Contacts of the helix formed by residues 446 - 461 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358H VAL* 4.7 18.8 - - - +
442H VAL* 5.4 1.6 - - + +
443H THR* 2.8 48.3 + - - +
444H LYS 3.2 0.6 - - - -
445H LYS* 1.3 81.5 - - + +
447H VAL* 1.3 64.4 + - - +
448H PHE 3.4 2.5 - - - -
449H GLU* 3.6 27.0 - - + +
450H THR* 3.2 34.7 + - - +
9J T 5.9 0.4 + - - -
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Residues in contact with VAL 447 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408H ALA* 3.9 14.8 - - + +
442H VAL* 4.0 9.9 - - + -
443H THR 2.8 22.4 - - - +
444H LYS* 3.2 26.7 + - + +
445H LYS 3.4 0.4 - - - -
446H LYS* 1.3 79.5 - - - +
448H PHE* 1.3 59.6 + - - +
450H THR* 5.0 0.2 - - - -
451H LEU* 3.0 26.0 + - - +
502H THR* 3.9 21.5 - - + +
505H MET* 4.5 10.3 - - + -
507H LEU* 3.6 25.1 - - + -
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Residues in contact with PHE 448 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444H LYS 5.0 0.2 + - - -
445H LYS 5.2 1.5 + - - +
446H LYS 3.4 0.8 - - - -
447H VAL* 1.3 76.7 - - - +
449H GLU* 1.3 60.3 + - + +
451H LEU* 3.1 5.5 + - - +
452H GLU* 2.7 68.0 + - - +
495H ARG* 4.5 5.6 - - + -
498H ALA* 4.1 2.0 - - + +
499H VAL* 3.4 40.8 - - + -
502H THR* 3.7 28.0 - - + +
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Residues in contact with GLU 449 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445H LYS 4.6 2.6 - - - +
446H LYS* 3.6 36.7 - - + +
448H PHE* 1.3 84.7 - - + +
450H THR* 1.3 62.7 + - - +
452H GLU* 3.5 11.4 - - - +
453H ALA* 2.9 27.9 + - - +
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Residues in contact with THR 450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408H ALA* 3.4 25.1 - - - +
410H SER* 4.9 2.2 - - - +
442H VAL* 3.9 16.4 - - + +
446H LYS* 3.2 26.7 + - - +
447H VAL* 4.5 1.8 - - - -
449H GLU* 1.3 78.1 - - - +
451H LEU* 1.3 62.7 + - - +
453H ALA* 3.4 7.6 + - - +
454H ARG* 3.0 40.6 + - - +
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Residues in contact with LEU 451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H LEU* 3.8 28.5 - - + +
407H HIS 4.4 2.0 - - - +
408H ALA* 4.1 16.4 - - + +
447H VAL 3.0 21.2 + - - +
448H PHE 3.1 3.1 + - - +
450H THR* 1.3 78.8 - - - +
452H GLU* 1.3 63.4 + - - +
454H ARG* 3.2 4.4 + - + +
455H MET* 3.1 42.8 + - + +
497H ALA 4.9 0.2 - - - +
498H ALA* 3.3 42.2 - - + +
501H GLN* 5.2 1.6 - - + +
502H THR* 4.1 6.3 - - + -
505H MET* 4.1 17.9 - - + -
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Residues in contact with GLU 452 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448H PHE* 2.7 42.6 + - - +
449H GLU* 3.5 10.5 - - - +
451H LEU* 1.3 84.5 - - - +
453H ALA* 1.3 57.2 + - - +
455H MET* 3.8 0.6 + - - -
456H THR* 3.0 26.8 + - - +
494H ILE* 3.8 19.3 - - + +
495H ARG* 3.0 44.9 - - - +
498H ALA* 3.8 6.9 - - + +
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Residues in contact with ALA 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449H GLU 2.9 18.2 + - - +
450H THR* 3.7 8.1 - - - +
451H LEU 3.2 0.4 - - - -
452H GLU* 1.3 75.3 - - - +
454H ARG* 1.3 68.2 + - - +
456H THR* 3.6 7.4 + - - -
457H GLU* 3.3 36.8 + - - +
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Residues in contact with ARG 454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H LEU* 3.4 18.8 - - + +
407H HIS 4.5 10.1 - - - +
408H ALA 4.3 12.6 - - - +
409H HIS 4.9 4.1 + - - -
410H SER* 3.7 20.1 + - - -
418H ASP* 3.1 41.8 + - - +
419H GLY* 3.5 13.2 - - - +
