Contacts of the helix formed by residues 646 - 667 (chain A) in PDB entry 5UT1
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 ASN 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644A CYS 4.1 1.9 + - - -
645A ILE* 1.3 73.9 - - - +
647A ILE* 1.3 68.4 + - + +
648A LEU* 3.2 16.9 + - - +
649A TRP* 3.1 23.5 + - - +
650A LYS* 3.0 27.4 + - - +
685A GLU* 4.9 5.9 + - - +
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Residues in contact with ILE 647 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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646A ASN* 1.3 80.3 - - + +
648A LEU* 1.3 74.2 + - + +
650A LYS* 3.2 18.2 + - + -
651A LEU* 2.8 36.2 + - + +
747A CYS* 5.8 1.8 - - - -
777A ALA* 5.9 1.6 - - + -
779A GLU* 3.6 52.3 - - + +
780A LEU* 5.0 10.5 - - + -
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Residues in contact with LEU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A ASN* 3.2 14.2 + - - +
647A ILE* 1.3 87.0 - - + +
649A TRP* 1.3 67.1 + - - +
651A LEU* 3.8 19.3 - - + +
652A GLU* 2.9 25.3 + - - +
685A GLU* 5.2 2.0 - - - +
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Residues in contact with TRP 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A LEU* 3.5 26.5 - - + -
637A TYR* 3.7 28.8 + + - -
638A LEU* 3.9 19.7 - - + -
644A CYS 5.5 1.8 - - - -
645A ILE* 3.4 35.4 - - + +
646A ASN* 3.1 25.9 + - - +
648A LEU* 1.3 76.4 - - - +
650A LYS* 1.3 68.3 + - + +
652A GLU* 3.2 6.7 + - - +
653A VAL* 3.0 44.2 + - + +
681A LEU* 4.2 11.6 - - + +
684A GLU* 5.7 0.4 - - - +
685A GLU* 3.6 45.9 + - + +
693A PRO* 3.6 19.0 - - + +
746A ILE* 4.9 1.6 - - + -
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Residues in contact with LYS 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A LEU* 5.7 0.2 - - - -
645A ILE* 3.7 34.0 + - + -
646A ASN 3.0 17.9 + - - +
647A ILE* 3.6 17.7 - - + +
649A TRP* 1.3 81.8 - - + +
651A LEU* 1.3 59.0 + - - +
653A VAL* 3.4 1.6 + - - +
654A ALA* 2.9 30.5 + - - +
746A ILE* 3.6 38.2 - - + +
747A CYS* 3.3 37.5 + - - -
749A GLY* 5.1 3.3 - - - +
777A ALA* 3.8 20.2 - - + +
780A LEU* 4.8 3.1 - - + +
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Residues in contact with LEU 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A ILE* 2.8 24.6 + - + +
648A LEU* 3.8 20.0 - - + +
650A LYS* 1.3 72.3 - - - +
652A GLU* 1.3 60.5 + - - +
654A ALA* 3.7 4.6 - - - +
655A LYS* 2.9 60.4 + - - +
780A LEU* 4.8 10.1 - - + -
805A LEU* 3.6 39.0 - - + +
808A LEU* 4.3 31.0 - - + +
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Residues in contact with GLU 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A LEU 2.9 18.3 + - - +
649A TRP* 3.6 4.7 - - - +
651A LEU* 1.3 76.8 - - - +
653A VAL* 1.3 57.2 + - - +
655A LYS* 3.3 16.2 + - - +
656A GLN* 2.8 66.2 + - - +
692A PRO* 3.6 29.8 - - + +
693A PRO* 4.0 11.2 - - + -
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Residues in contact with VAL 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A LEU* 4.0 16.6 - - + -
649A TRP* 3.0 49.8 + - + +
650A LYS* 3.8 3.4 - - - +
652A GLU* 1.3 73.9 - - - +
