Contacts of the helix formed by residues 446 - 461 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358D VAL* 4.9 17.4 - - - +
442D VAL* 4.8 3.5 - - + +
443D THR* 3.1 44.0 + - - +
445D LYS* 1.3 79.5 - - + +
447D VAL* 1.3 58.3 + - - +
448D PHE 3.5 2.0 - - - -
449D GLU* 3.7 26.7 - - + +
450D THR* 2.8 35.5 + - - +
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Residues in contact with VAL 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D ALA* 3.7 15.0 - - + +
442D VAL* 4.1 9.2 - - + -
443D THR 3.0 15.0 - - - +
444D LYS* 2.9 34.5 + - + +
445D LYS 3.3 1.4 - - - -
446D LYS* 1.3 76.4 - - - +
448D PHE* 1.3 61.5 + - - +
451D LEU* 3.1 24.8 + - - +
502D THR* 3.9 21.5 - - + +
505D MET* 4.6 11.2 - - + -
507D LEU* 3.8 24.2 - - + -
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Residues in contact with PHE 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D LYS 5.0 2.4 + - - +
446D LYS 3.5 0.2 - - - -
447D VAL* 1.3 76.4 - - - +
449D GLU* 1.3 61.2 + - + +
451D LEU* 3.0 5.5 + - - +
452D GLU* 2.7 64.9 + - - +
495D ARG* 4.4 5.8 - - + -
498D ALA* 4.0 3.8 - - + -
499D VAL* 3.3 42.6 - - + -
502D THR* 3.7 27.6 - - + +
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Residues in contact with GLU 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D LYS 4.7 2.8 - - - +
446D LYS* 3.7 39.1 - - + +
448D PHE* 1.3 88.5 - - + +
450D THR* 1.3 62.0 + - - +
452D GLU* 3.6 9.1 - - - +
453D ALA* 3.0 27.4 + - - +
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Residues in contact with THR 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D ALA* 3.2 26.2 - - - +
410D SER* 5.1 3.4 - - - +
442D VAL* 3.7 16.6 - - + +
446D LYS* 2.8 30.6 + - - +
447D VAL* 4.3 2.5 - - - -
448D PHE 3.2 0.6 - - - -
449D GLU* 1.3 78.6 - - - +
451D LEU* 1.3 63.6 + - - +
453D ALA* 4.0 5.7 - - - +
454D ARG* 3.2 34.3 + - + +
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Residues in contact with LEU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D LEU* 3.7 30.1 - - + +
407D HIS 4.4 1.1 - - - +
408D ALA* 4.1 16.1 - - + +
447D VAL 3.1 19.1 + - - +
448D PHE 3.0 4.6 + - - +
450D THR* 1.3 77.1 - - - +
452D GLU* 1.3 65.5 + - - +
454D ARG* 3.3 4.8 + - + +
455D MET* 3.1 41.0 + - + +
497D ALA 5.0 0.2 - - - +
498D ALA* 3.4 40.2 - - + +
501D GLN* 5.1 3.8 - - + +
502D THR* 4.2 7.4 - - + -
505D MET* 4.0 17.3 - - + -
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Residues in contact with GLU 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D PHE* 2.7 39.5 + - - +
449D GLU* 3.6 10.0 - - - +
450D THR 3.3 0.2 - - - -
451D LEU* 1.3 85.3 - - - +
453D ALA* 1.3 59.5 + - - +
455D MET* 3.5 2.1 + - - -
456D THR* 3.0 28.0 + - - +
494D ILE* 3.7 17.5 - - + +
495D ARG* 2.8 46.0 - - - +
498D ALA* 4.2 7.4 - - + +
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Residues in contact with ALA 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D GLU 3.0 17.5 + - - +
450D THR* 4.0 7.0 - - - +
452D GLU* 1.3 74.3 - - - +
454D ARG* 1.3 67.7 + - - +
455D MET 3.4 0.2 - - - -
456D THR* 3.6 9.4 - - - -
457D GLU* 3.2 36.8 + - - +
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Residues in contact with ARG 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D LEU* 3.5 19.0 - - + +
407D HIS 4.6 10.3 - - - +
408D ALA 4.6 11.4 - - - +
409D HIS 5.2 3.4 + - - +
410D SER* 3.9 19.6 + - - -
418D ASP* 3.3 23.8 + - - +
419D GLY* 3.5 24.6 - - - +
