Contacts of the helix formed by residues 650 - 671 (chain A) in PDB entry 3LLT
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 HIS 650 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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649A PHE* 1.3 75.6 - - - +
651A ILE* 1.3 75.1 + - + +
652A GLU* 3.2 57.4 + - + +
653A ASP* 3.0 30.8 + - - +
654A ILE* 3.0 11.0 + - - +
695A ILE* 4.4 4.7 - - + -
696A THR 5.6 0.4 - - - -
697A VAL* 3.8 41.3 - - + -
708A ILE* 3.9 8.6 - - - +
710A ARG* 3.8 12.4 + - - +
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Residues in contact with ILE 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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649A PHE 3.7 1.4 + - - -
650A HIS* 1.3 87.0 - - + +
652A GLU* 1.3 67.7 + - + +
654A ILE* 4.1 11.2 - - + -
655A LYS* 3.1 21.1 + - - +
768A TYR* 3.9 26.2 - - + -
844A HIS* 4.1 29.4 - - + +
847A PHE* 4.2 14.8 - - + -
873A PHE* 3.5 34.3 - - + -
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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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650A HIS* 3.2 28.8 + - + +
651A ILE* 1.3 81.9 - - + +
653A ASP* 1.3 62.5 + - - +
655A LYS* 3.4 24.3 - - - +
656A LEU* 3.6 15.3 + - - +
710A ARG* 3.6 19.8 + - - +
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Residues in contact with ASP 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A PHE* 4.6 8.3 - - + -
650A HIS* 3.0 23.9 + - - +
652A GLU* 1.3 74.4 - - - +
654A ILE* 1.3 66.2 + - - +
656A LEU* 3.1 9.3 + - - +
657A TYR* 3.0 47.4 + - + -
695A ILE* 4.7 0.3 - - - +
710A ARG* 3.0 49.1 + - - +
711A THR* 4.8 3.8 + - - +
714A THR* 4.0 12.6 + - - +
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Residues in contact with ILE 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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649A PHE* 3.4 34.3 - - + +
650A HIS 3.0 13.2 + - - +
651A ILE* 3.7 12.8 - - + +
653A ASP* 1.3 76.1 - - - +
655A LYS* 1.3 56.5 + - - +
657A TYR* 3.4 8.1 + - - +
658A CYS* 2.8 33.4 + - + +
764A LEU* 4.6 11.8 - - + +
767A LEU* 3.7 26.0 - - + +
768A TYR* 3.7 29.4 - - + -
847A PHE* 4.0 30.1 - - + -
873A PHE* 4.7 3.8 - - + -
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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 ILE 3.1 13.1 + - - +
652A GLU* 3.4 17.5 - - - +
653A ASP 3.2 0.2 - - - -
654A ILE* 1.3 76.6 - - - +
656A LEU* 1.3 68.8 + - + +
658A CYS* 3.4 2.9 - - - +
659A ILE* 3.1 39.0 + - + +
872A LYS 5.2 0.2 + - - -
873A PHE* 2.8 52.0 + - + +
874A LEU* 3.6 10.8 - - + +
875A GLU 3.9 24.0 + - - +
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Residues in contact with LEU 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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652A GLU 3.6 15.7 + - - +
653A ASP* 3.1 8.3 + - - +
655A LYS* 1.3 82.7 - - + +
657A TYR* 1.3 65.5 + - - +
658A CYS 3.2 1.1 - - - -
659A ILE* 3.4 20.0 + - + +
660A GLU* 3.1 28.6 + - + +
714A THR* 3.5 37.2 - - + +
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Residues in contact with TYR 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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637A LEU* 3.8 23.0 - - + +
640A ILE* 4.9 0.2 - - - +
649A PHE* 3.8 44.6 - + - -
653A ASP* 3.0 35.4 + - + +
654A ILE* 3.8 7.9 - - - +
656A LEU* 1.3 74.6 - - - +
658A CYS* 1.3 57.4 + - - +
660A GLU* 3.2 4.1 + - - +
661A ILE* 2.9 46.4 + - + +
685A LEU* 4.1 9.8 - - + +
