Contacts of the helix formed by residues 363 - 384 (chain D) in PDB entry 5HP1
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 363 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402C TRP* 5.6 0.2 - - - -
410C TRP* 3.3 29.5 - - + +
359D GLY* 2.7 17.2 + - - +
362D THR* 1.3 81.3 - - + +
364D ASP* 1.3 62.4 + - - +
365D VAL* 2.9 12.1 + - - +
366D LYS* 2.7 37.8 + - + +
367D GLN* 3.2 25.9 + - - +
405D TYR* 2.4 35.6 + - - -
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Residues in contact with ASP 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C TRP* 3.1 34.3 - - - +
408C ALA* 4.2 5.6 - - + -
409C THR 3.3 33.0 + - - +
410C TRP* 4.3 1.2 - - - -
331D LYS* 2.8 37.5 + - - -
337D TRP* 3.6 12.7 - - + -
362D THR 4.1 1.2 + - - -
363D ASN* 1.3 72.4 + - - +
365D VAL* 1.3 58.1 + - - +
367D GLN* 3.4 18.2 + - - +
368D LEU* 3.0 25.5 + - - +
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Residues in contact with VAL 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ALA* 4.9 1.8 - - - -
409C THR* 4.3 4.9 - - - +
410C TRP* 3.7 26.0 - - + +
363D ASN* 2.9 6.9 + - - +
364D ASP* 1.3 73.2 - - - +
366D LYS* 1.3 66.8 + - - +
368D LEU* 3.3 5.7 + - - +
369D THR* 3.0 29.5 + - - +
393D ILE* 4.2 18.4 - - + -
397D THR* 4.1 24.9 - - + +
398D TRP* 4.4 11.7 - - + -
401D TRP* 4.0 26.9 - - + -
402D TRP 4.8 2.9 - - - +
405D TYR* 4.5 7.0 - - + -
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Residues in contact with LYS 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D ARG* 3.6 25.6 - - - +
359D GLY* 3.8 13.1 - - - +
363D ASN* 2.7 31.1 + - + +
365D VAL* 1.3 70.1 - - - +
367D GLN* 1.3 65.3 + - - +
369D THR* 3.1 3.6 + - - -
370D GLU* 3.0 46.0 + - - +
405D TYR* 3.6 47.3 - - + -
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Residues in contact with GLN 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C TRP* 5.5 0.2 - - - -
335D GLY* 3.1 23.8 - - - +
337D TRP* 3.1 33.2 + - + +
354D TYR* 4.2 4.2 - - - -
357D MET* 4.7 10.8 + - + +
358D ARG 4.1 7.0 - - - +
359D GLY 3.5 7.5 + - - -
360D ALA* 3.4 37.5 - - + +
361D HIS* 3.5 8.3 - - - +
362D THR 4.7 0.2 - - - +
363D ASN 3.2 14.0 + - - +
364D ASP* 3.5 23.7 + - - +
366D LYS* 1.3 78.7 - - - +
368D LEU* 1.3 57.2 + - - +
370D GLU* 3.3 6.1 + - - +
371D ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ALA* 4.2 9.2 - - + -
329D ILE* 3.8 32.3 - - + -
337D TRP* 3.8 26.2 - - + -
364D ASP 3.0 16.4 + - - +
365D VAL* 3.8 6.3 - - - +
367D GLN* 1.3 75.6 - - - +
369D THR* 1.3 63.9 + - - +
371D ALA* 3.2 5.7 + - + +
372D VAL* 2.9 26.6 + - + +
391D LEU* 4.6 4.0 - - + -
392D PRO* 4.4 12.6 - - + +
393D ILE* 4.0 30.7 - - + -
398D TRP* 3.9 20.2 - - + -
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Residues in contact with THR 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D VAL* 3.0 14.9 + - - +
366D LYS 3.5 8.7 - - - -
368D LEU* 1.3 77.4 - - - +
370D GLU* 1.3 62.9 + - + +
372D VAL* 3.3 3.7 + - - +
373D GLN* 3.1 31.3 + - - +
398D TRP* 3.2 23.9 - - - -
402D TRP* 4.1 14.1 + - - +
405D TYR* 3.9 28.2 - - + +
406D TRP* 3.5 27.6 - - + +
