Contacts of the helix formed by residues 462 - 478 (chain A) in PDB entry 3OEH
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 ARG 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A ILE* 4.0 32.3 - - + +
459A GLU* 2.8 38.0 + - + +
461A SER* 1.3 83.7 - - - +
463A ILE* 1.3 50.1 + - - +
464A GLY 3.0 6.9 + - - -
465A GLU* 3.2 47.7 + - + +
466A PHE* 2.7 36.8 + - + +
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Residues in contact with ILE 463 (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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425A ARG* 3.7 24.5 - - + +
428A GLN* 3.7 11.7 - - + -
429A LEU* 4.0 31.0 - - + +
455A LEU* 4.2 29.2 - - + +
458A ILE* 3.6 29.2 - - + +
459A GLU 3.7 1.0 + - - +
460A LEU* 3.7 30.7 + - + +
461A SER 3.7 0.8 - - - -
462A ARG* 1.3 75.5 - - - +
464A GLY* 1.3 61.8 + - - +
466A PHE* 3.8 10.6 - - + +
467A GLU* 3.4 18.4 + - - +
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Residues in contact with GLY 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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428A GLN* 4.8 10.5 - - - +
461A SER 4.4 4.4 + - - -
462A ARG* 3.0 2.6 - - - +
463A ILE* 1.3 74.2 - - - +
465A GLU* 1.3 58.4 + - - -
466A PHE 2.8 10.3 + - - -
467A GLU* 3.0 16.1 + - - +
468A SER* 3.3 9.5 + - - -
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Residues in contact with GLU 465 (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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461A SER 5.0 2.1 + - - +
462A ARG* 3.2 62.1 + - + +
464A GLY* 1.3 72.1 - - - +
466A PHE* 1.3 57.7 + - - +
468A SER* 3.6 9.3 - - - -
469A SER* 3.0 34.1 + - - -
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Residues in contact with PHE 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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429A LEU* 5.8 2.7 - - + -
446A LEU* 5.0 4.3 - - + -
449A ALA* 4.6 8.1 - - + -
455A LEU* 3.5 35.9 - - + -
458A ILE* 3.6 31.6 - - + -
462A ARG* 2.7 22.7 + - + +
463A ILE* 3.8 15.7 - - + +
464A GLY 2.8 1.6 + - - -
465A GLU* 1.3 72.3 - - - +
467A GLU* 1.3 62.3 + - + +
469A SER* 3.2 4.6 + - - -
470A PHE* 2.8 65.2 + + + +
503A THR* 5.6 0.4 - - + -
506A PHE* 3.6 29.3 - + - -
507A VAL* 4.5 17.7 - - + -
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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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153A LYS* 2.4 33.4 + - - -
429A LEU* 3.9 9.1 - - + +
438A LEU* 4.6 8.9 - - - +
446A LEU* 3.3 39.7 - - + +
463A ILE 3.4 8.9 + - - +
464A GLY* 3.0 9.3 + - - +
466A PHE* 1.3 87.5 - - + +
468A SER* 1.3 64.6 + - - +
470A PHE* 4.6 0.2 - - - -
471A LEU* 3.2 35.2 + - + +
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Residues in contact with SER 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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464A GLY 3.3 8.1 + - - -
465A GLU* 3.6 13.7 - - - -
467A GLU* 1.3 86.6 + - - +
469A SER* 1.3 53.7 + - - +
471A LEU* 4.2 3.5 - - - +
472A SER* 2.7 30.0 + - - -
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Residues in contact with SER 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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465A GLU* 3.0 22.9 + - - -
466A PHE* 3.2 1.8 + - - -
468A SER* 1.3 77.0 + - - +
470A PHE* 1.3 61.4 + - - +
472A SER* 3.0 15.0 + - - -
473A TYR* 3.2 18.0 + - - +
506A PHE* 3.5 19.6 - - - -
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Residues in contact with PHE 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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445A PRO* 3.7 26.9 - - + -
