Contacts of the helix formed by residues 459 - 477 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 4.4 4.3 - - - -
457B CYS* 3.1 12.7 - - - -
458B ILE* 1.3 81.4 - - - +
460B GLU* 1.3 57.2 + - - +
461B THR 3.4 2.0 - - - -
462B ILE* 3.8 10.6 - - - +
463B ALA* 2.8 32.4 + - - +
601B HEM 3.7 26.3 - - - +
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Residues in contact with GLU 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B PHE* 3.5 42.7 - - + +
456B LYS* 4.8 12.0 + - - +
457B CYS* 3.3 16.6 - - - +
458B ILE 3.4 2.2 - - - -
459B GLY* 1.3 77.1 - - - +
461B THR* 1.3 63.8 + - + +
463B ALA* 3.2 2.8 + - - +
464B ARG* 2.4 69.3 + - - +
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Residues in contact with THR 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.9 23.0 - - + +
458B ILE 5.2 3.1 + - - -
459B GLY 5.0 0.3 - - - -
460B GLU* 1.3 83.0 + - + +
462B ILE* 1.3 75.9 + - - +
464B ARG* 3.3 6.8 + - - +
465B TRP* 3.0 46.0 + - + +
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Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.6 42.8 - - + -
146B SER* 3.5 30.3 - - - +
147B ILE* 5.1 5.6 - - + -
159B LEU* 4.0 26.2 - - + +
198B ILE* 6.2 1.6 - - + -
201B ILE* 5.1 5.6 - - + -
458B ILE 5.0 1.1 - - - +
459B GLY* 3.5 11.8 + - - +
460B GLU 3.3 0.4 - - - -
461B THR* 1.3 88.1 + - - +
463B ALA* 1.3 57.7 + - - +
465B TRP* 3.9 1.0 - - - -
466B GLU* 2.8 49.8 + - - +
601B HEM 4.8 11.9 - - + -
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Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 4.1 16.4 - - + -
376B PHE* 5.8 0.2 - - - -
450B PHE* 4.0 7.9 - - + -
459B GLY 2.8 18.8 + - - +
460B GLU 3.6 3.4 - - - +
462B ILE* 1.3 78.3 - - - +
464B ARG* 1.3 58.0 + - - +
466B GLU* 4.5 0.7 - - - -
467B VAL* 2.8 37.4 + - + +
601B HEM 3.6 37.9 - - + +
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Residues in contact with ARG 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ARG* 3.7 29.6 + - - +
369B GLU* 4.3 8.7 + - - -
372B ILE* 4.9 7.8 - - + +
373B LEU* 4.0 21.8 - - - +
376B PHE* 4.8 15.9 - - + -
444B SER 5.4 2.6 + - - -
447B VAL* 5.0 9.7 + - - +
449B ILE* 5.6 0.6 - - - +
450B PHE* 3.6 25.8 - - + -
460B GLU* 2.4 62.6 + - - +
461B THR* 3.8 6.3 - - - +
463B ALA* 1.3 76.1 - - - +
465B TRP* 1.3 65.5 + - + +
467B VAL* 4.2 3.7 - - - +
468B PHE* 3.2 23.4 + - - +
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Residues in contact with TRP 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 3.7 43.1 - - + -
159B LEU* 3.9 20.6 - - + -
359B LEU* 3.2 41.1 - - + -
362B ARG* 3.5 42.4 - - - +
461B THR* 3.0 31.5 + - + +
464B ARG* 1.3 77.5 - - + +
466B GLU* 1.3 60.0 + - - +
468B PHE* 3.2 6.4 + - - +
469B LEU* 2.9 34.6 + - - +
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Residues in contact with GLU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LEU* 4.3 7.2 - - + +