420H VAL* 5.7 3.1 - - - -
450H THR* 3.0 27.5 + - - +
451H LEU* 3.2 8.7 + - + +
453H ALA* 1.3 81.0 - - - +
455H MET* 1.3 62.2 + - - +
456H THR 3.2 0.4 - - - -
457H GLU* 3.5 25.7 + - - +
458H ALA* 3.2 24.1 + - - +
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Residues in contact with MET 455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H LEU* 4.0 7.6 - - + -
451H LEU* 3.1 35.7 + - + +
452H GLU 4.1 0.2 - - - +
453H ALA 3.4 0.2 - - - -
454H ARG* 1.3 75.1 - - - +
456H THR* 1.3 58.7 + - - +
458H ALA* 3.9 0.6 - - - -
459H CYS* 2.9 36.0 + - - -
468H LEU 4.5 0.7 - - - +
469H VAL* 3.5 40.7 - - + +
494H ILE* 3.7 33.4 - - + +
497H ALA* 3.7 13.2 - - + +
498H ALA* 3.8 3.6 - - - -
501H GLN* 3.3 41.7 - - - +
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Residues in contact with THR 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452H GLU* 3.0 15.6 + - - +
453H ALA* 3.7 11.3 - - - -
454H ARG 3.2 0.2 - - - -
455H MET* 1.3 76.9 - - - +
457H GLU* 1.3 60.7 + - + +
459H CYS* 3.1 4.2 + - - +
460H ILE* 2.9 51.5 + - + +
486H LEU* 4.1 20.6 - - + +
494H ILE* 4.1 9.7 - - - +
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Residues in contact with GLU 457 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418H ASP* 3.1 46.0 - - + +
453H ALA* 3.3 24.9 + - - +
454H ARG* 3.5 23.1 + - - +
456H THR* 1.3 80.8 - - + +
458H ALA* 1.3 57.2 + - - +
460H ILE* 4.0 11.4 - - + -
461H ARG* 2.9 39.5 + - + +
463H TYR* 5.2 1.1 - - - -
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Residues in contact with ALA 458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396H GLN* 4.7 4.0 - - - +
406H LEU* 4.0 17.3 - - + -
454H ARG 3.2 17.5 + - - +
455H MET* 4.0 3.8 - - - +
456H THR 3.1 0.4 - - - -
457H GLU* 1.3 76.0 - - - +
459H CYS* 1.3 61.3 + - - +
460H ILE 3.4 0.4 - - - -
462H GLY 3.2 2.2 + - - -
463H TYR* 2.9 53.4 + - + +
465H PRO* 2.9 11.1 - - + +
468H LEU* 6.4 0.4 - - + -
469H VAL* 4.9 5.6 - - + -
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Residues in contact with CYS 459 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455H MET 2.9 24.7 + - - +
456H THR 3.1 5.3 + - - +
458H ALA* 1.3 76.7 - - - +
460H ILE* 1.3 64.5 + - - +
462H GLY 3.7 3.7 + - - -
465H PRO* 3.7 12.3 - - - -
469H VAL* 4.2 9.0 - - - -
473H LEU* 3.4 34.3 - - - -
476H LEU* 3.6 23.1 - - + +
482H GLY 3.5 14.7 - - - +
486H LEU* 4.0 16.8 - - + +
494H ILE* 3.5 12.6 - - - -
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Residues in contact with ILE 460 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456H THR* 2.9 34.6 + - + +
457H GLU* 4.1 10.8 - - + +
459H CYS* 1.3 79.4 - - - +
461H ARG* 1.3 65.6 + - + +
462H GLY 3.6 0.3 + - - -
482H GLY 3.8 14.0 + - - +
483H ASP 4.0 6.2 - - - +
484H ARG* 3.1 54.5 + - - +
486H LEU* 3.3 23.1 - - + +
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Residues in contact with ARG 461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392H LYS* 5.1 1.8 - - - +
417H GLU* 5.1 9.5 + - - -
418H ASP* 5.0 11.3 + - - +
422H THR* 5.4 3.6 + - - +
457H GLU* 2.9 25.9 + - + +
460H ILE* 1.3 80.0 - - + +
462H GLY* 1.3 63.2 + - - +
463H TYR* 3.4 53.7 + - + -
478H ALA* 3.2 20.1 - - - +
481H GLY* 5.7 0.7 - - - -
482H GLY 4.9 2.1 + - - -
484H ARG* 3.9 26.3 - - - +
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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
------------------------------------------------------------
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