Contacts of the helix formed by residues 467 - 490 (chain B) in PDB entry 3N2Z
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 PRO 467 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B PRO* 3.7 21.5 - - + -
304B TRP* 5.6 0.4 - - + -
450B ILE* 5.5 0.2 - - + -
451B SER 4.5 0.4 - - - +
452B GLU* 4.1 37.2 - - + +
457B LEU* 4.8 3.6 - - + -
465B LEU 3.4 9.6 - - - +
466B ASP* 1.4 87.9 - - - +
468B MET* 1.3 67.1 + - - +
469B SER* 3.2 20.0 - - - +
470B VAL* 3.2 25.7 + - + +
471B LEU* 3.4 4.5 - - - +
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Residues in contact with MET 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B PRO* 1.3 73.5 - - - +
469B SER* 1.4 54.4 + - - +
470B VAL 3.3 0.3 + - - -
471B LEU* 3.4 28.6 + - + +
472B LEU* 2.8 49.9 + - + +
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Residues in contact with SER 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B THR 4.7 4.3 - - - +
450B ILE* 4.1 8.5 - - - +
451B SER* 2.7 49.3 + - - -
452B GLU* 4.2 2.1 + - - -
467B PRO* 3.6 14.6 - - - +
468B MET* 1.4 74.4 - - - +
470B VAL* 1.4 55.0 + - - -
472B LEU* 3.9 8.5 - - - +
473B ALA* 3.2 25.8 + - - +
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ILE* 3.9 17.0 - - + +
457B LEU* 4.0 12.1 - - + -
458B ASP* 3.8 21.8 - - + +
466B ASP* 3.5 23.6 - - + -
467B PRO* 3.2 29.2 - - + +
469B SER* 1.4 76.7 + - - +
471B LEU* 1.4 52.9 + - - +
473B ALA* 2.8 9.5 + - - +
474B ARG* 2.7 66.7 + - + +
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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
----------------------------------------------------------
462B LYS* 5.5 6.1 - - + -
466B ASP* 3.4 40.2 - - + +
467B PRO 3.4 9.6 - - - +
468B MET* 3.4 35.4 + - + +
470B VAL* 1.4 74.3 - - - +
472B LEU* 1.3 56.8 + - - +
474B ARG* 3.4 19.2 + - - +
475B SER* 2.9 31.6 + - - -
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Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B MET* 2.8 35.5 + - + +
469B SER* 3.9 8.1 - - - +
471B LEU* 1.3 71.4 - - - +
473B ALA* 1.4 57.7 + - + +
475B SER* 3.1 21.8 + - - +
476B LEU* 3.3 17.4 + - + +
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Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B VAL* 3.4 30.1 - - + +
449B THR 5.1 1.3 - - - +
450B ILE* 3.8 16.8 - - + -
458B ASP* 5.4 2.2 - - + -
469B SER 3.2 16.3 + - - +
470B VAL* 2.8 14.2 + - - +
472B LEU* 1.4 69.7 - - - +
474B ARG* 1.4 58.0 + - - +
475B SER 3.1 1.6 - - - -
476B LEU* 3.0 7.8 + - - +
477B GLU* 2.9 37.0 + - - +
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Residues in contact with ARG 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.7 22.8 - - + +
108B ASP* 5.9 1.6 - - - -
457B LEU* 3.0 26.5 + - - +
458B ASP* 2.8 30.8 + - + +
460B ARG* 3.3 23.0 + - - +
461B THR 4.5 1.0 + - - -
462B LYS* 4.1 14.9 - - - +
466B ASP* 3.6 34.1 + - - +
470B VAL* 2.7 40.2 + - + +
471B LEU* 3.7 17.5 - - - +
473B ALA* 1.4 70.1 - - - +
475B SER* 1.3 58.5 + - - +
477B GLU* 3.4 13.1 + - - +
478B VAL* 3.1 26.9 + - - +
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Residues in contact with SER 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B LEU 2.9 16.6 + - - -
472B LEU* 3.1 12.1 + - - +
