Contacts of the helix formed by residues 489 - 503 (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 ARG 489 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475D TYR* 6.0 1.1 - - - -
487D THR* 3.3 7.3 + - - +
488D ASP* 1.3 77.0 - - - +
490D GLU* 1.3 65.0 + - + +
491D LYS 3.3 0.7 - - - -
492D GLU* 3.2 32.5 - - - +
493D ILE* 3.3 39.7 + - - +
496D GLN* 4.3 13.5 - - - +
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Residues in contact with GLU 490 (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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473D LEU* 4.7 7.4 - - + -
475D TYR* 3.3 38.6 + - - +
476D LEU* 3.7 15.8 - - + +
483D ASP* 4.1 4.5 - - - +
485D GLN 4.1 1.8 - - - +
486D LEU* 2.8 24.8 - - + +
487D THR* 2.4 57.8 + - + +
489D ARG* 1.3 79.4 - - + +
491D LYS* 1.3 58.9 + - - +
492D GLU 3.2 0.7 - - - -
493D ILE* 3.5 8.1 + - - +
494D ILE* 2.8 37.6 + - + +
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Residues in contact with LYS 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486D LEU* 2.8 43.6 + - + -
487D THR 3.1 20.1 + - - +
488D ASP* 3.6 28.2 + - - +
489D ARG 3.3 0.2 - - - -
490D GLU* 1.3 77.1 - - - +
492D GLU* 1.3 57.4 + - - +
494D ILE* 4.0 7.3 - - - +
495D ARG* 3.2 57.1 + - - +
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Residues in contact with GLU 492 (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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488D ASP 3.3 16.8 + - - +
489D ARG* 3.2 28.9 - - - +
490D GLU 3.2 0.2 - - - -
491D LYS* 1.3 78.1 - - - +
493D ILE* 1.3 57.1 + - - +
494D ILE 3.4 0.2 - - - -
495D ARG* 2.6 43.9 + - - +
496D GLN* 2.8 44.4 + - - +
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Residues in contact with ILE 493 (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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469D VAL* 5.3 0.2 - - + -
470D HIS* 3.6 37.4 - - + -
472D ASP* 3.3 22.7 - - - +
473D LEU* 3.9 25.8 - - + -
475D TYR* 5.8 0.9 - - - +
489D ARG* 3.3 40.5 + - - +
490D GLU* 3.7 8.5 - - - +
491D LYS 3.4 0.2 - - - -
492D GLU* 1.3 76.7 - - - +
494D ILE* 1.3 59.8 + - - +
496D GLN* 3.5 7.8 + - - +
497D ALA* 3.0 27.2 + - - +
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Residues in contact with ILE 494 (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* 3.7 35.7 - - + +
455D MET* 3.6 31.5 - - + +
456D THR* 4.1 8.1 - - - +
459D CYS* 3.7 12.3 - - + -
469D VAL* 3.9 6.3 - - + -
473D LEU* 3.6 26.2 - - + -
486D LEU* 4.3 11.4 - - + -
490D GLU* 2.8 29.2 + - + +
491D LYS* 4.0 7.9 - - - +
492D GLU 3.4 0.2 - - - -
493D ILE* 1.3 77.3 - - - +
495D ARG* 1.3 59.0 + - - +
497D ALA* 4.4 1.1 - - - -
498D ALA* 2.9 30.0 + - - +
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Residues in contact with ARG 495 (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* 4.4 6.1 - - + -
452D GLU* 2.8 31.8 - - - +
488D ASP 4.9 1.4 + - - -
491D LYS* 3.2 45.6 + - - +
492D GLU* 2.6 39.1 + - - +
493D ILE 3.4 0.4 - - - -
494D ILE* 1.3 76.9 - - - +
496D GLN* 1.3 58.1 + - + +
498D ALA* 3.9 1.4 - - - +
499D VAL* 3.3 27.0 + - - +
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Residues in contact with GLN 496 (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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489D ARG* 4.3 15.2 - - - +
492D GLU* 2.8 40.6 + - - +
493D ILE* 3.8 9.1 - - - +
494D ILE 3.2 0.6 - - - -
495D ARG* 1.3 78.9 - - + +
497D ALA* 1.3 60.6 + - - +
498D ALA 3.3 0.2 - - - -
499D VAL* 3.1 22.4 - - + +
500D GLN* 3.3 15.2 - - - +
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Residues in contact with ALA 497 (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* 3.6 13.9 - - + -
469D VAL* 3.2 31.0 - - + +
470D HIS* 4.5 9.4 - - + +
493D ILE 3.0 17.5 + - - +
494D ILE 3.4 2.2 + - - +
496D GLN* 1.3 73.2 - - - +
498D ALA* 1.3 60.4 + - - +
500D GLN* 3.9 3.9 - - - +
501D GLN* 2.9 39.8 + - - +
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Residues in contact with ALA 498 (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* 4.0 9.6 - - + +
451D LEU* 3.4 28.7 - - + -
452D GLU* 4.2 22.0 - - + +
455D MET* 3.8 1.7 - - - -
494D ILE 2.9 18.6 + - - +
495D ARG 3.9 4.7 - - - +
497D ALA* 1.3 75.4 - - - +
499D VAL* 1.3 62.5 + - - +
501D GLN* 3.3 2.3 + - - +
502D THR* 2.9 31.9 + - - +
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Residues in contact with VAL 499 (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* 3.3 25.5 - - + -
495D ARG 3.3 14.2 + - - +
496D GLN* 3.1 20.4 - - + +
498D ALA* 1.3 78.3 - - - +
500D GLN* 1.3 69.1 - - + +
502D THR* 3.0 13.8 + - - -
503D LYS* 3.8 10.6 + - - +
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Residues in contact with GLN 500 (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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496D GLN 3.3 17.5 + - - +
497D ALA* 3.9 5.2 - - - +
498D ALA 3.2 0.6 - - - -
499D VAL* 1.3 87.1 - - - +
501D GLN* 1.3 60.1 + - + +
503D LYS* 2.7 67.3 - - - +
504D GLU* 4.6 1.4 + - - +
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Residues in contact with GLN 501 (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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405D HIS* 3.0 56.8 + - + +
406D LEU 4.2 6.1 + - - +
451D LEU* 5.1 3.7 - - + +
455D MET* 3.3 22.1 - - + +
468D LEU 3.6 2.5 + - - +
469D VAL 3.0 26.9 + - - -
497D ALA* 2.9 21.1 + - - +
498D ALA* 4.1 2.9 - - - +
500D GLN* 1.3 77.9 - - + +
502D THR* 1.3 61.8 + - - +
503D LYS 3.4 0.2 - - - -
504D GLU* 3.7 20.3 + - - +
505D MET* 3.8 17.0 - - + +
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Residues in contact with THR 502 (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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447D VAL* 3.9 22.7 - - + +
448D PHE* 3.7 36.4 - - + -
451D LEU* 4.2 13.7 - - + -
498D ALA 2.9 19.6 + - - +
499D VAL* 3.0 17.0 + - - -
501D GLN* 1.3 74.8 - - - +
503D LYS* 1.3 60.8 + - - +
504D GLU* 2.9 6.8 + - - -
505D MET* 4.1 12.7 + - + +
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Residues in contact with LYS 503 (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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499D VAL 3.8 7.0 + - - +
500D GLN* 2.7 51.8 - - - +
502D THR* 1.3 80.5 + - - +
504D GLU* 1.3 80.6 + - + +
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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