Contacts of the helix formed by residues 446 - 461 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B VAL* 4.9 16.6 - - - +
442B VAL* 4.6 3.0 - - + +
443B THR* 2.9 47.0 + - - +
444B LYS 3.2 0.8 - - - -
445B LYS* 1.3 81.4 - - + +
447B VAL* 1.3 58.7 + - - +
448B PHE 3.6 1.6 - - - -
449B GLU* 3.6 27.4 - - - +
450B THR* 2.4 41.7 + - - +
23Y T 5.4 2.2 + - - -
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ALA* 4.0 17.7 - - + +
442B VAL* 4.1 14.1 - - + -
443B THR 2.9 17.3 - - - +
444B LYS* 2.9 33.9 + - + +
445B LYS 3.4 0.8 - - - -
446B LYS* 1.3 77.4 - - - +
448B PHE* 1.3 66.9 + - - +
450B THR 4.0 0.5 - - - -
451B LEU* 3.1 22.9 + - - +
502B THR* 3.9 19.3 - - + +
505B MET* 4.1 15.0 - - + -
507B LEU* 4.3 14.4 - - + -
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Residues in contact with PHE 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B LYS 5.0 0.2 + - - -
445B LYS 5.1 2.1 + - - +
447B VAL* 1.3 79.5 - - - +
449B GLU* 1.3 64.3 + - + +
451B LEU* 3.0 5.4 + - - +
452B GLU* 3.0 60.1 + - - +
495B ARG* 4.6 5.6 - - + -
498B ALA* 3.7 8.1 - - + -
499B VAL* 3.3 39.9 - - + -
502B THR* 3.6 28.9 - - + +
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Residues in contact with GLU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B LYS 4.7 3.2 + - - +
446B LYS* 3.6 38.8 - - - +
448B PHE* 1.3 88.8 - - + +
450B THR* 1.3 66.8 + - - +
452B GLU* 3.8 9.1 - - - +
453B ALA* 3.3 22.3 + - - +
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Residues in contact with THR 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ALA* 3.9 20.2 - - - +
410B SER* 4.9 2.2 - - - +
442B VAL* 4.1 14.2 - - + +
446B LYS* 2.4 34.7 + - - +
447B VAL 4.2 1.8 - - - -
448B PHE 3.2 0.6 - - - -
449B GLU* 1.3 83.1 - - - +
451B LEU* 1.3 57.8 + - - +
453B ALA* 3.7 5.9 + - + +
454B ARG* 3.2 42.0 + - - +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LEU* 4.1 20.2 - - + +
407B HIS 4.8 1.1 - - - +
408B ALA* 4.5 11.8 - - + +
447B VAL 3.1 20.0 + - - +
448B PHE 3.0 4.2 + - - +
450B THR* 1.3 76.0 - - - +
452B GLU* 1.3 60.2 + - - +
453B ALA 3.4 0.2 - - - -
454B ARG* 3.6 5.1 + - + +
455B MET* 2.8 53.5 + - + +
497B ALA 4.9 0.4 - - - +
498B ALA* 3.2 42.0 - - + +
501B GLN* 4.8 6.3 - - + +
502B THR* 4.4 9.4 - - + -
505B MET* 4.1 23.6 - - + -
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Residues in contact with GLU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B PHE* 3.0 41.1 + - - +
449B GLU* 3.8 9.2 - - - +
451B LEU* 1.3 83.3 - - - +
453B ALA* 1.3 62.6 + - - +
455B MET* 3.3 6.4 + - - +
456B THR* 3.1 27.9 + - - +
494B ILE* 3.9 16.6 - - + +
495B ARG* 2.9 45.6 - - - +
498B ALA* 4.0 6.4 - - + +
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Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B GLU 3.3 16.7 + - - +
450B THR* 3.7 9.0 - - + +
452B GLU* 1.3 81.2 - - - +
454B ARG* 1.3 62.1 + - - +
456B THR* 3.5 6.8 + - - -
457B GLU* 3.2 39.1 + - - +
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Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LEU* 3.6 20.4 - - + +
407B HIS 4.6 13.9 - - - +
408B ALA 5.0 4.5 - - - +
409B HIS 5.0 2.1 + - - -
410B SER* 2.9 29.3 + - - -
418B ASP* 3.1 40.7 + - - +