474B ARG* 1.3 74.3 - - - +
476B LEU* 1.4 57.4 + - - +
477B GLU 3.2 0.2 - - - -
478B VAL* 3.4 11.9 - - - +
479B ARG* 2.9 56.6 + - - +
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Residues in contact with LEU 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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423B VAL* 5.8 0.4 - - - -
446B VAL* 6.1 0.4 - - + -
447B ALA 5.5 0.7 - - - +
448B VAL* 3.7 32.1 - - + -
472B LEU* 3.3 15.8 + - + +
473B ALA* 3.0 11.3 + - - +
475B SER* 1.4 77.4 + - - +
477B GLU* 1.4 64.6 + - - +
479B ARG* 3.4 18.1 - - + +
480B HIS* 3.0 56.3 + - + +
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Residues in contact with GLU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.6 21.7 - - + -
200B LEU* 3.6 26.2 - - + +
423B VAL* 4.3 14.4 - - + +
425B SER* 3.3 16.6 - - - -
448B VAL* 4.4 5.5 - - + +
458B ASP* 3.0 34.3 - - - +
473B ALA* 2.9 19.2 + - - +
474B ARG* 3.4 20.6 - - - +
475B SER 3.2 0.2 - - - -
476B LEU* 1.4 74.5 - - - +
478B VAL* 1.4 58.7 + - - +
480B HIS* 3.0 9.1 + - - +
481B MET* 2.9 35.1 + - + +
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 5.2 0.9 - - + -
109B VAL* 3.9 26.5 - - + -
112B GLU* 5.0 6.7 - - + +
113B LEU* 4.0 11.9 - - + -
474B ARG 3.1 18.4 + - - +
475B SER* 3.4 15.7 - - - +
477B GLU* 1.4 69.7 - - - +
479B ARG* 1.3 65.1 + - - +
481B MET* 3.0 12.8 + - + +
482B LYS* 2.8 50.5 + - + +
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Residues in contact with ARG 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B SER* 2.9 39.1 + - - +
476B LEU* 3.4 23.6 - - + +
477B GLU 3.3 0.2 - - - -
478B VAL* 1.3 76.3 - - - +
480B HIS* 1.3 60.5 + - + +
482B LYS* 3.6 10.1 - - + +
483B ASN* 3.0 32.7 + - - +
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Residues in contact with HIS 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B VAL* 4.4 8.5 - - + +
443B ASP 4.4 7.5 + - - -
444B THR* 5.4 5.2 - - - -
446B VAL* 3.8 38.0 - - + +
476B LEU* 3.0 45.9 + - + +
477B GLU 3.0 9.0 + - - +
479B ARG* 1.3 73.2 - - + +
481B MET* 1.3 66.3 + - - +
483B ASN* 3.1 23.5 + - + +
484B TRP* 3.1 45.4 + + + -
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Residues in contact with MET 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.7 3.6 - - - -
105B PHE* 3.5 38.4 - - + -
109B VAL* 4.6 2.0 - - + -
113B LEU* 4.0 25.1 - - + -
174B ILE* 3.8 16.8 - - + +
176B ILE* 3.9 24.5 - - - -
200B LEU* 4.7 6.3 - - + -
423B VAL* 5.6 0.9 - - + -
477B GLU* 2.9 14.3 + - + +
478B VAL* 3.0 23.5 + - + +
480B HIS* 1.3 74.8 - - - +
482B LYS* 1.4 59.2 + - - +
484B TRP* 2.9 44.4 + - + +
485B ILE* 3.2 17.8 + - - +
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Residues in contact with LYS 482 (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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112B GLU* 2.7 33.4 + - - -
113B LEU* 3.9 15.9 - - + +
478B VAL* 2.8 42.0 + - + +
479B ARG* 3.6 11.7 - - + +
481B MET* 1.4 72.1 - - - +
483B ASN* 1.3 55.0 + - - +
485B ILE* 4.0 10.9 - - + +
486B ARG* 3.1 57.9 + - - +
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Residues in contact with ASN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ARG* 3.0 24.7 + - - +
480B HIS* 3.1 22.3 + - + +
