Contacts of the helix formed by residues 443 - 454 (chain F) in PDB entry 3HX0
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 443 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403F ALA* 6.3 0.2 - - + -
406F PHE* 4.2 13.8 - - + -
410F LEU* 3.8 25.4 - - + -
432F ILE* 3.6 34.8 - - + -
439F SER 3.6 14.6 - - - +
440F HIS 3.4 17.5 - - - +
441F ARG 3.0 13.9 + - - +
442F GLY* 1.3 74.2 - - - +
444F PHE* 1.3 63.0 + - + +
445F SER 3.4 0.9 - - - -
446F ARG* 3.3 14.2 + - - +
447F LEU* 2.9 32.5 + - + +
493F VAL* 3.9 18.4 - - + -
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Residues in contact with PHE 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442F GLY* 3.4 3.6 - - - -
443F ILE* 1.3 78.0 - - + +
445F SER* 1.3 67.5 + - - +
446F ARG 2.8 2.5 + - - -
447F LEU* 4.4 9.2 - - + +
448F LEU* 2.8 49.4 + - + +
470F GLN* 3.0 50.7 - - + +
471F GLN 3.2 32.5 - - - -
472F LYS 4.3 2.2 - - - -
473F TYR* 3.7 20.4 - + + -
491F ILE* 3.9 19.5 - - + -
492F ILE* 4.3 0.4 - - - -
493F VAL* 3.5 31.9 - - + -
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Residues in contact with SER 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442F GLY* 4.7 9.5 + - - -
443F ILE 3.4 0.2 - - - -
444F PHE* 1.3 77.7 - - - +
446F ARG* 1.3 61.8 + - - +
448F LEU* 4.6 2.4 - - - +
449F ASP* 3.4 17.7 + - - +
465F GLU* 5.4 6.7 - - - -
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Residues in contact with ARG 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406F PHE* 3.3 58.5 - - + +
442F GLY 4.3 16.5 + - - +
443F ILE* 3.3 8.7 + - - +
444F PHE 2.8 1.4 + - - -
445F SER* 1.3 79.2 - - - +
447F LEU* 1.3 57.2 + - - +
449F ASP* 2.7 27.2 + - - +
450F SER* 2.9 12.9 + - - -
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Residues in contact with LEU 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399F VAL* 4.1 12.6 - - + +
402F ALA* 4.0 12.6 - - + +
403F ALA* 3.8 34.8 - - + +
406F PHE* 3.6 9.1 - - + -
432F ILE* 3.4 33.2 - - + -
443F ILE* 2.9 23.2 + - + +
444F PHE* 4.0 10.1 - - + +
446F ARG* 1.3 76.2 - - - +
448F LEU* 1.3 60.7 + - + +
449F ASP 2.8 6.1 + - - -
450F SER* 3.1 2.7 + - - +
451F LEU* 3.1 40.0 + - + +
491F ILE* 4.6 12.6 - - + -
493F VAL* 5.8 0.4 - - + -
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Residues in contact with LEU 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444F PHE* 2.8 32.6 + - + +
445F SER 4.6 2.0 - - - +
447F LEU* 1.3 74.5 - - + +
449F ASP* 1.3 55.5 + - - +
451F LEU* 4.5 1.8 - - + -
452F ARG* 2.8 43.3 + - - +
457F LEU* 3.9 11.5 - - + +
463F SER* 3.5 18.4 - - - +
465F GLU* 3.5 26.2 - - - +
470F GLN* 3.9 15.5 - - - +
473F TYR* 3.6 50.5 - - + -
491F ILE* 5.3 4.3 - - + -
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Residues in contact with ASP 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445F SER 3.4 14.1 - - - +
446F ARG* 2.7 12.2 + - - +
448F LEU* 1.3 79.2 - - - +
450F SER* 1.3 58.7 + - - +
451F LEU 3.2 1.6 - - - -
452F ARG* 3.1 9.0 + - - +
453F GLN* 2.9 29.7 + - - +
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Residues in contact with SER 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F ALA* 3.9 30.0 + - - +
405F ALA* 5.5 2.3 - - - +
406F PHE* 4.8 5.6 - - - -
446F ARG 2.9 11.2 + - - -
447F LEU* 3.1 9.6 + - - -
449F ASP* 1.3 77.2 - - - +
451F LEU* 1.3 61.9 + - - +
453F GLN* 3.4 19.3 + - - +
454F GLU* 3.6 12.6 + - - +
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Residues in contact with LEU 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398F THR* 3.9 26.0 - - + +
399F VAL* 4.5 10.8 - - + -
402F ALA* 3.4 29.8 - - + -
447F LEU* 3.1 31.4 + - + +
448F LEU* 5.4 1.1 - - + -
450F SER* 1.3 76.8 - - - +
452F ARG* 1.3 59.1 + - - +
453F GLN 3.4 0.2 - - - -
454F GLU* 3.6 7.1 - - - +
455F GLY 3.5 0.9 + - - -
456F PHE* 2.8 44.2 + - + +
457F LEU* 3.2 31.3 + - + -
491F ILE* 4.5 16.4 - - + -
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Residues in contact with ARG 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448F LEU* 2.8 33.8 + - - +
449F ASP* 3.1 9.8 + - - +
451F LEU* 1.3 79.0 - - - +
453F GLN* 1.3 65.0 + - - +
455F GLY* 3.1 13.1 + - - +
457F LEU* 4.1 24.5 - - + +
460F ASP* 2.5 41.2 + - - -
463F SER* 5.4 1.8 + - - -
465F GLU* 3.6 30.8 + - - -
473F TYR* 5.3 0.2 - - - -
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Residues in contact with GLN 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449F ASP 2.9 12.3 + - - +
450F SER* 3.5 13.5 - - - +
451F LEU 3.4 0.2 - - - -
452F ARG* 1.3 79.0 - - - +
454F GLU* 1.3 59.9 + - - +
455F GLY* 3.0 4.5 + - - -
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Residues in contact with GLU 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398F THR* 4.2 13.0 - - - +
402F ALA* 4.4 7.1 - - - +
450F SER* 3.6 17.1 + - - +
451F LEU* 3.6 23.1 - - - +
453F GLN* 1.3 77.9 - - - +
455F GLY* 1.3 60.1 + - - +
456F PHE* 3.6 19.1 + - - +
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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