654A ALA* 1.3 65.0 + - - +
656A GLN* 3.3 7.8 + - - +
657A LEU* 3.0 23.3 + - + +
679A ILE* 5.7 0.2 - - + -
693A PRO* 3.7 19.1 - - + -
695A ILE* 3.9 23.6 - - + +
746A ILE* 3.7 23.8 - - + -
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Residues in contact with ALA 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A LYS 2.9 18.7 + - - +
651A LEU* 3.7 6.5 - - - +
653A VAL* 1.3 77.0 - - - +
655A LYS* 1.3 58.8 + - - +
657A LEU* 3.3 5.3 + - - +
658A ALA* 2.8 30.0 + - - +
739A PHE* 4.2 2.4 - - - -
743A LEU* 3.4 32.1 - - + -
746A ILE* 4.8 2.7 - - + +
780A LEU* 4.4 5.2 - - + -
805A LEU* 4.0 21.1 - - + +
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Residues in contact with LYS 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A LEU* 2.9 43.0 + - + +
652A GLU* 3.5 17.0 + - - +
653A VAL 3.3 0.2 - - - -
654A ALA* 1.3 76.8 - - - +
656A GLN* 1.3 57.7 + - + +
658A ALA* 3.4 3.3 + - - +
659A ALA* 2.9 28.1 + - - +
802A ILE* 5.0 5.2 - - + +
805A LEU* 3.7 40.4 + - + -
806A ASN* 3.3 29.3 + - - +
808A LEU 5.3 1.8 + - - -
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Residues in contact with GLN 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A HIS* 3.4 33.2 - - + +
652A GLU* 2.8 43.2 + - - +
653A VAL* 3.7 2.5 - - - +
655A LYS* 1.3 73.5 - - + +
657A LEU* 1.3 67.5 + - - +
659A ALA* 3.2 6.1 + - - +
660A ALA* 3.0 19.9 + - - +
692A PRO* 4.5 2.4 - - - +
693A PRO* 2.8 25.2 + - - +
694A PHE* 3.3 7.9 - - - +
695A ILE* 3.0 44.7 + - + +
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Residues in contact with LEU 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A VAL 3.0 16.4 + - - +
654A ALA* 3.7 4.0 - - - +
656A GLN* 1.3 75.6 - - - +
658A ALA* 1.3 64.0 + - - +
660A ALA* 3.1 5.6 + - + +
661A MET* 2.9 39.3 + - + +
674A VAL* 4.3 6.3 - - + -
679A ILE* 3.9 30.1 - - + -
695A ILE* 3.6 12.5 - - + +
697A LEU* 4.2 26.9 - - + -
739A PHE* 3.6 29.6 - - + +
742A THR* 3.9 16.8 - - + -
743A LEU* 5.3 2.2 - - + -
746A ILE* 4.8 8.5 - - + -
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Residues in contact with ALA 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A ALA 2.8 21.4 + - - +
655A LYS 3.6 4.9 - - - +
657A LEU* 1.3 72.6 - - - +
659A ALA* 1.3 58.8 + - - +
661A MET* 3.3 1.6 + - - +
662A HIS* 2.8 30.5 + - - +
739A PHE* 3.7 16.2 - - + -
798A PHE* 4.1 8.1 - - + -
801A ILE* 4.2 5.4 - - + -
802A ILE* 3.6 24.0 - - + +
805A LEU* 3.8 16.6 - - + -
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Residues in contact with ALA 659 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606A HIS* 4.6 6.4 + - + -
607A LYS* 6.2 0.7 - - - -
608A HIS* 4.3 13.2 - - + +
655A LYS 2.9 14.2 + - - +
656A GLN* 3.2 9.6 + - - +
658A ALA* 1.3 77.6 - - - +
660A ALA* 1.3 63.2 + - - +
662A HIS* 3.4 3.8 + - - +
663A PHE* 3.0 22.9 + - - +
802A ILE* 4.1 13.2 - - + +
904A GOL 5.2 4.5 + - - -
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Residues in contact with ALA 660 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606A HIS* 4.6 3.1 - - - -
608A HIS* 3.8 30.6 - - + +
609A LEU* 4.5 12.1 - - + +
656A GLN 3.0 12.5 + - - +