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Residues in contact with GLU 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LYS* 5.5 8.8 + - - -
354D TYR* 3.6 15.5 + - + +
357D MET* 3.1 22.7 - - + +
358D ARG* 3.3 39.0 + - - +
366D LYS* 3.0 27.4 + - + +
367D GLN 3.6 5.6 - - - +
369D THR* 1.3 74.6 - - + +
371D ALA* 1.3 64.4 + - - +
373D GLN* 3.1 17.7 + - - +
374D LYS* 2.9 26.0 + - + +
405D TYR* 5.6 4.0 - - + +
407D GLN* 5.7 1.8 - - - +
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Residues in contact with ALA 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D ILE* 4.5 7.4 - - + -
337D TRP* 4.9 11.9 - - + -
354D TYR* 3.8 25.2 - - + -
367D GLN 2.9 14.7 + - - +
368D LEU* 3.2 20.6 + - + +
370D GLU* 1.3 77.1 - - - +
372D VAL* 1.3 63.3 + - - +
374D LYS* 3.2 3.0 + - - +
375D ILE* 3.0 34.6 + - + +
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Residues in contact with VAL 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D ILE* 3.9 12.1 - - + -
368D LEU* 2.9 20.7 + - + +
369D THR* 3.6 8.1 - - - +
371D ALA* 1.3 73.7 - - - +
373D GLN* 1.3 58.6 + - - +
376D THR* 2.9 34.0 + - - -
389D PHE* 3.5 31.5 - - + -
391D LEU* 3.7 29.4 - - + -
398D TRP* 4.5 7.2 - - + -
406D TRP* 4.1 12.8 - - + -
412D PRO* 3.9 17.3 - - + -
414D TRP* 5.2 5.6 - - + -
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Residues in contact with GLN 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D THR* 3.1 30.8 + - - +
370D GLU* 3.1 17.9 + - - +
372D VAL* 1.3 76.5 - - - +
374D LYS* 1.3 62.4 + - + +
376D THR 3.4 0.5 + - - -
377D THR* 2.9 28.5 + - - +
405D TYR 4.0 7.9 + - - -
406D TRP* 3.6 28.5 - - + -
407D GLN* 3.0 31.8 + - - +
408D ALA* 3.3 14.6 + - + +
410D TRP* 3.7 16.6 - - + -
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Residues in contact with LYS 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D TYR* 3.2 49.0 + - + +
370D GLU* 2.9 15.4 + - + +
371D ALA* 3.8 7.4 - - - +
373D GLN* 1.3 75.7 - - + +
375D ILE* 1.3 60.0 + - + +
377D THR* 3.2 7.4 + - - +
378D GLU* 2.9 43.3 + - + +
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Residues in contact with ILE 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ALA* 4.3 6.1 - - + -
329D ILE* 3.8 24.0 - - + -
339D TYR* 3.4 50.0 - - + -
341D ILE* 3.7 30.1 - - + -
371D ALA* 3.0 23.0 + - + +
374D LYS* 1.3 76.7 - - + +
376D THR* 1.3 64.2 + - - +
378D GLU* 3.2 9.3 + - - +
379D SER* 2.8 29.7 + - - +
387D PRO* 4.4 0.2 - - + -
389D PHE* 3.8 20.4 - - + -
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Residues in contact with THR 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D VAL 2.9 18.9 + - - -
375D ILE* 1.3 77.6 - - - +
377D THR* 1.3 55.8 + - - +
379D SER* 3.2 2.4 + - - -
380D ILE* 2.9 32.0 + - + +
386D THR* 3.7 33.4 - - + -
387D PRO* 4.2 8.3 - - - -
389D PHE* 3.1 20.8 - - - -
410D TRP* 3.5 34.4 - - + -
412D PRO* 3.9 8.7 - - + +
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Residues in contact with THR 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D VAL* 5.6 2.0 - - + -
188D TYR* 5.0 8.0 + - + -
234D LEU* 3.6 39.3 - - + -
239D TRP* 5.0 2.0 - - + -
373D GLN* 2.9 19.8 + - - +