482B LYS* 1.3 75.5 - - - +
484B TRP* 1.4 63.1 + - + +
486B ARG* 2.9 31.7 + - - +
487B ASP* 2.9 36.1 + - - +
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Residues in contact with TRP 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 3.8 23.6 - - + -
197B VAL* 3.9 23.8 - - + +
198B GLY* 3.8 10.1 - - - -
199B ALA 3.4 34.8 - - - -
200B LEU 4.7 0.4 - - - -
421B ASN* 3.3 56.9 - - + +
422B ILE 4.0 2.9 - - - -
423B VAL* 3.5 19.3 - - + -
444B THR* 5.0 1.3 + - - +
480B HIS* 3.2 40.4 + + + -
481B MET* 2.9 25.5 + - + +
483B ASN* 1.4 83.5 - - + +
485B ILE* 1.3 62.4 + - - +
487B ASP* 3.6 4.1 + - - +
488B PHE* 3.2 23.6 + - - +
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Residues in contact with ILE 485 (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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83B GLY 5.2 1.6 - - - +
84B GLY 4.3 5.2 - - - +
85B SER* 3.7 21.5 - - - +
113B LEU* 4.0 23.3 - - + +
172B PRO* 3.9 23.3 - - + -
174B ILE* 3.7 22.0 - - + -
481B MET 3.2 16.6 + - - +
482B LYS* 4.0 9.0 - - + +
484B TRP* 1.3 73.4 - - - +
486B ARG* 1.4 59.4 + - - +
488B PHE* 3.0 5.4 + - - +
489B TYR* 3.0 54.6 + - + -
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Residues in contact with ARG 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LYS* 3.1 47.8 + - - +
483B ASN* 2.9 33.1 + - - +
485B ILE* 1.4 75.3 - - - +
487B ASP* 1.3 61.4 + - - +
489B TYR* 3.5 4.5 + - - -
490B ASP* 3.0 43.5 + - - +
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Residues in contact with ASP 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ASN* 2.9 27.4 + - - +
484B TRP* 4.0 5.2 - - - +
485B ILE 3.3 0.8 - - - -
486B ARG* 1.3 79.4 - - - +
488B PHE* 1.3 60.4 + - - +
490B ASP* 3.7 9.3 + - - +
491B SER* 3.6 19.1 + - - -
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Residues in contact with PHE 488 (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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162B LYS* 5.1 4.0 - - - -
170B ASN* 3.1 30.7 - - + -
171B GLN 3.7 11.9 - - - -
172B PRO* 3.4 34.8 - - + -
197B VAL* 3.7 23.1 - - + -
484B TRP 3.2 13.9 + - - +
485B ILE 3.0 8.2 + - - +
487B ASP* 1.3 75.4 - - - +
489B TYR* 1.3 74.3 + + - +
491B SER* 3.2 22.9 + - - -
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Residues in contact with TYR 489 (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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83B GLY* 3.3 34.0 - - - -
84B GLY 2.8 29.6 + - - -
170B ASN 3.9 17.9 - - - -
171B GLN* 3.4 13.9 - - - +
172B PRO* 3.4 13.4 - - + +
485B ILE* 3.0 34.7 + - + +
486B ARG* 4.0 5.6 - - - +
488B PHE* 1.3 84.7 - + - +
490B ASP* 1.3 59.6 + - - +
491B SER 3.2 7.8 + - - +
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Residues in contact with ASP 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ARG* 3.0 35.7 + - - +
487B ASP* 3.9 5.6 - - - +
488B PHE 3.2 1.0 - - - -
489B TYR* 1.3 77.8 - - - +
491B SER* 1.4 64.6 + - - +
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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) + - + + + + + -
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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