394R GLN 3.3 1.2 + - - -
395R GLY 3.9 1.6 + - - -
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Residues in contact with PHE 393 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147R ILE* 4.9 5.4 - - + -
150R VAL* 5.0 6.3 - - + -
151R GLY* 3.5 30.7 - - - -
154R LEU* 5.1 11.7 - - + -
389R SER* 2.9 26.1 + - - +
390R PHE* 3.3 11.6 + + + +
392R SER* 1.3 81.3 + - - +
394R GLN* 1.3 58.8 + - - +
395R GLY 3.2 0.4 - - - -
396R LEU* 3.1 19.7 + - + +
397R MET* 2.9 37.2 + - + +
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Residues in contact with GLN 394 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187R PHE* 3.9 18.2 - - + -
190R ARG* 5.7 1.2 + - - -
240R ASN* 5.6 0.3 + - - -
241R TYR* 5.9 0.2 - - - -
244R LEU* 3.4 18.9 - - - +
358R PRO* 3.1 33.7 + - + +
361R GLY* 3.3 23.0 - - - -
363R HIS* 3.2 24.5 + - + -
364R GLU* 4.6 4.7 - - - +
390R PHE 2.9 15.8 + - - +
391R THR* 3.9 14.5 - - - +
392R SER 3.2 1.4 - - - -
393R PHE* 1.3 77.0 - - - +
395R GLY* 1.3 57.7 + - - +
397R MET* 3.2 8.1 + - - +
398R VAL* 3.0 28.3 + - - +
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Residues in contact with GLY 395 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R TYR* 6.3 0.2 - - - -
155R SER* 4.0 5.4 - - - -
159R LEU* 3.3 30.9 - - - +
187R PHE* 3.9 16.0 - - - -
391R THR 4.8 0.8 + - - -
392R SER 3.9 4.2 + - - -
393R PHE 3.2 0.6 - - - -
394R GLN* 1.3 77.6 - - - +
396R LEU* 1.3 63.1 + - - +
398R VAL* 3.3 10.7 - - - +
399R ALA* 3.0 19.1 + - - +
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Residues in contact with LEU 396 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154R LEU* 3.6 40.8 - - + +
155R SER* 3.5 17.5 - - - +
158R ALA* 4.4 13.9 - - + -
393R PHE* 3.1 24.8 + - + +
395R GLY* 1.3 75.5 - - - +
397R MET* 1.3 74.0 + - + +
399R ALA* 3.2 1.0 + - - +
400R ILE* 3.0 48.4 + - + +
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Residues in contact with MET 397 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354R LEU 5.7 2.0 - - - +
358R PRO* 3.8 21.3 - - + -
393R PHE* 2.9 27.1 + - + +
394R GLN* 3.2 8.9 + - - +
396R LEU* 1.3 91.4 - - - +
398R VAL* 1.3 58.5 + - - +
400R ILE* 3.4 18.4 - - + +
401R LEU* 2.9 48.1 + - + +
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Residues in contact with VAL 398 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159R LEU* 4.6 0.7 - - + -
183R LEU* 5.4 0.9 - - + -
184R PHE* 4.0 18.6 - - + -
187R PHE* 3.9 23.1 - - + -
358R PRO* 3.3 36.3 - - + +
359R LEU* 3.8 14.8 - - + +
394R GLN 3.0 11.1 + - - +
395R GLY* 3.3 19.7 - - - +
397R MET* 1.3 78.6 - - - +
399R ALA* 1.3 57.4 + - - +
402R TYR* 2.9 47.0 + - + +
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Residues in contact with ALA 399 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R ALA* 3.6 39.3 - - + +
159R LEU* 3.7 15.9 - - + -
162R ALA* 4.2 3.4 - - + -
184R PHE* 4.5 6.3 - - - -
395R GLY 3.0 18.7 + - - +
396R LEU 3.2 1.1 + - - +
398R VAL* 1.3 77.8 - - - +
400R ILE* 1.3 62.5 + - - +
403R CYS* 3.5 9.0 + - - +
404R PHE* 3.5 23.2 + - + -
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Residues in contact with ILE 400 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R ALA* 5.3 2.5 - - + -
396R LEU* 3.0 40.0 + - + +
397R MET* 3.4 22.9 - - + +
399R ALA* 1.3 80.1 - - + +
401R LEU* 1.3 81.4 + - + +
402R TYR 3.4 0.4 - - - -
404R PHE* 3.4 26.0 + - + -
405R VAL* 3.1 39.4 + - + +
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Residues in contact with LEU 401 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU* 5.2 8.3 - - - +
351R LYS* 5.2 2.7 - - - +
354R LEU 4.0 4.0 - - - +
355R THR* 3.7 48.2 - - + +
358R PRO* 3.9 19.5 - - + -
397R MET* 2.9 30.0 + - + +
400R ILE* 1.3 92.8 - - + +
402R TYR* 1.3 79.6 + - + +
403R CYS 3.8 0.2 - - - -
405R VAL* 3.8 23.6 - - + +
406R ASN* 4.7 4.6 + - - +
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Residues in contact with TYR 402 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TYR* 4.1 27.2 + + - +
392A GLU* 6.1 0.9 - - + -
393A LEU* 5.2 1.2 - - - +
166R LEU* 4.9 3.5 - - - +
176R ARG* 5.9 0.6 + - - -
177R ASN* 5.1 1.7 - - - +
180R HIS* 3.6 36.0 + + - +
184R PHE* 4.1 9.9 - - + -
355R THR* 2.5 33.5 + - - -
356R LEU* 4.0 4.7 - - - +
359R LEU* 3.3 49.0 - - + +
398R VAL* 2.9 29.6 + - + +
401R LEU* 1.3 96.5 - - + +
403R CYS* 1.3 70.0 + - - +
406R ASN* 4.2 19.0 + - - +
409R VAL* 4.9 1.2 - - - +
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Residues in contact with CYS 403 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162R ALA* 3.6 9.6 - - - -
165R ILE* 3.9 13.7 - - + -
166R LEU* 3.6 25.6 - - - -
184R PHE* 3.5 28.5 - - - -
399R ALA 3.5 8.2 + - - +
402R TYR* 1.3 84.2 - - - +
404R PHE* 1.3 82.4 + - + +
405R VAL 3.3 2.2 - - - -
406R ASN 3.3 8.6 + - - +
409R VAL* 3.3 30.6 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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