Contacts of the helix formed by residues 458 - 474 (chain A) in PDB entry 1EJI
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 ILE 458 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A LEU* 4.9 11.3 - - + +
435A ILE* 3.7 28.3 - - + -
438A HIS* 5.1 4.9 - - + -
451A LYS* 3.2 66.6 - - + +
452A LEU* 4.9 6.3 - - + -
455A ASP* 2.7 20.6 + - - +
457A LYS* 1.3 78.8 - - + +
459A GLN* 1.3 61.1 + - - +
460A SER 3.1 2.8 + - - -
461A ALA* 3.4 15.3 + - + +
462A VAL* 3.5 11.4 + - + +
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Residues in contact with GLN 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ALA* 6.2 1.0 - - - +
451A LYS 5.4 0.2 - - - +
452A LEU* 3.2 25.8 + - - +
453A ALA* 3.2 21.6 + - - +
454A GLY 3.7 5.4 - - - +
455A ASP 4.6 2.9 - - - +
456A GLU* 2.7 20.6 + - - +
458A ILE* 1.3 77.6 - - - +
460A SER* 1.3 60.8 + - - +
461A ALA 3.3 0.9 - - - -
462A VAL* 2.9 21.9 - - + +
463A ALA* 2.9 21.8 - - + +
466A ARG* 4.7 11.7 - - - +
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Residues in contact with SER 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A GLU* 2.6 22.7 + - - +
457A LYS* 3.5 13.6 + - - -
458A ILE 3.1 0.2 - - - -
459A GLN* 1.3 77.2 - - - +
461A ALA* 1.3 57.2 + - - +
463A ALA* 3.8 6.5 - - - +
464A THR* 2.7 33.3 + - - -
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Residues in contact with ALA 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 4.2 19.5 - - + -
457A LYS 3.9 4.8 + - - +
458A ILE* 3.4 14.0 + - + +
459A GLN 3.3 0.2 - - - -
460A SER* 1.3 77.3 - - - +
462A VAL* 1.3 66.3 + - - +
464A THR* 3.1 15.8 + - - -
465A LEU* 3.1 13.5 + - - +
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A VAL* 6.1 0.9 - - + -
379A ALA* 3.3 33.2 - - + +
380A CYS* 3.3 31.4 - - - -
431A LEU* 4.1 11.1 - - + +
452A LEU* 5.7 4.9 - - + -
458A ILE* 3.5 5.2 + - + +
459A GLN* 2.9 42.4 - - + +
461A ALA* 1.3 79.6 - - - +
463A ALA* 1.3 64.6 + - - +
464A THR 3.0 0.9 + - - -
465A LEU* 3.0 2.3 + - - +
466A ARG* 2.6 41.1 + - - +
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Residues in contact with ALA 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLN* 2.9 18.3 + - + +
460A SER* 3.8 8.3 - - - +
462A VAL* 1.3 81.2 - - - +
464A THR* 1.3 60.6 + - - +
466A ARG* 3.8 29.1 + - - +
467A GLU* 3.3 21.7 + - - +
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Residues in contact with THR 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ARG* 6.2 1.6 - - - +
460A SER 2.7 19.6 + - - -
461A ALA* 3.1 10.0 + - - -
462A VAL 3.0 0.8 - - - -
463A ALA* 1.3 75.1 - - - +
465A LEU* 1.3 66.0 - - - +
467A GLU* 3.1 23.3 + - - +
468A GLU* 3.1 16.5 + - + +
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A CYS* 4.1 22.7 - - + -
382A ILE* 5.6 1.3 - - + -
424A PHE* 3.7 25.8 - - + +
427A ARG* 3.6 55.2 - - + +
428A GLY* 4.0 15.7 - - - +
431A LEU* 5.0 7.6 - - + -
461A ALA 3.1 8.1 + - - +
462A VAL* 3.0 6.1 + - - +
464A THR* 1.3 76.0 - - - +
466A ARG* 1.3 67.1 + - - +
467A GLU 3.2 0.2 + - - -
468A GLU* 3.2 4.3 + - - +
469A VAL* 2.9 33.6 + - + +
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Residues in contact with ARG 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ALA* 3.3 21.1 + - - +
380A CYS* 3.9 19.4 - - - +