419B GLY* 3.5 7.5 - - - +
420B VAL* 5.6 4.0 - - - -
450B THR* 3.2 31.6 + - - +
451B LEU* 4.0 9.4 - - + +
452B GLU 3.2 0.4 - - - -
453B ALA* 1.3 82.8 - - - +
455B MET* 1.3 59.5 + - - +
457B GLU* 3.6 21.4 + - - +
458B ALA* 3.1 28.2 + - - +
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Residues in contact with MET 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LEU* 3.8 8.7 - - + -
451B LEU* 2.8 47.9 + - + +
452B GLU 3.3 3.5 + - - +
454B ARG* 1.3 74.2 - - - +
456B THR* 1.3 61.3 + - - +
458B ALA* 3.4 1.3 + - - +
459B CYS* 3.0 35.9 + - - -
468B LEU 4.3 1.6 - - - +
469B VAL* 3.3 50.9 - - + -
494B ILE* 4.0 15.7 - - + +
497B ALA* 3.7 6.3 - - + -
498B ALA* 4.0 12.3 - - - -
501B GLN* 3.3 37.7 - - - +
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Residues in contact with THR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B GLU* 3.1 16.4 + - - +
453B ALA* 3.6 10.7 - - - -
455B MET* 1.3 74.4 - - - +
457B GLU* 1.3 62.0 + - + +
458B ALA 3.0 1.8 - - - -
459B CYS* 3.0 3.5 + - - +
460B ILE* 2.9 47.8 + - + +
486B LEU* 3.6 26.4 - - + +
494B ILE* 3.7 14.3 - - - +
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Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B ASP* 3.4 44.0 - - + +
453B ALA* 3.2 25.0 + - - +
454B ARG* 3.8 22.4 + - - +
455B MET 3.5 0.2 - - - -
456B THR* 1.3 81.0 - - + +
458B ALA* 1.3 57.9 + - - +
460B ILE* 4.0 10.7 - - + +
461B ARG* 3.0 39.5 + - + +
463B TYR* 5.0 0.6 - - - -
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Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLN* 4.6 7.0 - - - +
406B LEU* 3.9 17.9 - - + -
454B ARG 3.1 18.6 + - - +
455B MET* 3.7 5.4 - - - +
456B THR 3.0 0.8 - - - -
457B GLU* 1.3 78.4 - - - +
459B CYS* 1.3 58.0 + - - +
462B GLY 3.3 0.9 + - - -
463B TYR* 2.9 48.9 + - + +
465B PRO* 3.2 8.7 - - + +
468B LEU* 6.5 0.2 - - + -
469B VAL* 4.8 4.7 - - + -
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Residues in contact with CYS 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B MET 3.0 23.2 + - - +
456B THR 3.0 5.1 + - - +
458B ALA* 1.3 76.8 - - - +
460B ILE* 1.3 62.8 + - - +
462B GLY 3.7 2.3 + - - -
465B PRO* 3.6 19.1 - - - -
469B VAL* 3.7 12.3 - - - -
473B LEU* 3.3 32.5 - - + -
476B LEU* 3.4 33.4 - - + +
482B GLY 3.4 10.7 - - - +
486B LEU* 4.0 15.5 - - + +
494B ILE* 3.7 5.6 - - + -
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B THR* 2.9 34.2 + - + +
457B GLU* 4.0 9.9 - - + +
459B CYS* 1.3 76.5 - - - +
461B ARG* 1.3 65.3 + - - +
482B GLY 3.1 23.4 + - - +
483B ASP 3.6 5.3 - - - +
484B ARG* 3.4 51.0 + - - +
486B LEU* 3.1 29.8 - - + +
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Residues in contact with ARG 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B LYS* 4.9 3.4 - - - +
417B GLU* 5.4 6.9 + - - -
418B ASP* 5.2 9.1 + - - +
457B GLU* 3.0 24.0 + - + +
460B ILE* 1.3 79.1 - - + +
462B GLY* 1.3 59.3 + - - +
463B TYR* 3.4 54.1 + - + +
478B ALA* 3.2 25.4 - - - +
481B GLY* 5.2 1.2 - - - -
482B GLY 4.2 3.3 + - - -
484B ARG* 3.7 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
------------------------------------------------------------
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