163B VAL* 3.9 15.3 - - + -
194B VAL* 3.8 18.5 - - - +
197B VAL* 3.7 27.2 - - - +
198B ILE* 5.1 4.0 + - - +
322B VAL* 3.9 21.5 - - + +
462B ILE* 2.8 37.3 + - - +
463B ALA* 4.0 3.4 - - - +
465B TRP* 1.3 74.3 - - - +
467B VAL* 1.3 61.1 + - - +
469B LEU* 3.5 1.6 + - - +
470B PHE* 3.1 57.8 + - + -
601B HEM 5.3 1.4 - - - +
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.9 23.3 - - + -
325B ALA* 4.1 21.1 - - + -
326B ILE* 4.5 14.8 - - + +
329B SER* 4.8 6.3 - - - +
372B ILE* 4.2 19.5 - - + -
376B PHE* 4.8 9.0 - - + -
463B ALA* 2.8 29.3 + - + +
464B ARG* 4.2 3.8 - - - +
466B GLU* 1.3 72.3 - - - +
468B PHE* 1.3 63.4 + - - +
470B PHE* 4.1 1.0 - - - +
471B LEU* 3.3 42.0 + - + +
601B HEM 5.2 0.4 - - + -
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Residues in contact with PHE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B PRO* 5.1 3.6 - - + -
358B ARG 3.7 24.2 - - - -
359B LEU* 4.6 3.1 - - + -
361B ASP* 4.3 4.3 - - + -
362B ARG* 3.5 50.3 - - + +
365B LEU* 4.3 16.4 - - + -
368B MET* 3.7 28.9 - - + +
369B GLU* 5.8 2.2 - - - +
372B ILE* 3.9 14.8 - - + +
464B ARG 3.2 19.6 + - - +
465B TRP* 3.2 9.3 + - - +
467B VAL* 1.3 78.7 - - - +
469B LEU* 1.3 69.4 + - + +
471B LEU* 3.3 2.1 + - - +
472B ALA* 2.8 44.3 + - + +
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Residues in contact with LEU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 5.7 1.3 - - + -
160B GLU* 3.9 19.3 - - + +
163B VAL* 3.6 34.1 - - + -
164B SER* 4.8 2.7 - - - +
357B PRO* 4.0 24.0 - - + +
358B ARG* 4.4 5.2 - - - +
359B LEU* 3.2 36.1 - - + -
465B TRP 2.9 16.0 + - - +
466B GLU 4.0 0.4 - - - +
468B PHE* 1.3 85.1 - - + +
470B PHE* 1.3 65.1 + - - +
472B ALA* 3.0 1.7 + - - -
473B ILE* 2.8 48.0 + - + +
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Residues in contact with PHE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B VAL* 3.7 19.3 - - + -
166B GLU* 4.4 2.2 - - + -
167B ALA* 4.2 24.0 - - + -
170B LEU* 4.5 14.4 - - + -
190B VAL* 6.2 0.9 - - + -
193B SER* 4.1 30.1 - - - -
194B VAL* 4.4 8.5 - - + -
197B VAL* 3.9 19.5 - - + -
326B ILE* 3.7 29.8 - - + -
466B GLU* 3.1 52.0 + - + +
467B VAL 4.1 2.0 - - - +
469B LEU* 1.3 79.5 - - - +
471B LEU* 1.3 64.5 + - + +
473B ILE* 4.2 2.0 - - - -
474B LEU* 3.2 33.3 + - + +
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Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B ILE* 4.6 17.9 - - + -
329B SER* 3.8 35.2 - - - +
330B LEU* 4.7 13.5 - - + -
333B LEU* 4.8 9.2 - - + -
368B MET* 4.0 21.8 - - + -
371B PHE* 4.1 3.8 - - + -
372B ILE* 4.0 17.7 - - + -
467B VAL* 3.3 31.0 + - + +
468B PHE 3.8 2.2 - - - +
469B LEU 3.2 0.6 - - - -
470B PHE* 1.3 78.3 - - + +
472B ALA* 1.3 63.5 + - - +
474B LEU* 4.7 4.3 - - + -
475B LEU* 3.0 35.1 + - + +
