Contacts of the helix formed by residues 487 - 502 (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 THR 487 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483F ASP* 5.6 2.9 - - - +
485F GLN 4.5 5.8 - - - +
486F LEU* 1.3 78.6 - - - +
488F ASP* 1.3 61.3 + - - +
489F ARG* 3.6 5.8 + - - +
490F GLU* 2.6 49.6 + - - +
491F LYS* 3.3 26.5 + - - +
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Residues in contact with ASP 488 (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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487F THR* 1.3 74.7 - - - +
489F ARG* 1.3 65.0 + - - +
490F GLU 3.1 1.3 - - - -
491F LYS* 3.5 25.8 + - - +
492F GLU* 3.3 24.6 + - - +
495F ARG* 5.2 1.0 + - - -
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Residues in contact with ARG 489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F TYR* 6.0 1.3 - - - -
487F THR* 3.5 6.4 + - - +
488F ASP* 1.3 78.1 - - - +
490F GLU* 1.3 63.2 + - + +
491F LYS 3.4 0.2 - - - -
492F GLU* 3.5 22.7 + - - +
493F ILE* 3.4 39.7 + - - +
496F GLN* 4.3 11.3 - - - +
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Residues in contact with GLU 490 (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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473F LEU* 5.0 6.8 - - + +
475F TYR* 2.6 45.0 + - - +
476F LEU* 3.4 15.7 - - + +
483F ASP* 3.8 5.0 - - - +
485F GLN 4.1 1.6 - - - +
486F LEU* 3.0 22.4 - - + +
487F THR* 2.6 57.3 + - - +
488F ASP 3.1 0.2 - - - -
489F ARG* 1.3 78.1 - - + +
491F LYS* 1.3 65.7 + - - +
492F GLU 3.1 2.4 + - - -
493F ILE* 3.3 9.5 + - - +
494F ILE* 3.1 27.5 + - + +
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Residues in contact with LYS 491 (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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486F LEU* 3.2 36.7 + - + -
487F THR 3.3 11.4 + - - +
488F ASP* 3.5 28.6 + - - +
490F GLU* 1.3 77.7 - - - +
492F GLU* 1.3 58.8 + - - +
494F ILE* 3.4 11.2 - - - +
495F ARG* 3.0 53.7 + - - +
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Residues in contact with GLU 492 (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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488F ASP 3.3 15.2 + - - +
489F ARG* 3.5 27.4 - - - +
490F GLU 3.1 0.2 - - - -
491F LYS* 1.3 76.1 - - - +
493F ILE* 1.3 65.7 + - - +
494F ILE 3.1 1.1 - - - -
495F ARG* 2.6 40.9 + - - +
496F GLN* 3.0 37.3 + - - +
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Residues in contact with ILE 493 (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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469F VAL* 5.2 0.4 - - + -
470F HIS* 3.4 42.4 - - + +
472F ASP* 3.7 18.8 - - - +
473F LEU* 4.2 24.2 - - + -
489F ARG* 3.4 43.3 + - - +
490F GLU* 3.3 7.1 + - - +
492F GLU* 1.3 76.8 - - - +
494F ILE* 1.3 57.3 + - - +
496F GLN* 3.2 12.9 + - - +
497F ALA* 3.0 27.9 + - - +
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Residues in contact with ILE 494 (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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452F GLU* 3.9 23.8 - - + +
455F MET* 4.0 15.6 - - + +
456F THR* 3.8 21.8 - - - +
459F CYS* 3.6 24.7 - - + -
469F VAL* 3.6 25.8 - - + -
473F LEU* 3.8 7.6 - - + -
486F LEU* 4.7 6.7 - - + -
490F GLU* 3.1 18.2 - - + +
491F LYS* 3.4 11.9 - - - +
493F ILE* 1.3 77.3 - - - +
495F ARG* 1.3 57.1 + - - +
497F ALA* 3.3 4.8 + - - +
498F ALA* 2.9 32.6 + - - +
