Contacts of the helix formed by residues 676 - 690 (chain B) in PDB entry 1GUX
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 LEU 676 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670B LEU* 4.0 10.8 - - + -
673B HIS* 3.5 31.0 - - + +
674B PRO 3.2 0.2 - - - -
675B GLU* 1.3 94.1 - - + +
677B GLU* 1.3 55.2 + - - +
679B ILE* 2.8 8.7 + - + +
680B ILE* 2.7 47.8 + - + +
711B ILE* 4.2 8.5 - - + +
712B CYS* 3.9 18.6 - - - -
715B LYS* 3.4 39.0 - - + -
717B ILE* 3.7 19.7 - - + -
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Residues in contact with GLU 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B TYR* 2.4 35.1 + - + -
662B LEU* 3.7 16.6 - - + +
663B ASN* 2.8 33.9 + - - +
666B CYS* 3.7 30.8 - - + +
667B GLU* 4.7 2.6 - - - +
670B LEU* 5.2 0.8 - - - +
673B HIS 4.6 0.6 + - - -
674B PRO* 4.1 10.8 + - + +
675B GLU 3.5 1.0 - - - -
676B LEU* 1.3 76.2 - - - +
678B HIS* 1.3 54.0 + - - +
680B ILE* 3.4 3.9 + - - +
681B TRP* 2.8 32.9 + - - +
782B ILE* 4.8 5.0 - - - +
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Residues in contact with HIS 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B TYR* 6.1 0.2 - - - -
674B PRO 4.9 2.1 + - - +
675B GLU* 3.8 8.3 + - - +
676B LEU 3.2 0.4 - - - -
677B GLU* 1.3 80.9 + - - +
679B ILE* 1.3 57.9 + - - +
681B TRP* 3.6 6.1 - - - +
682B THR* 2.8 30.1 + - - -
779B LEU* 3.6 31.4 - - + +
780B SER 2.6 31.7 + - - -
781B PRO* 4.5 1.0 - - + +
782B ILE* 3.7 37.4 + - + +
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Residues in contact with ILE 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B GLU* 3.6 27.4 - - + +
676B LEU* 2.8 13.7 + - + +
678B HIS* 1.3 76.1 - - - +
680B ILE* 1.3 66.3 + - - +
681B TRP 3.1 0.2 - - - -
682B THR* 3.1 12.0 + - - -
683B LEU* 3.1 13.2 + - - +
711B ILE* 3.7 23.5 - - + +
715B LYS* 3.9 25.4 - - - +
771B TYR* 3.5 30.7 - - + -
777B PRO* 4.4 13.2 - - + -
779B LEU* 4.0 23.8 - - + -
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Residues in contact with ILE 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B LEU* 3.7 23.8 - - + -
666B CYS* 3.9 13.7 - - - -
670B LEU* 3.6 30.7 - - + -
676B LEU* 2.7 27.6 + - + +
677B GLU* 3.6 4.0 - - - +
679B ILE* 1.3 71.3 - - - +
681B TRP* 1.3 57.6 + - - +
683B LEU* 3.1 4.7 + - - +
684B PHE* 2.9 28.0 + - + +
704B MET 4.8 0.4 - - - +
707B SER* 4.0 6.2 - - - -
708B MET* 3.8 36.8 - - + +
711B ILE* 3.7 29.2 - - + -
712B CYS* 4.7 2.0 - - - -
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Residues in contact with TRP 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B TYR* 3.5 41.5 - + + -
658B ALA* 4.0 9.9 - - + -
659B TYR* 3.8 38.1 - + + -
662B LEU* 3.8 11.7 - - + -
677B GLU 2.8 18.3 + - - +
678B HIS* 3.6 11.0 - - - +
680B ILE* 1.3 76.5 - - - +
682B THR* 1.3 58.2 + - - +
684B PHE* 3.3 20.9 + + - +
685B GLN* 2.8 49.9 + - + +
688B LEU* 5.1 0.4 - - + -
780B SER* 3.6 27.0 + - - -
781B PRO 3.1 20.7 + - - -
782B ILE* 4.2 9.4 - - + -
783B PRO* 3.4 20.0 - - + +
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Residues in contact with THR 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B HIS* 2.8 20.4 + - - -
679B ILE 3.1 8.2 + - - -
681B TRP* 1.3 77.2 - - - +
683B LEU* 1.3 57.5 + - - +
685B GLN* 3.9 0.9 - - - +
686B HIS* 2.9 32.2 + - + +
771B TYR* 3.4 19.5 - - - +
778B THR 3.9 12.3 - - - +
779B LEU* 3.2 13.5 - - + +
780B SER* 2.9 45.6 + - - +
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Residues in contact with LEU 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B ILE 3.1 11.8 + - - +
680B ILE 3.4 7.4 - - - +