381A SER* 3.5 14.4 - - - +
459A GLN* 4.7 11.9 - - - +
462A VAL* 2.6 28.8 + - - +
463A ALA* 3.8 35.2 + - - +
465A LEU* 1.3 72.1 - - - +
467A GLU* 1.3 59.2 + - - +
469A VAL* 3.3 1.4 + - - +
470A GLU* 2.8 59.8 + - - +
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Residues in contact with GLU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A ALA 3.3 11.4 + - - +
464A THR* 3.1 19.2 + - - +
466A ARG* 1.3 78.1 - - - +
468A GLU* 1.3 64.6 + - - +
469A VAL 2.9 0.3 + - - -
470A GLU* 3.0 7.7 + - - +
471A ASN* 2.7 49.3 + - - +
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Residues in contact with GLU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A PHE* 3.4 21.4 - - + -
427A ARG* 2.5 34.3 + - - +
464A THR* 3.1 12.2 + - + +
465A LEU 3.8 6.1 - - - +
467A GLU* 1.3 81.7 + - - +
469A VAL* 1.3 60.3 + - - +
471A ASN* 3.7 10.3 - - - +
472A PHE* 3.2 21.7 + - - +
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Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.9 23.6 - - + +
380A CYS 3.6 22.0 - - - +
381A SER* 3.9 17.5 - - - +
382A ILE* 4.2 10.1 - - + -
424A PHE* 3.6 33.2 - - + -
465A LEU* 2.9 25.2 + - + +
466A ARG 3.4 7.4 - - - +
468A GLU* 1.3 75.8 - - - +
470A GLU* 1.3 61.5 + - - +
472A PHE* 3.0 4.5 + - - +
473A ALA* 2.8 27.9 + - + +
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Residues in contact with GLU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.2 38.1 - - + +
381A SER* 3.3 21.4 + - - +
466A ARG* 2.8 50.7 + - - +
467A GLU* 3.7 5.8 - - - +
469A VAL* 1.3 72.9 - - - +
471A ASN* 1.3 53.3 + - - +
473A ALA* 3.8 6.9 - - - +
474A SER* 2.6 39.5 + - - -
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Residues in contact with ASN 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A GLU* 2.7 51.6 + - - +
468A GLU* 3.6 8.8 - - - +
470A GLU* 1.3 75.9 - - - +
472A PHE* 1.3 57.6 + - - +
474A SER* 3.0 16.7 + - - -
475A ASN* 2.5 30.1 + - - +
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Residues in contact with PHE 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.1 16.8 - - + -
413A LEU* 3.8 20.0 - - + -
417A ASP* 3.8 22.9 - - + -
420A LYS* 4.0 24.5 - - + -
421A VAL* 3.9 22.0 - - + -
424A PHE* 3.5 26.5 - + + -
468A GLU 3.2 12.8 + - - +
469A VAL 3.0 6.7 + - - +
471A ASN* 1.3 80.3 - - - +
473A ALA* 1.3 62.8 + - - +
475A ASN* 3.3 16.0 + - - +
476A PHE* 3.2 39.3 - + - -
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Residues in contact with ALA 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG 3.9 5.4 - - - +
46A VAL 3.8 0.9 - - - -
47A GLY* 3.3 41.1 - - - +
48A LEU* 4.4 9.9 - - + -
411A ARG* 3.7 6.3 + - - +
469A VAL 2.8 14.8 + - - +
470A GLU* 3.8 4.5 - - - +
472A PHE* 1.3 77.3 - - - +
474A SER* 1.3 53.8 + - - +
475A ASN 2.5 18.5 + - - -
476A PHE* 2.8 25.5 + - - +
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Residues in contact with SER 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 3.6 38.9 + - - +
46A VAL* 3.6 9.2 - - - +
411A ARG* 4.8 1.1 - - - +
470A GLU 2.6 21.3 + - - -
471A ASN* 3.0 16.6 + - - -
473A ALA* 1.3 74.1 - - - +
475A ASN* 1.3 59.6 + - - +
476A PHE 3.2 8.8 + - - +
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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