Contacts of the helix formed by residues 459 - 478 (chain B) in PDB entry 3OEE
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 GLU 459 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B ARG* 4.5 2.7 - - - +
457B GLY 3.7 3.3 + - - +
458B ILE* 1.3 81.8 - - - +
460B LEU* 1.3 65.6 + - - +
461B SER* 3.5 16.1 + - - +
462B ARG* 3.4 32.4 + - + +
463B ILE* 3.2 22.0 + - - +
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Residues in contact with LEU 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B GLU* 3.1 34.5 - - + +
425B ARG* 3.8 36.5 - - - +
428B GLN* 4.2 35.2 + - + +
459B GLU* 1.3 69.4 - - - +
461B SER* 1.3 61.1 + - - +
462B ARG 2.9 10.3 + - - -
463B ILE* 3.0 18.3 + - + +
464B GLY 4.3 1.2 + - - -
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Residues in contact with SER 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B GLU* 4.4 13.2 + - - +
460B LEU* 1.3 76.2 - - - +
462B ARG* 1.3 63.6 + - - +
463B ILE 3.7 0.2 - - - -
464B GLY* 4.7 3.8 + - - -
465B GLU* 5.0 3.1 + - - +
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Residues in contact with ARG 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B ILE* 4.2 22.9 - - + +
459B GLU* 3.4 37.1 + - + +
460B LEU 2.9 1.4 + - - -
461B SER* 1.3 85.1 - - - +
463B ILE* 1.3 54.3 + - - +
464B GLY 3.1 2.9 - - - -
465B GLU* 2.9 49.0 + - - +
466B PHE* 2.7 36.8 + - - +
509B THR 5.3 6.3 + - - -
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Residues in contact with ILE 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ARG* 3.8 23.1 - - + +
428B GLN* 3.8 29.6 - - + +
429B LEU* 4.3 21.1 - - + +
455B LEU* 3.8 41.7 - - + -
458B ILE* 4.3 8.0 - - + +
459B GLU 3.2 18.1 + - - +
460B LEU* 3.0 12.9 + - + +
462B ARG* 1.3 76.3 - - - +
464B GLY* 1.3 61.3 + - - +
466B PHE* 3.7 7.8 - - + +
467B GLU* 3.3 22.5 + - + +
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Residues in contact with GLY 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLN* 5.5 3.8 - - - +
460B LEU 4.3 2.6 + - - -
461B SER 4.7 2.7 + - - -
462B ARG* 3.1 1.8 - - - +
463B ILE* 1.3 80.9 - - - +
465B GLU* 1.3 60.7 + - - +
467B GLU* 3.4 16.7 + - - +
468B SER* 3.4 12.4 + - - -
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Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B SER 5.0 2.1 + - - +
462B ARG* 2.9 57.9 + - - +
464B GLY* 1.3 70.1 - - - +
466B PHE* 1.3 67.1 + - - +
467B GLU 3.3 0.2 + - - -
468B SER* 3.3 8.7 + - - -
469B SER* 3.1 37.7 + - - +
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Residues in contact with PHE 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 5.6 4.7 - - + -
446B LEU* 4.9 4.7 - - + -
449B ALA* 4.7 9.2 - - + -
455B LEU* 3.6 26.0 - - + -
458B ILE* 3.4 33.9 - - + -
462B ARG* 2.7 22.6 + - - +
463B ILE* 3.7 13.5 - - + +
465B GLU* 1.3 75.0 - - - +
467B GLU* 1.3 61.2 + - + +
469B SER* 3.3 4.4 + - - -
470B PHE* 2.8 73.7 + + + +
506B PHE* 3.6 30.7 - + - -
507B VAL* 4.1 18.2 - - + -
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 3.3 28.7 + - - -
428B GLN 5.5 1.7 - - - +
429B LEU* 5.6 8.0 - - + -
431B LYS 4.9 0.9 - - - +
432B GLN* 5.9 0.2 - - - +
438B LEU* 4.0 14.4 - - - +
446B LEU* 3.7 32.2 - - + +
463B ILE* 3.3 13.5 + - + +
464B GLY* 3.7 10.0 - - - +
465B GLU 3.2 0.6 - - - -
466B PHE* 1.3 89.1 - - + +
468B SER* 1.3 62.9 + - - +
470B PHE* 3.9 1.1 - - - +
471B LEU* 3.2 32.2 + - + +
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Residues in contact with SER 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B GLY 3.4 9.9 + - - -
465B GLU* 3.3 15.2 + - - -
467B GLU* 1.3 81.3 - - - +
469B SER* 1.3 54.4 + - - +
471B LEU* 3.5 6.9 + - - +
472B SER* 2.7 31.6 + - - -
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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
----------------------------------------------------------
465B GLU* 3.1 28.8 + - - +
466B PHE* 3.8 1.6 - - - -
468B SER* 1.3 77.8 + - - +
470B PHE* 1.3 62.1 + - - +