682B THR* 1.3 76.1 - - - +
684B PHE* 1.3 54.6 + - - +
686B HIS* 3.3 4.0 + - - +
687B THR* 2.8 38.1 + - - +
706B CYS 5.1 0.2 - - - +
707B SER* 3.6 40.2 - - - +
711B ILE* 4.1 18.6 - - + +
760B PHE* 4.1 6.7 - - + -
764B LEU* 3.6 23.8 - - + -
767B ASN* 3.4 24.7 - - - +
768B ILE* 4.0 25.4 - - + -
771B TYR* 4.7 4.2 + - + -
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Residues in contact with PHE 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B ALA* 3.5 36.8 - - + -
662B LEU* 4.3 10.1 - - + -
680B ILE* 2.9 17.4 + - + +
681B TRP* 3.5 21.8 - + + +
683B LEU* 1.3 75.1 - - - +
685B GLN* 1.3 62.9 + - - +
687B THR* 3.1 13.6 + - - -
688B LEU* 3.1 19.3 + - + +
700B LEU* 3.6 27.1 - - + -
701B ASP* 5.9 0.4 - - - -
703B ILE* 3.6 25.8 - - + -
704B MET* 3.4 44.0 - - + -
707B SER* 3.5 14.5 + - - +
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Residues in contact with GLN 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B TYR* 3.1 34.7 + - + -
681B TRP* 2.8 45.6 + - + +
682B THR 4.0 1.3 + - - +
684B PHE* 1.3 73.4 - - - +
686B HIS* 1.3 67.9 + - - +
688B LEU* 3.3 10.8 + - - +
689B GLN* 2.8 49.9 + - - +
780B SER* 2.8 31.1 + - - +
781B PRO* 5.9 0.4 - - - +
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Residues in contact with HIS 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B THR* 2.9 22.1 + - + +
683B LEU* 3.5 5.8 - - - +
685B GLN* 1.3 83.1 - - - +
687B THR* 1.3 54.4 + - - +
690B ASN* 2.7 77.4 + - + +
691B GLU* 4.0 18.3 + - - +
764B LEU* 3.6 19.3 - - + +
767B ASN* 3.4 39.4 + - - +
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Residues in contact with THR 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B LEU* 2.8 21.9 + - - +
684B PHE* 3.3 9.0 - - - -
686B HIS* 1.3 77.8 - - - +
688B LEU* 1.3 57.1 + - + +
691B GLU* 2.8 51.8 + - + +
692B TYR* 3.7 0.3 - - - -
694B LEU* 4.1 13.0 - - + -
695B MET* 5.9 1.5 - - + +
703B ILE* 3.6 26.0 - - + -
707B SER* 4.5 0.3 + - - -
760B PHE* 4.2 6.2 - - + -
764B LEU* 3.4 34.3 - - + +
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Residues in contact with LEU 688 (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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563A TRP* 4.8 3.8 - - + -
651B TYR* 2.7 32.6 + - + -
654B VAL* 4.3 9.0 - - + -
655B TYR* 3.9 31.0 - - + -
658B ALA* 4.5 6.1 - - + -
681B TRP* 5.1 0.7 - - + -
684B PHE* 3.1 39.3 + - + +
685B GLN* 3.8 5.4 - - - +
687B THR* 1.3 76.0 - - - +
689B GLN* 1.3 56.4 + - - +
692B TYR* 3.3 14.1 - - - +
695B MET* 3.9 26.2 - - + -
700B LEU* 3.6 27.8 - - + -
703B ILE* 4.5 6.3 - - + -
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Residues in contact with GLN 689 (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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573A ILE* 5.4 0.2 - - - +
577A LYS* 3.2 41.3 + - - +
651B TYR* 4.2 8.2 + - + -
655B TYR* 3.6 10.3 + - - +
685B GLN* 2.8 40.6 + - - +
686B HIS 4.2 0.9 - - - +
688B LEU* 1.3 78.7 - - - +
690B ASN* 1.3 72.3 + - - +
692B TYR* 3.6 14.1 - - - -
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Residues in contact with ASN 690 (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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577A LYS* 3.4 25.8 + - - +
686B HIS* 2.7 59.4 + - + +
689B GLN* 1.3 89.8 - - - +
691B GLU* 1.3 65.3 + - + +
692B TYR* 3.5 9.1 + - - -
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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
------------------------------------------------------------
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