Contacts of the helix formed by residues 446 - 461 (chain F) in PDB entry 5UH8
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 VAL 446 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1046C THR* 5.8 3.1 - - - +
1047C GLY* 5.8 7.2 - - - +
1049C TYR* 6.4 1.3 - - - -
444F ALA 4.4 6.5 - - - +
445F VAL* 1.3 73.3 - - - +
447F ALA* 1.3 69.1 + - - +
448F VAL* 3.6 24.9 - - + -
449F ASP* 4.1 22.8 - - + +
450F ALA* 3.2 23.2 + - - +
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Residues in contact with ALA 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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1046C THR* 4.5 16.1 + - + +
1049C TYR* 5.7 3.9 - - + +
1099C ARG* 4.9 4.5 - - + +
1100C VAL* 4.7 20.5 - - + +
1103C TYR* 3.8 34.8 - - + -
445F VAL 3.4 4.8 + - - -
446F VAL* 1.3 74.6 - - - +
448F VAL* 1.3 64.8 + - - +
450F ALA* 3.9 2.1 - - - +
451F VAL* 3.2 26.2 + - - +
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Residues in contact with VAL 448 (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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1046C THR* 5.6 3.4 - - - +
1103C TYR* 3.7 32.3 - - + +
457D MET* 5.1 4.5 - - + -
469D ILE* 5.4 9.3 - - + +
470D LYS* 5.2 9.0 - - + -
473D LYS* 3.5 45.1 - - + +
446F VAL* 3.6 18.6 - - + -
447F ALA* 1.3 75.7 - - + +
449F ASP* 1.3 69.4 + - - +
451F VAL* 3.2 4.7 + - - +
452F SER* 3.0 28.4 + - - -
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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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470D LYS* 4.2 16.6 - - - -
473D LYS* 5.3 2.9 - - - +
445F VAL* 6.3 0.4 - - + -
446F VAL* 3.6 26.3 + - + +
447F ALA 3.4 0.4 - - - -
448F VAL* 1.3 91.1 - - - +
450F ALA* 1.3 61.3 - - - +
452F SER* 2.5 23.4 + - - -
453F PHE* 3.1 10.4 + - - +
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Residues in contact with ALA 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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1100C VAL* 4.9 14.4 - - + -
445F VAL* 3.6 20.8 - - + +
446F VAL 3.2 16.2 + - - +
447F ALA 3.9 3.4 - - - +
449F ASP* 1.3 79.1 - - - +
451F VAL* 1.3 60.4 + - - +
453F PHE* 3.3 17.9 - - - +
454F THR* 3.1 17.3 + - - -
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Residues in contact with VAL 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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1100C VAL* 4.2 11.4 - - + +
1103C TYR* 4.3 6.3 - - + -
1104C GLU* 3.7 41.1 - - + +
1107C VAL* 4.0 24.9 - - + -
1108C LYS* 6.1 1.8 - - - -
469D ILE* 5.1 6.5 - - + -
447F ALA 3.2 16.3 + - - +
448F VAL* 3.5 9.9 - - - +
449F ASP 3.2 0.2 - - - -
450F ALA* 1.3 75.2 - - - +
452F SER* 1.3 61.7 + - - +
454F THR* 2.8 26.5 + - - -
455F LEU* 3.1 21.8 + - + +
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Residues in contact with SER 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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468D ASN* 6.2 0.2 - - - -
469D ILE* 3.9 27.6 - - - -
470D LYS* 4.1 25.7 + - - +
448F VAL* 3.0 11.6 + - - -
449F ASP* 2.5 30.1 + - - -
451F VAL* 1.3 75.3 - - - +
453F PHE* 1.3 61.3 + - - +
455F LEU* 3.2 5.4 + - - +
456F LEU* 3.1 20.5 + - - +
526F TYR* 4.6 7.2 - - - -
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Residues in contact with PHE 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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815C THR* 3.4 39.0 - - + -
817C GLU* 4.5 8.5 - - + -
818C GLU* 5.8 4.3 - - + -
449F ASP 3.1 8.0 + - - +
450F ALA* 3.3 15.0 - - - +
451F VAL 3.1 0.2 - - - -
452F SER* 1.3 83.6 + - - +
454F THR* 1.3 61.4 + - - +
456F LEU* 3.0 35.6 + - + +
457F GLN* 3.3 36.0 + - + +