711A THR* 2.7 29.3 + - - +
714A THR* 3.5 36.3 - - + -
716A ILE* 3.8 12.3 - - + -
767A LEU* 4.5 11.7 - - + -
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Residues in contact with CYS 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 ILE* 2.8 20.5 + - + +
655A LYS* 3.4 7.4 - - - +
657A TYR* 1.3 77.3 - - - +
659A ILE* 1.3 61.1 + - - +
661A ILE* 3.4 8.2 + - - +
662A LEU* 3.0 32.9 + - - +
760A PHE* 3.8 15.4 - - - -
764A LEU* 4.2 13.2 - - + +
850A PHE* 3.5 38.6 - - - -
873A PHE* 4.6 3.4 - - + -
874A LEU* 3.8 11.4 - - + -
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Residues in contact with ILE 659 (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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655A LYS* 3.1 32.7 + - + +
656A LEU* 3.7 19.7 - - + +
657A TYR 3.4 0.2 - - - -
658A CYS* 1.3 74.8 - - - +
660A GLU* 1.3 66.8 + - - +
662A LEU* 3.4 3.5 + - - +
663A LYS* 3.1 57.2 + - - +
869A LEU* 4.2 11.3 - - + +
874A LEU* 3.7 37.5 - - + +
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Residues in contact with GLU 660 (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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609A ASN* 4.6 9.8 + - - -
612A ASN* 2.7 52.2 + - - +
656A LEU* 3.1 17.0 + - + +
657A TYR 3.2 3.8 + - - +
659A ILE* 1.3 85.4 - - - +
661A ILE* 1.3 64.6 + - - +
663A LYS* 3.4 17.3 + - - +
664A ALA 3.5 4.3 + - - -
714A THR* 3.9 17.0 - - - +
715A GLY* 4.4 10.0 - - - -
716A ILE* 3.7 16.6 - - + +
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Residues in contact with ILE 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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637A LEU* 4.5 6.3 - - + -
657A TYR* 2.9 38.4 + - + +
658A CYS* 4.0 1.8 - - - +
660A GLU* 1.3 72.1 - - - +
662A LEU* 1.3 57.7 + - - +
664A ALA* 3.3 6.0 + - - +
665A LEU* 3.0 33.1 + - + +
678A LEU* 5.9 2.9 - - + -
683A ILE* 4.0 29.8 - - + -
716A ILE* 3.7 23.8 - - + -
718A LEU* 4.5 15.3 - - + -
760A PHE* 3.6 36.1 - - + -
763A VAL* 5.0 2.5 - - + -
764A LEU* 5.1 0.9 - - + -
767A LEU* 4.7 8.7 - - + -
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Residues in contact with LEU 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 CYS* 3.0 27.0 + - - +
659A ILE 3.7 4.7 - - - +
661A ILE* 1.3 75.4 - - - +
663A LYS* 1.3 59.2 + - - +
665A LEU* 4.3 8.5 - - + +
666A ASN* 2.8 32.7 + - - +
757A MET* 4.9 0.9 - - + -
760A PHE* 3.9 17.5 - - + -
850A PHE* 4.2 2.9 - - + -
865A PRO* 3.9 24.1 - - + +
868A LEU* 3.8 35.7 - - + -
869A LEU* 3.9 18.3 - - + +
874A LEU* 3.6 30.7 - - + -
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Residues in contact with LYS 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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611A ASN* 4.2 10.1 - - - +
612A ASN* 3.9 10.3 - - - +
659A ILE* 3.1 38.6 + - + +
660A GLU* 3.6 19.9 + - - +
662A LEU* 1.3 75.7 - - - +
664A ALA* 1.3 61.6 + - - +
666A ASN* 3.7 7.0 + - - +
667A TYR* 3.2 23.2 + - - +
869A LEU* 4.3 21.8 - - + -
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Residues in contact with ALA 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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611A ASN 3.2 21.5 + - - +
612A ASN* 3.8 17.9 - - + +
613A ILE* 4.1 3.7 - - + +
660A GLU 3.5 3.2 + - - +
661A ILE* 3.3 10.9 + - - +
662A LEU 3.2 0.2 - - - -
663A LYS* 1.3 80.4 - - - +
665A LEU* 1.3 57.9 + - - +
667A TYR* 3.3 3.9 + - - +
668A LEU* 3.0 33.1 + - - +
