Contacts of the helix formed by residues 487 - 502 (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 THR 487 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483H ASP* 5.8 1.8 - - - +
485H GLN 4.6 4.9 - - - +
486H LEU* 1.3 77.7 - - - +
488H ASP* 1.3 62.5 + - - +
489H ARG* 3.5 6.8 + - - +
490H GLU* 2.5 54.0 + - - +
491H LYS* 3.1 23.7 + - - +
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Residues in contact with ASP 488 (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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487H THR* 1.3 73.8 - - - +
489H ARG* 1.3 65.7 + - - +
490H GLU 3.3 0.7 - - - -
491H LYS* 3.4 25.9 + - - +
492H GLU* 3.5 23.7 + - - +
495H ARG* 5.0 1.6 + - - -
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Residues in contact with ARG 489 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475H TYR* 6.0 1.1 - - - -
487H THR* 3.4 6.8 + - - +
488H ASP* 1.3 76.4 - - - +
490H GLU* 1.3 62.5 + - + +
492H GLU* 3.2 25.9 + - - +
493H ILE* 3.2 38.5 + - - +
496H GLN* 4.2 14.7 - - - +
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Residues in contact with GLU 490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473H LEU* 4.7 6.5 - - + -
475H TYR* 2.9 42.5 + - - +
476H LEU* 3.7 16.3 - - + +
483H ASP* 4.2 4.9 - - - +
485H GLN 4.3 0.9 - - - +
486H LEU* 3.0 22.4 - - + +
487H THR* 2.5 57.1 + - - +
489H ARG* 1.3 76.7 - - + +
491H LYS* 1.3 61.9 + - - +
492H GLU 3.1 2.0 - - - -
493H ILE* 3.3 10.2 + - - +
494H ILE* 2.9 33.4 + - + +
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Residues in contact with LYS 491 (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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486H LEU* 3.0 41.2 + - + -
487H THR 3.1 16.4 + - - +
488H ASP* 3.4 28.7 + - - +
489H ARG 3.4 0.6 - - - -
490H GLU* 1.3 77.4 - - - +
492H GLU* 1.3 57.6 + - - +
494H ILE* 3.8 9.3 + - - +
495H ARG* 3.1 53.4 + - - +
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Residues in contact with GLU 492 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488H ASP 3.5 12.7 + - - +
489H ARG* 3.2 29.1 + - - +
491H LYS* 1.3 77.8 - - - +
493H ILE* 1.3 63.8 + - - +
494H ILE 3.3 0.2 - - - -
495H ARG* 2.7 44.0 + - - +
496H GLN* 3.1 41.4 + - - +
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Residues in contact with ILE 493 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470H HIS* 3.7 33.2 - - + +
472H ASP* 3.4 21.8 - - - +
473H LEU* 3.6 31.9 - - + -
475H TYR* 5.8 0.9 - - - +
489H ARG* 3.2 43.1 - - - +
490H GLU* 3.3 9.4 + - - +
492H GLU* 1.3 77.6 - - - +
494H ILE* 1.3 57.4 + - - +
496H GLN* 3.5 7.1 + - - +
497H ALA* 3.0 26.5 + - - +
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Residues in contact with ILE 494 (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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452H GLU* 3.8 33.4 - - + +
455H MET* 3.7 20.0 - - + +
456H THR* 4.1 7.9 - - - +
459H CYS* 3.5 26.0 - - - -
469H VAL* 3.9 16.2 - - + -
473H LEU* 3.7 11.0 - - + -
486H LEU* 4.2 13.5 - - + -
490H GLU* 2.9 29.9 + - + +
491H LYS* 3.9 7.2 - - - +
493H ILE* 1.3 77.8 - - - +
495H ARG* 1.3 56.0 + - - +
497H ALA* 3.7 6.0 - - - +
498H ALA* 2.7 33.4 + - - +
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Residues in contact with ARG 495 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448H PHE* 4.5 5.2 - - + -
452H GLU* 3.0 31.5 - - - +
488H ASP 5.0 1.0 + - - -
491H LYS* 3.1 45.6 + - - +
492H GLU* 2.7 42.1 + - - +
493H ILE 3.4 0.4 - - - -
494H ILE* 1.3 75.8 - - - +
496H GLN* 1.3 61.0 + - + +
498H ALA* 3.8 1.4 - - - +
499H VAL* 3.3 26.7 + - - +
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Residues in contact with GLN 496 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489H ARG* 4.2 19.0 - - - +
492H GLU* 3.1 33.8 + - + +
493H ILE* 3.8 6.7 - - - +
495H ARG* 1.3 76.1 - - + +
497H ALA* 1.3 63.4 + - - +
499H VAL* 2.9 25.2 - - + +
500H GLN* 3.2 14.2 + - - +
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Residues in contact with ALA 497 (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* 3.7 13.5 - - + -
469H VAL* 3.3 30.7 - - + +
470H HIS* 4.5 9.4 - - + +
493H ILE 3.0 18.8 + - - +
494H ILE 3.2 3.1 + - - +
496H GLN* 1.3 73.6 - - - +
498H ALA* 1.3 64.8 + - - +
500H GLN* 3.6 3.6 + - - +
501H GLN* 3.0 34.0 + - - +
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Residues in contact with ALA 498 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448H PHE* 4.1 7.6 - - + +
451H LEU* 3.3 29.2 - - + +
452H GLU* 3.8 29.4 - - + +
455H MET* 3.8 1.8 - - - -
494H ILE 2.7 22.2 + - - +
495H ARG 3.8 0.9 - - - +
497H ALA* 1.3 74.0 - - - +
499H VAL* 1.3 57.7 + - - +
501H GLN* 3.8 0.7 - - - -
502H THR* 2.8 35.3 + - - +
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Residues in contact with VAL 499 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448H PHE* 3.4 25.3 - - + -
495H ARG 3.3 12.7 + - - +
496H GLN* 2.9 31.0 - - + +
498H ALA* 1.3 79.1 - - - +
500H GLN* 1.3 67.4 + - + +
502H THR* 3.1 12.2 + - - +
503H LYS* 3.7 11.8 + - - +
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Residues in contact with GLN 500 (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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496H GLN 3.2 17.1 + - - +
497H ALA* 4.1 4.5 - - - +
499H VAL* 1.3 83.5 + - - +
501H GLN* 1.3 63.6 + - + +
502H THR 3.3 0.4 - - - -
503H LYS* 2.9 63.8 - - - +
504H GLU* 4.5 1.9 + - - +
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Residues in contact with GLN 501 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405H HIS* 2.9 56.7 + - + +
406H LEU 4.2 6.2 + - - +
451H LEU* 5.2 1.4 - - + +
455H MET* 3.3 23.8 - - + +
468H LEU 3.6 1.8 + - - +
469H VAL 3.0 28.1 + - - -
497H ALA* 3.0 18.6 + - - +
498H ALA* 4.1 2.5 - - - +
500H GLN* 1.3 78.3 - - + +
502H THR* 1.3 61.0 + - - +
503H LYS 3.4 0.2 - - - -
504H GLU* 3.6 12.9 + - - +
505H MET* 3.6 26.2 - - + +
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Residues in contact with THR 502 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447H VAL* 3.9 30.1 - - + +
448H PHE* 3.7 28.3 - - - -
451H LEU* 4.1 14.4 - - + -
498H ALA 2.8 21.6 + - - +
499H VAL* 3.1 15.6 + - - +
501H GLN* 1.3 74.8 - - - +
503H LYS* 1.3 59.7 + - - +
504H GLU* 3.0 6.7 + - - -
505H MET* 4.3 11.2 + - + +
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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