Contacts of the helix formed by residues 459 - 476 (chain D) in PDB entry 6DWN
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 GLY 459 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D LEU* 4.1 9.4 - - - -
457D CYS* 3.1 12.9 - - - -
458D ILE* 1.3 79.7 - - - +
460D GLU* 1.3 58.2 + - - +
461D THR 3.3 2.5 - - - -
462D ILE* 3.3 11.2 + - - +
463D ALA* 2.8 32.4 + - - +
601D HEM 3.9 21.5 - - - +
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Residues in contact with GLU 460 (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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450D PHE* 3.6 39.5 - - + +
456D LYS* 5.0 9.7 - - - +
457D CYS* 3.1 22.4 + - - +
458D ILE 3.4 2.8 - - - -
459D GLY* 1.3 76.1 - - - +
461D THR* 1.3 65.7 + - - +
463D ALA* 3.2 1.9 + - - +
464D ARG* 2.7 59.1 + - - +
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Residues in contact with THR 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D ILE* 4.3 17.5 - - + -
458D ILE 5.3 0.8 + - - -
459D GLY 3.3 0.4 - - - -
460D GLU* 1.3 79.1 - - - +
462D ILE* 1.3 64.9 + - - +
464D ARG* 3.4 5.4 + - - +
465D TRP* 3.1 65.0 + - + +
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Residues in contact with ILE 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU* 3.2 46.7 - - + -
146D SER* 3.3 30.3 - - - +
147D ILE* 4.9 11.7 - - + -
159D LEU* 3.7 31.3 - - + +
198D ILE* 6.3 0.9 - - + -
201D ILE* 5.0 6.3 - - + -
458D ILE 5.1 0.4 - - - +
459D GLY* 3.3 11.7 + - - +
461D THR* 1.3 77.2 - - - +
463D ALA* 1.3 58.1 + - - +
465D TRP* 5.3 0.9 - - - -
466D GLU* 2.8 38.8 + - - +
601D HEM 4.9 11.4 - - + -
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Residues in contact with ALA 463 (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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322D VAL* 4.2 15.3 - - + -
376D PHE* 5.9 0.7 - - - -
450D PHE* 4.1 5.4 - - + -
459D GLY 2.8 21.9 + - - +
460D GLU 3.6 3.8 - - - +
462D ILE* 1.3 74.0 - - - +
464D ARG* 1.3 57.5 + - - +
466D GLU* 3.8 0.6 - - - -
467D VAL* 2.9 37.2 + - - +
601D HEM 3.6 41.5 - - + +
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Residues in contact with ARG 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D ARG* 3.8 26.9 + - - +
369D GLU* 4.0 13.1 + - - +
372D ILE* 4.9 6.2 - - + +
373D LEU* 3.7 24.8 - - - +
376D PHE* 4.4 18.6 - - + -
444D SER 5.4 2.4 + - - -
447D VAL* 5.0 9.9 + - - +
449D ILE* 5.4 0.8 - - - +
450D PHE* 3.3 33.2 - - + -
460D GLU* 2.7 50.6 + - - +
461D THR* 4.0 6.1 - - - +
463D ALA* 1.3 76.1 - - - +
465D TRP* 1.3 63.1 + - + +
467D VAL* 4.3 3.2 - - - +
468D PHE* 3.2 27.2 + - - +
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Residues in contact with TRP 465 (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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434B THR* 5.2 2.2 - - + -
435B PRO* 4.0 29.8 - - + -
436B ASP* 3.4 37.5 + - + +
147D ILE* 3.9 32.3 - - + -
157D CYS* 4.7 3.6 - - - -
159D LEU* 3.6 26.5 - - + -
359D LEU* 3.5 34.5 - - + -
362D ARG* 3.8 23.7 - - - +
461D THR* 3.1 37.1 + - + +
462D ILE* 5.4 0.4 - - - -
464D ARG* 1.3 81.1 - - + +
466D GLU* 1.3 60.7 + - - +
468D PHE* 3.3 2.9 + - - +