657A LEU* 3.1 11.4 + - + +
659A ALA* 1.3 76.8 - - - +
661A MET* 1.3 59.0 + - - +
663A PHE* 3.3 9.8 + - - +
664A LEU* 3.0 30.6 + - - +
695A ILE* 6.1 0.7 - - + -
697A LEU* 4.7 13.0 - - + +
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Residues in contact with MET 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A LEU* 2.9 24.8 + - + +
660A ALA* 1.3 72.9 - - - +
662A HIS* 1.3 62.2 + - - +
664A LEU* 3.3 19.6 + - + +
665A GLU* 2.8 30.0 + - - +
671A HIS* 4.3 0.9 - - + -
674A VAL* 3.7 17.9 - - + -
697A LEU* 3.5 29.4 - - - -
735A ASP* 3.6 36.3 - - + +
739A PHE* 4.2 10.3 - - + -
798A PHE* 3.4 40.3 - - + -
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Residues in contact with HIS 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A ALA 2.8 17.0 + - - +
659A ALA* 3.6 5.8 - - - +
661A MET* 1.3 74.7 - - - +
663A PHE* 1.3 61.1 + - - +
665A GLU* 3.3 6.2 + - - +
666A GLU* 2.9 53.1 + - + +
798A PHE* 3.8 12.4 - - + +
799A ARG* 3.6 60.2 + - + -
802A ILE* 3.8 20.2 - - + -
904A GOL 6.1 1.8 - - - -
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Residues in contact with PHE 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604A LEU* 3.5 35.4 - - + -
605A SER 3.7 16.8 - - - -
606A HIS* 3.3 45.3 - + + +
609A LEU* 4.0 12.3 - - + -
659A ALA 3.0 14.2 + - - +
660A ALA* 3.4 9.2 - - - +
662A HIS* 1.3 81.4 - - - +
664A LEU* 1.3 66.1 + - + +
666A GLU* 3.3 4.1 + - + +
667A ASN* 2.8 47.4 + - - -
904A GOL 3.8 10.8 - - - +
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Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A MET* 5.4 5.2 - - - -
604A LEU* 4.6 2.2 - - + -
609A LEU* 4.2 27.8 - - + -
660A ALA 3.0 15.4 + - - +
661A MET* 3.6 36.8 - - + +
662A HIS 3.2 0.2 - - - -
663A PHE* 1.3 80.8 - - + +
665A GLU* 1.3 59.1 + - - +
667A ASN* 3.1 6.2 + - - +
668A THR 2.9 22.7 + - - -
669A LEU* 2.9 48.4 + - + +
670A ILE 5.5 0.2 - - - -
671A HIS* 4.2 16.6 - - + +
697A LEU* 4.0 14.4 - - + -
732A LEU* 6.0 0.2 - - + -
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Residues in contact with GLU 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A MET 2.8 20.6 + - - +
662A HIS* 3.8 9.0 + - - +
664A LEU* 1.3 74.0 - - - +
666A GLU* 1.3 61.7 + - + +
668A THR* 3.0 19.5 + - - +
732A LEU* 4.4 22.9 - - + +
736A LYS* 2.6 36.1 + - - +
797A SER* 4.0 9.4 - - - -
798A PHE* 2.8 36.6 + - + +
799A ARG 4.4 1.4 + - - -
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Residues in contact with GLU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A HIS* 2.9 47.4 + - + +
663A PHE* 3.8 5.6 - - + +
664A LEU 3.2 0.2 - - - -
665A GLU* 1.3 78.5 - - + +
667A ASN* 1.3 61.5 + - - +
668A THR* 3.2 7.0 + - - +
799A ARG* 3.8 24.6 + - - -
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Residues in contact with ASN 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604A LEU* 3.5 36.7 - - + +
663A PHE* 2.8 52.1 + - - +
664A LEU 3.1 4.8 + - - +
666A GLU* 1.3 79.4 - - - +
668A THR* 1.3 75.7 + - - +
669A LEU* 3.2 4.8 + - - +
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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