716A ILE* 5.1 0.2 - - + -
718A LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 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 ILE* 3.0 24.0 + - + +
662A LEU* 3.3 8.0 + - + +
664A ALA* 1.3 74.0 - - - +
666A ASN* 1.3 60.0 + - - +
668A LEU* 3.4 22.5 + - + +
669A ARG* 3.0 28.6 + - - +
678A LEU* 3.7 27.4 - - + -
718A LEU* 4.4 9.4 - - + -
756A ASP* 4.4 10.5 - - + +
757A MET* 4.5 13.7 - - - -
760A PHE* 4.1 37.7 - - + -
865A PRO* 3.7 16.0 - - + +
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Residues in contact with ASN 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 LEU 2.8 18.8 + - - +
663A LYS* 3.9 6.6 - - - +
665A LEU* 1.3 76.2 - - - +
667A TYR* 1.3 61.1 + - - +
669A ARG* 3.4 7.0 - - - +
670A LYS* 3.2 52.1 + - - +
865A PRO* 3.6 14.9 - - + +
866A ALA* 3.8 28.3 + - - +
869A LEU* 4.6 12.8 - - + +
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Residues in contact with TYR 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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602A LYS 4.6 0.7 + - - -
603A ILE* 2.9 44.7 + - + -
604A GLN 4.5 0.9 + - - -
605A ASN* 3.4 22.6 + - + +
611A ASN* 3.3 37.9 - - + +
613A ILE* 4.0 16.8 - - + -
663A LYS 3.2 18.2 + - - +
664A ALA 3.5 3.6 - - - +
666A ASN* 1.3 74.7 - - - +
668A LEU* 1.3 63.9 - - + +
670A LYS* 3.2 14.7 + - + +
671A MET* 3.0 59.8 + - + +
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Residues in contact with LEU 668 (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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603A ILE* 4.4 8.3 - - + -
613A ILE* 3.9 19.5 - - + -
664A ALA 3.0 18.0 + - - +
665A LEU* 3.8 18.2 - - + +
666A ASN 3.4 0.4 - - - -
667A TYR* 1.3 77.3 - - + +
669A ARG* 1.3 58.8 - - - +
671A MET* 3.3 4.6 + - - +
672A SER 3.0 7.1 + - - -
673A LEU* 2.8 68.7 + - + +
675A HIS* 4.3 15.0 - - + +
718A LEU* 4.0 24.0 - - + -
721A PHE* 4.0 15.3 - - + -
756A ASP* 4.8 1.3 - - - +
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Residues in contact with ARG 669 (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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665A LEU 3.0 16.6 + - - +
666A ASN* 3.4 13.7 - - - +
667A TYR 3.2 0.2 - - - -
668A LEU* 1.3 76.7 - - - +
670A LYS* 1.3 57.9 + - + +
672A SER* 3.0 22.5 + - - +
753A VAL* 3.6 55.4 + - + +
754A SER* 4.2 9.1 - - - +
757A MET* 4.2 13.3 - - - +
862A ARG 5.2 3.4 + - - -
863A PRO 4.7 1.6 + - - -
864A SER* 3.7 28.9 - - - +
865A PRO* 3.9 22.3 - - + +
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Residues in contact with LYS 670 (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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666A ASN* 3.2 40.0 + - - +
667A TYR* 3.2 17.8 + - + +
669A ARG* 1.3 80.1 - - + +
671A MET* 1.3 70.1 + - + +
672A SER* 3.3 4.0 + - - -
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Residues in contact with MET 671 (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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602A LYS 4.5 12.8 - - - +
603A ILE* 4.3 15.3 - - + -
667A TYR* 3.0 57.3 + - + +
668A LEU* 3.3 8.5 + - - +
669A ARG 3.2 0.2 - - - -
670A LYS* 1.3 85.7 - - + +
672A SER* 1.3 69.6 + - - +
673A LEU* 3.3 3.9 + - + +
726A PHE* 3.5 19.2 - - + -
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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
------------------------------------------------------------
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