469D LEU* 2.9 34.6 + - - +
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Residues in contact with GLU 466 (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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159D LEU* 4.0 9.7 - - + +
163D VAL* 4.0 13.2 - - + -
194D VAL* 3.5 31.8 - - - +
197D VAL* 3.9 15.8 - - - +
198D ILE* 5.1 3.3 + - - +
201D ILE* 6.0 0.2 - - - +
318D GLY 5.3 0.3 - - - +
322D VAL* 3.6 25.0 - - + +
462D ILE* 2.8 34.1 + - - +
463D ALA* 3.9 2.9 - - - +
465D TRP* 1.3 74.0 - - - +
467D VAL* 1.3 62.6 + - - +
469D LEU* 3.4 1.1 + - - +
470D PHE* 3.1 54.6 + - + -
601D HEM 5.2 1.6 - - - +
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Residues in contact with VAL 467 (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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322D VAL* 4.1 20.4 - - + -
325D ALA* 4.2 21.1 - - + -
326D ILE* 4.3 15.5 - - + -
329D SER* 4.8 6.1 - - - +
372D ILE* 3.9 27.4 - - + -
376D PHE* 4.8 11.0 - - + -
463D ALA* 2.9 24.0 + - + +
464D ARG* 4.3 4.0 - - - +
466D GLU* 1.3 76.2 - - - +
468D PHE* 1.3 65.6 + - - +
470D PHE* 4.1 0.7 - - - +
471D LEU* 3.2 35.8 + - + +
601D HEM 5.2 0.7 - - + -
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Residues in contact with PHE 468 (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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357D PRO* 5.7 0.9 - - + -
358D ARG 3.9 18.4 - - - -
359D LEU* 4.0 20.6 - - + -
362D ARG* 3.4 54.5 - - + +
365D LEU* 3.7 27.4 - - + -
368D MET* 3.7 24.6 - - + +
369D GLU* 5.3 2.9 - - + -
372D ILE* 3.8 15.0 - - + +
464D ARG 3.2 21.0 + - - +
465D TRP 3.3 2.4 + - - +
467D VAL* 1.3 79.0 - - - +
469D LEU* 1.3 65.7 + - + +
471D LEU* 3.8 1.8 - - - +
472D ALA* 2.8 43.3 + - + +
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Residues in contact with LEU 469 (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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159D LEU* 4.9 2.5 - - + -
160D GLU* 3.6 42.2 - - + +
163D VAL* 3.7 25.8 - - + -
164D SER* 5.0 1.3 - - - +
357D PRO 4.6 1.1 - - - +
358D ARG* 4.3 9.6 - - - +
359D LEU* 4.1 36.3 - - + +
465D TRP 2.9 20.0 + - - +
466D GLU 4.0 0.4 - - - +
468D PHE* 1.3 83.7 - - + +
470D PHE* 1.3 65.4 + - - +
472D ALA* 3.1 2.6 + - + -
473D ILE* 2.8 50.6 + - + +
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Residues in contact with PHE 470 (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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163D VAL* 3.7 20.8 - - + +
166D GLU* 4.3 2.5 - - + -
167D ALA* 4.0 29.2 - - + -
170D LEU* 4.7 12.3 - - + -
190D VAL* 6.5 0.7 - - + -
193D SER* 4.1 26.7 - - - -
194D VAL* 4.4 7.4 - - + -
197D VAL* 4.0 17.0 - - + -
326D ILE* 3.7 30.1 - - + -
466D GLU* 3.1 51.6 + - + +
467D VAL 4.1 1.3 - - - +
469D LEU* 1.3 79.5 - - - +
471D LEU* 1.3 63.3 + - + +
473D ILE* 5.1 1.8 - - - -
474D LEU* 3.3 34.6 + - + +
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Residues in contact with LEU 471 (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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326D ILE* 4.6 17.5 - - + -
329D SER* 4.0 25.6 - - - +
330D LEU* 4.6 8.1 - - + -