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Residues in contact with ARG 495 (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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448F PHE* 4.6 4.9 - - + -
452F GLU* 2.8 33.7 - - - +
488F ASP 5.2 0.6 + - - -
491F LYS* 3.0 44.6 + - - +
492F GLU* 2.6 38.9 + - - +
493F ILE 3.4 0.2 - - - -
494F ILE* 1.3 76.0 - - - +
496F GLN* 1.3 59.2 + - + +
498F ALA* 4.2 1.5 - - - +
499F VAL* 3.0 25.3 + - - +
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Residues in contact with GLN 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489F ARG* 4.3 18.6 - - - +
492F GLU* 3.0 34.0 + - - +
493F ILE* 3.6 11.0 - - - +
494F ILE 3.1 0.6 - - - -
495F ARG* 1.3 78.9 - - + +
497F ALA* 1.3 61.3 + - - +
499F VAL* 3.3 11.9 - - - +
500F GLN* 3.2 24.9 - - - +
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Residues in contact with ALA 497 (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* 3.5 15.0 - - + -
469F VAL* 3.5 29.4 - - + +
470F HIS* 4.8 7.0 - - + +
493F ILE 3.0 16.0 + - - +
494F ILE 3.3 2.0 + - - +
496F GLN* 1.3 74.8 - - - +
498F ALA* 1.3 57.7 + - - +
500F GLN* 4.5 2.9 - - - -
501F GLN* 2.8 44.4 + - - +
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Residues in contact with ALA 498 (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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448F PHE* 3.7 17.9 - - + -
451F LEU* 3.1 30.9 - - + +
452F GLU* 4.1 18.4 - - + +
455F MET* 3.9 2.6 - - - -
494F ILE 2.9 17.2 + - - +
495F ARG 4.2 0.7 - - - +
497F ALA* 1.3 77.0 - - - +
499F VAL* 1.3 52.0 + - - +
501F GLN* 3.7 1.4 - - - +
502F THR* 2.7 40.9 + - - +
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Residues in contact with VAL 499 (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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448F PHE* 3.3 15.9 - - + -
495F ARG 3.0 21.5 - - - +
496F GLN* 3.3 15.3 - - - +
498F ALA* 1.3 80.2 - - - +
500F GLN* 1.3 68.1 + - + +
502F THR* 3.0 18.1 + - - +
503F LYS* 3.7 10.7 + - - +
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Residues in contact with GLN 500 (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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496F GLN 3.2 18.0 - - - +
497F ALA* 3.4 5.5 + - - +
498F ALA 3.3 0.6 - - - -
499F VAL* 1.3 84.7 - - - +
501F GLN* 1.3 60.0 + - + +
503F LYS* 2.9 68.3 - - - +
504F GLU* 4.6 0.9 + - - +
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Residues in contact with GLN 501 (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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405F HIS* 3.0 55.2 + - + +
406F LEU 3.9 9.4 + - - +
451F LEU* 4.7 7.9 - - + +
455F MET* 3.3 20.9 - - - +
468F LEU 3.6 3.8 + - - +
469F VAL 3.2 24.9 + - - -
497F ALA* 2.8 19.8 + - - +
498F ALA* 3.9 3.8 - - - +
500F GLN* 1.3 77.6 - - + +
502F THR* 1.3 61.8 + - - +
503F LYS 3.2 2.4 + - - -
504F GLU* 3.5 20.3 + - - +
505F MET* 3.9 13.0 + - + +
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Residues in contact with THR 502 (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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447F VAL* 3.8 21.7 - - + +
448F PHE* 3.5 39.7 - - + -
451F LEU* 4.3 9.9 - - + -
498F ALA 2.7 23.3 + - - +
499F VAL* 3.0 19.1 + - - +
501F GLN* 1.3 72.6 - - - +
503F LYS* 1.3 60.3 + - - +
504F GLU* 3.1 6.4 + - - -
505F MET* 4.2 11.8 + - + +
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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