Contacts of the helix formed by residues 455 - 467 (chain A) in PDB entry 3IHO
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 ASP 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A LEU 3.2 13.9 + - - +
453A PHE 3.1 1.2 - - - -
454A HIS* 1.3 97.8 + - + +
456A PRO* 1.3 71.6 - - - +
457A TRP* 3.2 21.6 + - - +
458A LYS* 3.0 44.1 + - + +
459A LEU 3.2 1.7 + - - -
486A PRO 5.0 1.0 - - - +
487A SER* 6.0 0.3 - - - -
523A TYR* 4.3 2.3 + - - -
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Residues in contact with PRO 456 (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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453A PHE 4.6 1.1 - - - +
454A HIS 4.1 6.1 - - - +
455A ASP* 1.3 86.2 - - - +
457A TRP* 1.3 66.2 + - - +
458A LYS 3.0 0.3 + - - -
459A LEU* 3.1 1.4 + - - +
460A LEU* 2.8 30.7 + - + +
523A TYR* 3.8 18.6 - - + +
528A TRP* 5.1 3.4 - - + -
545A TYR* 3.9 31.9 - - + +
549A CYS* 4.0 20.9 - - + -
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Residues in contact with TRP 457 (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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455A ASP* 3.1 12.3 + - - +
456A PRO* 1.3 77.6 - - - +
458A LYS* 1.3 76.4 + - + +
460A LEU* 3.2 1.6 + - - +
461A ILE* 2.8 43.6 + - + +
481A PHE* 3.8 15.9 - + - -
482A LEU* 3.7 15.9 - - + -
485A TYR 3.3 27.1 - - - -
486A PRO 3.8 2.7 - - - -
487A SER* 3.6 18.8 - - - -
488A ALA* 3.5 29.3 - - + +
491A ALA* 3.7 13.9 - - + -
519A PHE* 3.4 26.5 - + - -
520A SER* 2.9 29.5 + - - -
523A TYR* 3.3 34.0 + + + -
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Residues in contact with LYS 458 (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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452A LEU* 4.1 28.0 - - + +
454A HIS* 5.0 8.6 + - + +
455A ASP* 3.0 36.2 + - + +
457A TRP* 1.3 90.7 - - + +
459A LEU* 1.3 54.1 + - - +
461A ILE* 3.2 8.8 + - - +
462A ALA* 2.8 33.7 + - - +
478A LEU* 4.9 1.6 - - - +
482A LEU* 4.3 22.1 - - + +
486A PRO* 3.4 33.1 + - - +
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Residues in contact with LEU 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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449A GLN* 3.6 44.4 - - + +
452A LEU* 3.6 21.3 - - + +
453A PHE* 3.9 14.6 - - - -
455A ASP 3.2 3.0 + - - +
456A PRO 3.1 5.3 + - - +
458A LYS* 1.3 80.4 - - - +
460A LEU* 1.3 71.9 + - + +
462A ALA* 3.2 6.4 - - - +
463A THR* 3.0 26.0 + - + +
544A SER* 4.0 23.6 - - - -
545A TYR* 4.0 8.5 - - - +
548A PHE* 4.0 9.2 - - + -
549A CYS* 3.8 22.7 - - - -
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Residues in contact with LEU 460 (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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456A PRO* 2.8 26.2 + - + +
459A LEU* 1.3 85.5 - - + +
461A ILE* 1.3 67.7 + - - +
463A THR* 2.8 25.4 + - - +
464A ILE* 3.1 8.5 + - - +
519A PHE* 3.5 36.1 - - + -
523A TYR* 4.1 16.4 - - + -
528A TRP* 5.2 1.6 - - + -
531A PRO* 3.8 34.8 - - + -
534A LEU* 4.7 0.7 - - + -
537A ILE* 4.2 13.2 - - + +
541A GLY* 4.0 21.5 - - - +
545A TYR* 4.4 4.7 - - + -
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Residues in contact with ILE 461 (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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457A TRP* 2.8 46.1 + - + +