333D LEU* 4.5 16.4 - - + -
368D MET* 3.8 30.7 - - + -
371D PHE* 4.0 6.1 - - + -
372D ILE* 3.9 10.8 - - + -
467D VAL* 3.2 35.7 + - + +
468D PHE 3.9 1.8 - - - +
469D LEU 3.2 0.4 - - - -
470D PHE* 1.3 77.7 - - + +
472D ALA* 1.3 62.6 + - - +
474D LEU* 4.8 4.3 - - + -
475D LEU* 3.1 35.1 + - + +
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Residues in contact with ALA 472 (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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347D LEU* 3.6 18.5 - - + +
357D PRO* 3.7 20.2 - - + +
365D LEU* 5.3 2.9 - - + -
368D MET* 4.3 8.0 - - + -
468D PHE* 2.8 41.2 + - + +
469D LEU* 3.7 4.9 - - + +
471D LEU* 1.3 78.5 - - - +
473D ILE* 1.3 64.2 + - + +
474D LEU 3.3 0.5 + - - -
476D GLN* 3.4 18.7 + - - +
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Residues in contact with ILE 473 (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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163D VAL* 4.7 1.1 - - + +
164D SER* 4.3 21.8 - - - +
167D ALA* 3.9 33.9 - - + -
168D GLU* 4.6 11.9 - - + +
171D ILE* 4.5 10.0 - - + +
356D ARG* 4.8 15.5 - - + +
357D PRO* 4.3 24.5 - - + +
469D LEU* 2.8 46.6 + - + +
470D PHE 4.3 0.9 - - - +
472D ALA* 1.3 73.1 - - - +
474D LEU* 1.3 65.9 + - + +
476D GLN* 3.9 4.3 + - - +
477D ARG* 3.8 19.7 - - - +
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Residues in contact with LEU 474 (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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167D ALA* 4.0 22.2 - - + +
170D LEU* 4.0 25.6 - - + -
171D ILE* 3.9 31.0 - - + -
174D LEU* 5.4 2.7 - - + -
326D ILE* 6.5 0.9 - - + -
330D LEU* 5.7 4.9 - - + -
470D PHE* 3.3 23.9 + - + +
471D LEU* 4.1 4.7 - - + +
472D ALA 3.2 0.6 - - - -
473D ILE* 1.3 75.8 - - - +
475D LEU* 1.3 56.9 + - + +
476D GLN 3.0 2.0 - - - -
477D ARG* 2.7 27.0 + - - +
478D VAL* 2.9 25.5 + - + +
480D PHE* 4.1 24.7 - - + -
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Residues in contact with LEU 475 (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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330D LEU* 5.8 0.2 - - + -
333D LEU* 4.0 30.5 - - + -
340D GLN* 4.0 26.0 - - + +
343D ILE* 3.7 37.7 - - + -
344D GLN* 3.2 20.1 + - + +
347D LEU* 4.5 3.8 - - + -
368D MET* 4.5 5.4 - - + -
471D LEU* 3.1 27.5 + - + +
472D ALA 4.6 0.9 - - - +
474D LEU* 1.3 75.0 - - + +
476D GLN* 1.3 59.2 + - - +
477D ARG 3.2 0.2 - - - -
478D VAL 3.4 7.7 - - - +
480D PHE* 4.1 19.3 - - + -
511D ARG* 2.8 20.3 + - - -
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Residues in contact with GLN 476 (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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347D LEU* 3.9 18.2 - - + +
348D ASP* 4.9 4.5 - - - +
351D ILE* 4.3 5.1 - - + +
352D GLY 3.6 16.9 + - - +
353D ARG* 3.7 33.1 + - - +
355D ARG 2.8 27.5 + - - -
356D ARG* 3.6 10.4 - - - +
357D PRO* 3.2 24.3 - - + +
472D ALA 3.4 16.1 + - - +
473D ILE 4.0 3.6 - - - +
474D LEU 2.9 1.0 + - - -
475D LEU* 1.3 78.2 - - - +
477D ARG* 1.3 72.1 + - - +
511D ARG* 3.3 19.9 + - - +
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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