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Residues in contact with THR 454 (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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1104C GLU* 4.7 17.4 + - - +
1108C LYS* 5.0 13.9 - - - +
450F ALA 3.1 13.7 + - - -
451F VAL* 2.8 12.4 + - - -
453F PHE* 1.3 82.1 - - - +
455F LEU* 1.3 61.9 + - - +
457F GLN* 3.2 26.5 + - + +
458F ASP* 3.4 13.7 - - - +
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Residues in contact with LEU 455 (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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1107C VAL* 5.8 3.6 - - + -
1108C LYS* 4.3 27.1 - - + -
469D ILE* 3.7 33.9 - - + +
451F VAL* 3.1 19.1 + - + +
452F SER* 3.6 8.7 - - - +
453F PHE 3.2 0.4 - - - -
454F THR* 1.3 76.3 - - + +
456F LEU* 1.3 62.2 + - - +
457F GLN 3.2 0.2 - - - -
458F ASP* 3.5 22.6 + - + +
459F GLN* 3.3 21.0 + - - +
526F TYR* 4.1 23.7 + - + +
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Residues in contact with LEU 456 (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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817C GLU* 3.5 31.9 - - + +
818C GLU* 5.1 11.9 - - + +
821C LEU* 3.7 29.6 - - + -
452F SER 3.1 10.1 + - - +
453F PHE* 3.0 24.3 + - + +
455F LEU* 1.3 76.6 - - - +
457F GLN* 1.3 63.7 + - + +
458F ASP 3.2 0.2 - - - -
459F GLN* 3.3 16.2 + - + +
460F LEU* 3.4 26.1 + - + +
526F TYR* 4.5 23.1 - - + +
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Residues in contact with GLN 457 (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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817C GLU* 3.0 41.5 + - - +
453F PHE* 3.3 37.5 + - + +
454F THR* 3.2 19.3 + - + +
456F LEU* 1.3 77.9 - - - +
458F ASP* 1.3 60.5 + - - +
459F GLN 3.1 2.0 - - - -
460F LEU* 3.6 5.1 + - - +
461F GLN* 3.2 27.4 + - - +
481F LEU* 4.8 5.2 - - - +
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Residues in contact with ASP 458 (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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1108C LYS* 4.9 9.3 + - - -
454F THR* 3.4 16.8 + - - +
455F LEU* 3.8 23.3 - - + +
456F LEU 3.2 1.0 - - - -
457F GLN* 1.3 79.8 - - - +
459F GLN* 1.3 62.2 + - + +
461F GLN* 4.0 19.7 - - - +
462F SER* 3.4 21.7 + - - -
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Residues in contact with GLN 459 (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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455F LEU 3.3 16.7 + - - +
456F LEU* 3.3 11.4 + - + +
457F GLN 3.1 0.6 - - - -
458F ASP* 1.3 82.1 - - + +
460F LEU* 1.3 65.1 + - + +
461F GLN 3.3 1.1 - - - -
462F SER* 3.4 16.6 + - - -
463F VAL* 3.4 16.5 + - - +
522F VAL* 3.6 38.6 + - - +
523F LEU* 4.4 13.9 - - + +
526F TYR* 3.2 38.5 + - + -
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Residues in contact with LEU 460 (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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817C GLU* 3.5 41.7 - - + +
820C LEU* 3.7 37.9 - - + -
821C LEU* 5.0 4.7 - - + -
456F LEU* 3.4 25.9 + - + +
457F GLN* 3.6 5.6 + - - +
459F GLN* 1.3 78.4 - - + +
461F GLN* 1.3 60.2 + - - +
462F SER 3.2 1.3 - - - -
463F VAL* 3.1 11.8 + - + +
464F LEU* 2.9 35.0 + - + +
481F LEU* 5.3 6.7 - - + -
523F LEU* 4.0 22.7 - - + -
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Residues in contact with GLN 461 (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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457F GLN 3.2 16.1 + - - +
458F ASP* 4.1 21.5 - - - +
460F LEU* 1.3 74.9 - - - +
462F SER* 1.3 58.2 + - - +
463F VAL 3.0 7.1 + - - -
464F LEU* 3.8 20.8 + - + +
465F ASP* 3.9 12.5 + - - +
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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