446A LEU* 4.0 18.6 - - + -
449A ALA* 4.6 6.1 - - + -
466A PHE* 2.8 36.4 + + + +
467A GLU 4.0 2.5 - - - +
468A SER 3.3 0.2 - - - -
469A SER* 1.3 70.7 - - - +
471A LEU* 1.3 61.1 + - + +
473A TYR* 3.5 2.5 + + - +
474A LEU* 2.8 68.4 + - + +
499A LEU* 5.4 0.9 - - + -
502A ALA 4.0 0.7 - - - -
503A THR* 3.6 33.9 - - + -
506A PHE* 3.5 46.2 - + + -
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Residues in contact with LEU 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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438A LEU* 4.0 20.9 - - + -
442A GLU* 3.4 44.6 - - + +
445A PRO* 4.4 9.9 - - + -
446A LEU* 3.8 29.6 - - + -
467A GLU* 3.2 23.4 + - + +
468A SER* 4.2 4.3 - - - +
470A PHE* 1.3 74.2 - - + +
472A SER* 1.3 54.1 + - - +
474A LEU* 3.1 11.8 + - + +
475A LYS* 2.7 45.4 + - - +
482A LEU* 5.0 2.3 - - + +
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Residues in contact with SER 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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468A SER 2.7 20.5 + - - -
469A SER* 3.0 15.9 + - - -
471A LEU* 1.3 75.5 - - - +
473A TYR* 1.3 50.6 + - - +
475A LYS* 3.1 14.2 + - - +
476A SER* 2.8 36.1 + - - -
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Residues in contact with TYR 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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469A SER 3.2 18.0 + - - +
470A PHE* 3.6 5.2 - + - +
472A SER* 1.3 77.0 - - - +
474A LEU* 1.3 70.7 + - + +
476A SER* 3.0 7.1 + - - -
477A ASN* 3.0 53.7 + - - +
478A HIS* 3.2 35.1 + + - -
502A ALA 3.9 13.9 - - - -
505A SER* 4.0 19.7 + - - -
506A PHE* 3.5 36.3 - + + -
509A THR* 5.6 6.1 - - + -
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PRO* 3.7 27.6 - - + -
470A PHE* 2.8 59.7 + - + +
471A LEU* 3.4 11.9 - - + +
473A TYR* 1.3 73.7 - - + +
475A LYS* 1.3 57.5 + - - +
478A HIS* 2.9 66.7 + - + +
479A ASN* 4.0 0.2 - - - -
481A LEU* 4.7 5.8 - - + -
482A LEU* 4.0 18.7 - - + +
499A LEU* 5.1 2.7 - - + -
502A ALA* 3.8 17.0 - - + -
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Residues in contact with LYS 475 (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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442A GLU* 3.2 31.3 + - - -
471A LEU* 2.7 26.9 + - + +
472A SER* 3.2 15.3 - - - +
474A LEU* 1.3 74.4 - - - +
476A SER* 1.3 62.6 + - - +
479A ASN* 3.7 24.0 - - - +
482A LEU* 4.0 18.8 - - + -
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Residues in contact with SER 476 (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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472A SER 2.8 23.9 + - - -
473A TYR* 3.0 6.9 + - - -
475A LYS* 1.3 76.8 - - - +
477A ASN* 1.3 74.4 + - - +
479A ASN* 5.3 1.2 + - - +
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Residues in contact with ASN 477 (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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473A TYR* 3.0 49.4 + - + +
476A SER* 1.3 91.2 - - - +
478A HIS* 1.3 83.3 + - + +
479A ASN 3.5 3.3 + - - -
480A GLU* 3.9 12.8 - - - +
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Residues in contact with HIS 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TYR* 3.2 35.7 + + - -
474A LEU* 2.9 43.5 + - + +
477A ASN* 1.3 85.9 + - + +
479A ASN* 1.3 60.8 + - - +
480A GLU* 3.0 21.0 + - - -
481A LEU* 3.3 33.1 + - + +
482A LEU* 3.6 8.7 + - - +
501A SER* 6.2 0.2 - - - -
502A ALA* 3.6 20.9 - - + +
505A SER* 6.1 0.9 - - - -
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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