472B SER* 3.7 8.9 + - - -
473B TYR* 3.3 16.1 + - - +
506B PHE* 3.5 27.4 - - - -
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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
----------------------------------------------------------
445B PRO* 4.1 15.3 - - + -
446B LEU* 4.0 14.1 - - + -
449B ALA* 4.3 17.0 - - + -
466B PHE* 2.8 41.5 + + + +
467B GLU 3.9 3.6 - - - +
468B SER 3.2 0.4 - - - -
469B SER* 1.3 75.0 - - - +
471B LEU* 1.3 61.6 + - - +
473B TYR* 3.4 8.3 + + - +
474B LEU* 3.0 59.1 + - + +
499B LEU* 6.0 0.7 - - + -
502B ALA 4.4 6.1 - - - -
503B THR* 4.3 24.9 - - + -
506B PHE* 3.6 40.2 - + + -
507B VAL* 6.3 0.2 - - + -
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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
----------------------------------------------------------
438B LEU* 4.6 17.9 - - + -
442B GLU* 3.3 43.1 - - + +
445B PRO* 4.9 0.7 - - + -
446B LEU* 4.1 28.0 - - + -
467B GLU* 3.2 26.0 + - + +
468B SER* 3.9 6.1 - - - +
469B SER 3.4 0.2 - - - -
470B PHE* 1.3 75.5 - - - +
472B SER* 1.3 64.2 + - - +
474B LEU* 3.2 17.2 + - + +
475B LYS* 2.9 39.7 + - - +
482B LEU* 5.9 2.7 - - + -
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Residues in contact with SER 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B SER 2.7 19.5 + - - -
469B SER* 3.7 9.3 - - - -
471B LEU* 1.3 76.4 - - - +
473B TYR* 1.3 62.1 - - - +
475B LYS* 3.1 8.2 + - - +
476B SER* 2.9 27.5 + - - -
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Residues in contact with TYR 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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469B SER 3.3 12.2 + - - +
470B PHE* 3.4 17.5 - + - +
472B SER* 1.3 78.2 - - - +
474B LEU* 1.3 59.1 + - + +
476B SER* 3.2 5.7 + - - -
477B ASN* 2.9 51.7 + - - +
478B HIS* 3.1 33.2 + + - -
502B ALA* 3.5 21.9 + - + -
505B SER* 3.2 26.0 + - - -
506B PHE* 3.7 32.8 - + + -
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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
----------------------------------------------------------
445B PRO* 3.6 29.2 - - + -
470B PHE* 3.0 56.4 + - + +
471B LEU* 3.2 12.5 + - + +
473B TYR* 1.3 76.8 - - + +
475B LYS* 1.3 59.4 + - - +
478B HIS* 2.9 61.2 + - + +
479B ASN* 3.1 0.9 + - - -
481B LEU* 5.7 1.8 - - + -
482B LEU* 4.1 22.2 - - + +
499B LEU* 5.1 10.5 - - + -
502B ALA* 4.5 9.4 - - + -
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Residues in contact with LYS 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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442B GLU* 2.6 37.6 + - - +
471B LEU* 2.9 30.0 + - + +
472B SER* 3.1 6.7 + - - +
474B LEU* 1.3 75.5 - - - +
476B SER* 1.3 60.3 + - - +
479B ASN* 3.0 38.1 - - - +
482B LEU* 4.2 14.1 - - + -
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Residues in contact with SER 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B SER 2.9 18.2 + - - -
473B TYR* 3.2 4.3 + - - -
475B LYS* 1.3 79.8 - - - +
477B ASN* 1.3 79.4 + - - +
479B ASN* 5.1 1.4 + - - +
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Residues in contact with ASN 477 (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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473B TYR* 2.9 32.6 + - + +
476B SER* 1.3 105.1 + - - +
478B HIS* 1.3 81.4 + - + +
479B ASN 3.6 1.5 + - - -
480B GLU* 6.1 0.2 - - - +
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Residues in contact with HIS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B TYR* 3.1 46.2 + + - -
474B LEU* 2.9 26.3 + - + +
477B ASN* 1.3 88.5 + - + +
479B ASN* 1.3 62.5 + - - +
480B GLU* 3.3 5.2 - - - +
481B LEU* 3.2 38.0 + - + +
482B LEU* 3.6 8.3 + - - +
501B SER* 6.3 0.9 - - - -
502B ALA* 3.6 24.3 - - + +
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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
------------------------------------------------------------
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