374D LYS* 3.5 8.0 - - - +
376D THR* 1.3 76.8 - - - +
378D GLU* 1.3 64.0 + - + +
380D ILE* 3.3 11.8 + - - +
381D VAL* 3.1 23.8 + - + +
410D TRP* 3.7 14.9 - - - -
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Residues in contact with GLU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D TRP* 3.7 43.4 + - + -
339D TYR* 2.6 34.7 + - - -
341D ILE* 5.2 2.8 - - + +
350D LYS* 3.1 19.2 - - + +
374D LYS* 2.9 28.8 + - + +
375D ILE* 3.6 6.9 - - - +
377D THR* 1.3 77.3 - - + +
379D SER* 1.3 57.1 + - - +
381D VAL* 3.3 1.4 + - - +
382D ILE* 2.8 42.0 + - + +
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Residues in contact with SER 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D LEU* 4.2 3.4 - - - -
341D ILE* 3.4 20.1 - - - +
375D ILE 2.8 17.6 + - - -
376D THR 3.6 3.6 - - - -
378D GLU* 1.3 76.7 - - - +
380D ILE* 1.3 54.3 + - - +
383D TRP* 2.7 49.8 + - - +
384D GLY 3.1 4.2 + - - -
385D LYS 3.2 19.5 - - - +
387D PRO* 3.5 19.9 - - - +
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Residues in contact with ILE 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D HIS* 3.4 4.7 - - - -
181D TYR* 3.9 10.0 - - + -
183D TYR* 3.9 32.3 - - + -
188D TYR* 3.6 42.8 - - + +
376D THR* 2.9 34.0 + - + +
377D THR* 3.6 5.2 - - - +
378D GLU 3.2 0.2 - - - -
379D SER* 1.3 77.5 - - - +
381D VAL* 1.3 60.5 + - - +
384D GLY* 2.6 29.0 + - - +
385D LYS 3.8 11.9 - - - +
386D THR* 4.0 8.3 - - + -
410D TRP* 3.8 22.2 - - + +
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Residues in contact with VAL 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D HIS* 3.2 15.1 + - - -
97D PRO 4.8 0.3 - - - +
100D LEU* 4.1 21.2 - - + +
101D LYS* 3.8 32.6 + - + +
106D VAL* 4.8 2.5 - - + -
188D TYR* 3.9 20.2 - - + -
234D LEU* 3.9 26.5 - - + -
236D PRO* 3.9 16.4 - - + -
239D TRP* 4.0 11.7 - - + -
377D THR 3.1 16.7 + - - +
378D GLU 3.8 2.9 - - - +
380D ILE* 1.3 76.9 - - - +
382D ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D HIS* 2.9 13.2 + - - -
101D LYS* 4.0 41.1 + - + -
239D TRP* 4.0 25.6 - - + -
350D LYS* 3.9 28.9 - - + -
378D GLU 2.8 27.9 + - - +
381D VAL* 1.3 75.1 - - - +
383D TRP* 1.3 97.9 + - + +
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Residues in contact with TRP 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D HIS* 3.5 19.8 - - - +
319D TYR* 3.5 62.5 + + + +
325D LEU* 3.7 19.3 - - + -
341D ILE* 3.9 29.4 - - + -
349D LEU* 3.7 31.6 - - + +
350D LYS* 4.0 22.7 - - + -
379D SER* 2.7 42.9 + - - +
382D ILE* 1.3 105.1 - - + +
384D GLY* 1.3 60.3 + - - +
385D LYS* 3.4 2.9 + - - +
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Residues in contact with GLY 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D HIS* 3.3 7.9 - - - -
181D TYR* 3.4 24.2 + - - -
183D TYR* 3.5 20.7 - - - -
379D SER 3.1 0.4 + - - -
380D ILE* 2.6 29.9 + - - -
383D TRP* 1.3 73.6 - - - +
385D LYS* 1.3 61.6 + - - +
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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
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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