Contacts of the helix formed by residues 446 - 462 (chain F) in PDB entry 3GUT
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 LYS 446 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358F VAL* 5.0 16.4 - - - +
442F VAL* 5.1 3.8 - - + +
443F THR* 3.0 47.6 + - - +
444F LYS 3.2 1.0 - - - -
445F LYS* 1.3 79.0 - - + +
447F VAL* 1.3 61.1 + - - +
448F PHE 3.5 1.8 - - - -
449F GLU* 3.7 25.6 - - - +
450F THR* 2.5 42.1 + - - +
23J T 5.2 2.2 + - - -
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Residues in contact with VAL 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F ALA* 4.1 6.1 - - + +
442F VAL* 4.2 10.8 - - + -
443F THR 3.2 12.8 + - - +
444F LYS* 2.8 33.0 + - + +
445F LYS 3.4 0.6 - - - -
446F LYS* 1.3 74.8 - - - +
448F PHE* 1.3 62.0 + - - +
450F THR* 3.8 1.2 - - - -
451F LEU* 2.9 31.2 + - + +
502F THR* 3.8 20.6 - - + +
505F MET* 4.1 26.2 - - + -
507F LEU* 4.1 20.2 - - + -
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Residues in contact with PHE 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445F LYS 5.0 2.8 + - - +
446F LYS 3.5 0.4 - - - -
447F VAL* 1.3 76.7 - - - +
449F GLU* 1.3 81.9 + - + +
451F LEU* 2.9 14.6 + - - +
452F GLU* 2.9 48.4 + - - +
495F ARG* 4.6 5.2 - - + -
498F ALA* 3.7 4.9 - - + -
499F VAL* 3.3 39.7 - - + -
502F THR* 3.5 30.3 - - + -
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Residues in contact with GLU 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 LYS 4.7 4.1 + - - +
446F LYS* 3.6 36.8 - - - +
448F PHE* 1.3 90.1 - - + +
450F THR* 1.3 68.3 + - - +
452F GLU* 3.4 9.1 + - - +
453F ALA* 3.1 23.2 + - - +
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Residues in contact with THR 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F ALA* 3.7 23.6 - - - +
410F SER* 5.0 1.6 - - - +
442F VAL* 4.1 12.7 - - + +
446F LYS* 2.5 34.7 + - - +
447F VAL 4.0 2.2 - - - -
449F GLU* 1.3 83.1 - - - +
451F LEU* 1.3 57.2 + - - +
453F ALA* 3.5 7.4 + - + +
454F ARG* 3.2 43.2 + - + +
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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
----------------------------------------------------------
406F LEU* 4.0 28.9 - - + +
407F HIS 4.9 1.1 - - - -
408F ALA* 4.6 12.5 - - + +
447F VAL 2.9 19.6 + - - +
448F PHE* 2.9 7.0 + - - +
450F THR* 1.3 73.0 - - - +
452F GLU* 1.3 62.1 + - - +
454F ARG* 3.5 3.9 + - + +
455F MET* 2.8 52.7 + - + +
497F ALA 4.8 0.2 - - - +
498F ALA* 3.1 43.1 - - + +
501F GLN* 4.7 6.1 - - + +
502F THR* 4.3 7.9 - - + -
505F MET* 4.0 15.7 - - + -
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Residues in contact with GLU 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448F PHE* 2.9 40.7 + - - +
449F GLU* 3.5 12.8 - - - +
451F LEU* 1.3 82.9 - - - +
453F ALA* 1.3 61.1 + - - +
454F ARG 3.3 0.2 + - - -
455F MET 3.4 1.7 + - - -
456F THR* 3.2 27.3 + - - +
494F ILE* 3.9 21.9 - - + +
495F ARG* 2.8 44.5 - - + +
498F ALA* 4.1 6.3 - - + +
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Residues in contact with ALA 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 GLU 3.1 15.3 + - - +
450F THR* 3.7 9.2 - - - +
451F LEU 3.4 0.2 - - - -
452F GLU* 1.3 79.5 - - - +
454F ARG* 1.3 66.1 + - - +
455F MET 3.5 0.2 - - - -
456F THR* 3.9 7.0 - - - -
457F GLU* 3.3 35.2 + - - +
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Residues in contact with ARG 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F LEU* 3.7 19.2 - - + +
407F HIS 4.7 14.4 - - - +
408F ALA* 5.1 1.8 - - - +
409F HIS 4.9 1.2 + - - -
410F SER* 2.6 36.7 + - - +
418F ASP* 3.0 36.6 + - - +
419F GLY* 3.6 7.0 + - - +
420F VAL* 5.5 4.3 - - - -
450F THR* 3.2 33.5 + - + +
451F LEU* 3.9 8.7 - - + +
452F GLU 3.2 0.2 - - - -
453F ALA* 1.3 78.5 - - - +
455F MET* 1.3 59.5 + - - +
456F THR 3.2 1.8 - - - -
457F GLU* 3.5 22.8 + - - +
458F ALA* 2.9 28.8 + - - +