420D VAL* 5.7 3.1 - - - -
450D THR* 3.2 28.4 + - - +
451D LEU* 3.3 8.7 + - + +
453D ALA* 1.3 81.1 - - - +
455D MET* 1.3 62.1 + - - +
456D THR 3.2 0.2 - - - -
457D GLU* 3.4 30.8 + - - +
458D ALA* 3.1 24.3 + - - +
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Residues in contact with MET 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D LEU* 4.1 7.0 - - + -
451D LEU* 3.1 40.0 + - + +
452D GLU 3.7 5.8 - - - +
454D ARG* 1.3 74.7 - - - +
456D THR* 1.3 60.1 + - - +
458D ALA* 3.4 1.6 + - - +
459D CYS* 3.0 37.4 + - - -
468D LEU 4.5 1.1 - - - +
469D VAL* 3.4 39.9 - - + +
494D ILE* 3.6 30.1 - - + +
497D ALA* 3.6 11.9 - - + -
498D ALA* 3.8 1.1 - - - -
501D GLN* 3.3 40.6 - - - +
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Residues in contact with THR 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D GLU* 3.0 16.4 + - - +
453D ALA* 3.6 13.7 - - - +
455D MET* 1.3 79.6 - - - +
457D GLU* 1.3 58.1 + - + +
459D CYS* 3.1 4.3 + - - +
460D ILE* 3.0 51.0 + - + +
486D LEU* 4.3 17.7 - - + +
494D ILE* 4.1 10.6 - - - +
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Residues in contact with GLU 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D ASP* 3.2 43.6 - - + +
453D ALA* 3.2 23.8 + - - +
454D ARG* 3.4 28.5 + - - +
455D MET 3.4 0.2 - - - -
456D THR* 1.3 82.2 - - + +
458D ALA* 1.3 57.5 + - - +
460D ILE* 4.0 8.9 - - + +
461D ARG* 3.0 39.8 + - + +
463D TYR* 5.3 0.5 - - - -
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Residues in contact with ALA 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D GLN* 4.7 3.8 - - - +
406D LEU* 3.9 17.0 - - + -
454D ARG 3.1 17.8 + - - +
455D MET* 3.9 4.7 - - - +
456D THR 3.2 0.2 - - - -
457D GLU* 1.3 75.9 - - - +
459D CYS* 1.3 60.0 + - - +
462D GLY 3.0 2.0 + - - -
463D TYR* 2.7 53.9 + - + +
465D PRO* 2.8 9.6 - - + +
468D LEU* 6.1 0.9 - - + -
469D VAL* 4.8 6.1 - - + -
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Residues in contact with CYS 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D MET 3.0 23.3 + - - +
456D THR 3.1 3.8 + - - +
458D ALA* 1.3 75.2 - - - +
460D ILE* 1.3 63.3 + - - +
462D GLY* 3.6 7.2 + - - -
465D PRO* 3.5 18.6 - - - -
469D VAL* 4.0 7.6 - - - -
473D LEU* 3.2 35.7 - - - -
476D LEU* 3.6 22.8 - - + +
482D GLY 3.6 12.0 - - - +
486D LEU* 4.0 17.7 - - + +
494D ILE* 3.7 9.0 - - - -
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Residues in contact with ILE 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D THR* 3.0 38.0 + - + +
457D GLU* 4.0 10.1 - - + +
459D CYS* 1.3 78.0 - - - +
461D ARG* 1.3 65.6 + - + +
462D GLY 3.2 0.6 + - - -
482D GLY 3.6 15.9 + - - +
483D ASP 4.0 5.1 - - - +
484D ARG* 3.2 52.5 + - - +
486D LEU* 3.3 24.5 - - + +
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Residues in contact with ARG 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D LYS* 5.2 2.2 - - - +
417D GLU* 5.5 6.5 + - - -
418D ASP* 5.1 12.9 + - - +
422D THR* 5.4 2.4 + - - -
457D GLU* 3.0 25.6 + - + +
460D ILE* 1.3 79.5 - - + +
462D GLY* 1.3 63.0 + - - +
463D TYR* 3.5 49.8 + - + -
478D ALA* 3.1 22.8 - - - +
481D GLY* 5.4 1.0 - - - -
482D GLY 4.7 1.9 + - - -
484D ARG* 3.8 29.3 - - - +
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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
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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