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Residues in contact with ALA 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B LEU* 4.4 18.1 - - + +
357B PRO* 3.7 27.0 - - + +
368B MET* 4.6 5.8 - - - -
468B PHE* 2.8 36.2 + - + +
469B LEU* 3.6 4.7 - - - +
471B LEU* 1.3 77.1 - - - +
473B ILE* 1.3 63.8 + - - +
474B LEU 3.2 0.7 + - - -
476B GLN* 3.3 24.9 + - - +
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Residues in contact with ILE 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B VAL 4.5 1.6 - - - +
164B SER* 4.1 22.4 - - - +
167B ALA* 3.6 36.3 - - + -
168B GLU* 5.0 5.6 - - + +
171B ILE* 4.1 15.0 - - + +
356B ARG* 5.1 9.2 - - + -
357B PRO* 4.0 25.4 - - + +
469B LEU* 2.8 44.2 + - + +
470B PHE 4.3 0.9 - - - +
472B ALA* 1.3 72.8 - - - +
474B LEU* 1.3 63.8 + - - +
476B GLN* 3.9 6.4 + - - +
477B ARG* 3.9 26.6 - - - +
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Residues in contact with LEU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ALA* 4.3 16.4 - - + +
170B LEU* 4.0 28.5 - - + -
171B ILE* 4.1 27.8 - - + -
174B LEU* 5.3 3.4 - - + -
190B VAL* 6.2 0.7 - - + -
326B ILE* 6.0 4.0 - - + -
330B LEU* 5.1 9.0 - - + -
470B PHE* 3.2 31.1 + - + +
471B LEU* 4.0 5.6 - - + +
472B ALA 3.2 0.8 - - - -
473B ILE* 1.3 77.1 - - - +
475B LEU* 1.3 61.8 + - + +
476B GLN 3.1 1.6 - - - -
477B ARG* 2.8 21.1 + - - +
478B VAL* 2.9 25.3 + - + +
480B PHE* 3.9 27.6 - - + -
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Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B LEU* 4.0 26.2 - - + -
340B GLN* 3.9 26.2 - - + +
343B ILE* 3.8 31.2 - - + -
344B GLN* 3.7 9.2 - - + +
347B LEU* 3.8 13.2 - - + -
368B MET* 4.7 6.7 - - + -
471B LEU* 3.0 25.9 + - + +
474B LEU* 1.3 76.0 - - + +
476B GLN* 1.3 60.4 + - - +
477B ARG 3.2 0.6 + - - -
478B VAL 3.4 15.7 - - - +
480B PHE* 3.9 24.2 - - + -
511B ARG* 3.5 16.5 + - - -
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Residues in contact with GLN 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B LEU* 3.8 16.5 - - + +
348B ASP* 5.6 1.6 - - - +
351B ILE* 4.3 4.2 - - + +
352B GLY 3.4 23.4 + - - +
353B ARG* 3.8 27.7 + - + +
355B ARG 2.5 31.1 + - - +
356B ARG* 4.1 2.1 - - - -
357B PRO* 3.7 20.3 - - + +
472B ALA 3.3 17.9 + - - +
473B ILE 3.9 3.2 - - - +
474B LEU 3.0 1.0 + - - -
475B LEU* 1.3 77.9 - - - +
477B ARG* 1.3 81.3 + - + +
511B ARG* 3.7 19.3 + - - +
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Residues in contact with ARG 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLU* 2.7 43.4 + - - -
171B ILE* 3.4 29.4 - - + +
356B ARG* 4.3 13.7 - - - +
473B ILE* 3.9 16.3 + - - +
474B LEU 2.8 5.8 + - - +
476B GLN* 1.3 99.9 + - - +
478B VAL* 1.3 67.9 + - + +
510B LEU* 3.5 19.1 - - + +
511B ARG* 3.2 27.3 + - - +
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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