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Residues in contact with MET 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F LEU* 3.7 15.3 - - + -
451F LEU* 2.8 48.4 + - + +
452F GLU 3.9 3.1 - - - +
454F ARG* 1.3 74.5 - - - +
456F THR* 1.3 59.5 + - - +
458F ALA* 3.6 1.1 - - - +
459F CYS* 2.9 36.4 + - - -
468F LEU 4.5 0.9 - - - +
469F VAL* 3.4 45.1 - - + -
494F ILE* 4.0 16.8 - - + +
497F ALA* 3.5 8.5 - - + -
498F ALA* 3.9 10.3 - - - +
501F GLN* 3.3 37.5 - - - +
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Residues in contact with THR 456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452F GLU* 3.2 17.7 + - - +
453F ALA* 3.9 7.8 - - - -
455F MET* 1.3 76.0 - - - +
457F GLU* 1.3 62.1 + - + +
458F ALA 3.0 1.1 - - - -
459F CYS* 2.9 2.9 + - - +
460F ILE* 2.8 49.5 + - + +
486F LEU* 3.7 26.3 - - + +
494F ILE* 3.8 14.2 - - - +
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Residues in contact with GLU 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418F ASP* 3.4 44.8 - - + +
453F ALA* 3.3 24.5 + - - +
454F ARG* 3.7 21.4 + - - +
456F THR* 1.3 81.0 - - + +
458F ALA* 1.3 58.4 + - - +
460F ILE* 4.1 9.1 - - + +
461F ARG* 3.1 39.4 + - + +
463F TYR* 5.0 0.9 - - - -
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Residues in contact with ALA 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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396F GLN* 4.7 5.6 - - - +
406F LEU* 3.8 18.2 - - + -
454F ARG 2.9 19.0 + - - +
455F MET* 3.6 5.6 - - - +
456F THR 3.0 0.2 - - - -
457F GLU* 1.3 80.0 - - - +
459F CYS* 1.3 57.2 + - - +
462F GLY 3.3 1.8 + - - -
463F TYR* 2.9 50.2 + - + +
465F PRO* 3.2 8.2 - - + +
468F LEU* 6.5 0.2 - - + -
469F VAL* 4.7 5.4 - - + -
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Residues in contact with CYS 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 MET 2.9 24.3 + - - +
456F THR 2.9 3.5 + - - +
458F ALA* 1.3 76.6 - - - +
460F ILE* 1.3 63.6 + - - +
462F GLY 3.7 3.6 + - - -
465F PRO* 3.8 17.9 - - - -
469F VAL* 3.8 9.0 - - - -
473F LEU* 3.2 34.3 - - + -
476F LEU* 3.5 28.7 - - + +
482F GLY 3.5 12.0 - - - +
486F LEU* 4.0 14.9 - - + +
494F ILE* 3.6 8.1 - - + -
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Residues in contact with ILE 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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456F THR* 2.8 37.4 + - + +
457F GLU* 4.1 10.1 - - + +
459F CYS* 1.3 75.9 - - - +
461F ARG* 1.3 64.5 + - + +
462F GLY 3.2 0.2 - - - -
482F GLY 3.0 23.2 + - - +
483F ASP 3.6 4.9 - - - +
484F ARG* 3.4 50.7 + - - +
486F LEU* 3.2 26.2 - - + +
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Residues in contact with ARG 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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392F LYS* 5.2 2.8 - - - +
417F GLU* 5.5 7.3 + - - -
418F ASP* 5.1 9.9 + - - +
422F THR* 5.8 1.0 + - - -
457F GLU* 3.1 25.1 + - + +
460F ILE* 1.3 78.3 - - + +
462F GLY* 1.3 59.1 + - - +
463F TYR* 3.4 52.9 + - + -
478F ALA* 3.1 26.2 - - - +
481F GLY* 5.0 1.6 - - - -
482F GLY 4.1 3.4 + - - -
484F ARG* 3.8 30.3 + - - +
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Residues in contact with GLY 462 (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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458F ALA 3.3 7.1 + - - -
459F CYS 3.7 3.8 + - - -
460F ILE 3.2 4.0 - - - -
461F ARG* 1.3 79.4 - - - +
463F TYR* 1.3 62.3 + - - +
464F ASN 3.1 7.8 + - - -
465F PRO* 3.2 10.6 - - - +
476F LEU 3.5 19.3 - - - +
477F GLN* 4.3 6.8 - - - +
478F ALA* 3.6 21.8 + - - +
482F GLY 4.7 1.3 - - - -
517F PHE* 4.9 4.2 - - - -
528F ARG* 5.3 0.3 - - - -
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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
------------------------------------------------------------
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