458A LYS* 3.3 9.2 - - - +
460A LEU* 1.3 73.6 - - - +
462A ALA* 1.3 66.3 + - - +
464A ILE* 2.8 20.2 + - + +
465A PHE* 3.0 36.9 + - + -
478A LEU* 3.7 12.3 - - + -
481A PHE* 3.9 11.2 - - + -
482A LEU* 4.5 2.5 - - + -
516A ILE* 3.9 31.0 - - + -
519A PHE* 3.5 25.3 - - + -
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Residues in contact with ALA 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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448A VAL* 4.3 7.4 - - + -
449A GLN* 6.0 2.7 - - - -
452A LEU* 3.9 13.2 - - + -
458A LYS 2.8 13.2 + - - +
459A LEU* 3.2 13.5 - - + +
460A LEU 3.0 0.2 - - - -
461A ILE* 1.3 73.7 - - - +
463A THR* 1.3 58.2 + - + +
465A PHE* 2.9 18.5 + - - +
466A LEU* 2.9 26.2 + - + +
478A LEU* 3.7 31.4 - - + -
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Residues in contact with THR 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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449A GLN* 4.3 10.3 - - - +
459A LEU* 3.0 19.0 + - + +
460A LEU* 2.8 19.5 + - - +
462A ALA* 1.3 75.9 - - + +
464A ILE* 1.3 59.0 + - - +
466A LEU* 4.6 1.3 - - - -
467A ASN* 2.8 31.4 + - - +
537A ILE* 4.5 3.6 - - - +
540A TYR* 3.6 25.7 - - - -
541A GLY* 3.6 20.2 + - - +
544A SER* 4.0 29.8 - - - +
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Residues in contact with ILE 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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460A LEU 3.1 11.1 + - - +
461A ILE* 2.8 22.4 + - + +
463A THR* 1.3 74.7 - - - +
465A PHE* 1.3 62.7 + - + +
467A ASN* 3.7 10.8 - - - +
512A ARG* 3.3 32.5 + - + +
515A THR* 4.2 29.4 - - + -
516A ILE* 4.3 17.5 - - + -
519A PHE* 3.9 29.8 - - + -
536A GLY 3.9 17.0 - - - +
537A ILE* 4.1 13.9 - - + -
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Residues in contact with PHE 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 ILE* 3.0 39.4 + - + -
462A ALA* 2.9 10.6 + - - +
464A ILE* 1.3 76.1 - - + +
466A LEU* 1.3 53.5 + - + +
469A THR* 2.5 26.9 + - - -
474A ALA* 3.8 15.9 - - + +
477A VAL* 3.6 18.2 - - + -
478A LEU* 3.7 23.8 - - + -
481A PHE* 3.7 18.4 - + + -
503A LEU* 3.4 35.0 - - + -
506A LEU* 3.8 16.0 - - + +
512A ARG* 3.1 19.2 + - - +
516A ILE* 3.7 20.2 - - + -
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Residues in contact with LEU 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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448A VAL* 4.2 22.4 - - + -
449A GLN* 5.3 2.2 - - - +
462A ALA* 2.9 40.3 + - + +
463A THR* 4.4 1.1 - - - +
465A PHE* 1.3 70.1 - - + +
467A ASN* 1.3 68.6 + - - +
468A ARG 2.8 1.7 + - - -
469A THR* 2.8 28.5 + - - +
471A GLY* 4.0 27.6 - - - +
474A ALA* 4.2 6.1 - - + -
475A ILE* 4.1 16.6 - - + -
478A LEU* 4.8 5.2 - - + -
540A TYR* 3.8 26.5 - - + +
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Residues in contact with ASN 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 THR 2.8 24.7 + - - +
464A ILE* 3.7 11.9 - - - +
465A PHE 3.3 1.0 - - - -
466A LEU* 1.3 70.1 - - - +
468A ARG* 1.3 68.4 + - - +
469A THR* 2.8 17.0 + - - -
512A ARG* 3.4 12.2 + - - +
540A TYR* 4.0 26.2 - - + +
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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