Contacts of the helix formed by residues 643 - 666 (chain A) in PDB entry 3DXD
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 ALA 643 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A VAL* 3.9 9.4 - - + -
618A VAL 3.0 16.4 + - - +
619A HIS 3.9 7.6 - - - +
620A THR 3.7 20.4 - - - +
621A PHE* 3.8 18.2 - - + -
639A CYS* 3.6 10.7 - - - +
642A ASN* 1.3 74.7 - - - +
644A ALA* 1.3 61.9 + - - +
645A SER 3.4 2.2 - - - -
646A LEU* 3.5 2.9 + - - +
647A SER* 2.9 27.0 + - - -
674B LEU* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ASN* 2.8 19.7 + - - +
643A ALA* 1.3 75.4 - - - +
645A SER* 1.3 62.0 + - - +
647A SER* 3.0 19.7 + - - -
648A GLU* 3.0 24.9 + - - +
670B GLU* 3.4 34.5 - - + +
674B LEU* 3.9 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A PHE* 3.5 23.3 - - - -
642A ASN* 4.4 3.6 + - - -
643A ALA 3.4 0.4 - - - -
644A ALA* 1.3 79.7 - - - +
646A LEU* 1.3 64.6 + - - +
648A GLU* 3.8 12.2 - - - +
649A ALA* 3.1 24.3 + - - +
670B GLU* 4.9 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A PHE* 3.7 35.9 - - + -
545A VAL* 4.4 8.5 - - + -
583A VAL* 3.8 36.1 - - + -
585A VAL* 4.5 0.4 - - + -
621A PHE* 3.5 29.2 - - + -
637A PHE* 4.4 7.0 - - + -
639A CYS* 3.9 26.5 - - + -
642A ASN 5.7 0.2 + - - -
643A ALA 3.5 6.9 + - - +
644A ALA 3.4 0.2 - - - -
645A SER* 1.3 76.7 + - - +
647A SER* 1.3 61.9 + - - +
649A ALA* 3.3 1.9 + - - +
650A VAL* 2.9 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 4.2 3.0 - - - +
614A VAL* 3.5 16.6 - - - +
621A PHE* 3.4 32.5 - - - -
643A ALA 2.9 22.5 + - - -
644A ALA* 3.0 12.5 + - - -
646A LEU* 1.3 77.8 - - - +
648A GLU* 1.3 54.1 + - - +
650A VAL* 3.4 1.0 + - - +
651A GLN* 2.8 36.3 + - - +
674B LEU* 5.1 0.3 - - - +
677B MET* 3.8 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A ALA* 3.0 30.6 + - - +
645A SER* 3.8 13.3 - - - +
647A SER* 1.3 78.3 + - - +
649A ALA* 1.3 53.4 + - - +
651A GLN* 3.4 5.5 + - - +
652A ALA* 2.8 37.2 + - - +
670B GLU* 4.2 19.6 - - - +
673B HIS* 3.6 40.0 + - + +
674B LEU 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 649 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 5.7 0.2 - - - +
540A VAL* 4.4 9.2 - - + -
543A PHE* 3.5 28.3 - - + -
585A VAL* 3.6 14.4 - - + +
645A SER 3.1 16.1 + - - +
646A LEU 3.6 3.6 - - - +
648A GLU* 1.3 77.4 - - - +
650A VAL* 1.3 57.8 + - - +
652A ALA* 3.5 5.9 + - - +
653A ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A VAL* 5.2 1.1 - - + -
585A VAL* 4.2 9.4 - - + -
590A LEU* 3.8 35.2 - - + -
609A LEU* 3.8 11.9 - - + -
612A LEU* 3.5 20.4 - - + -
621A PHE* 4.0 19.1 - - + -
646A LEU* 2.9 37.9 + - + +
647A SER 3.9 2.5 - - - +
649A ALA* 1.3 75.5 - - - +
651A GLN* 1.3 66.3 + - - +
653A ALA* 3.3 6.8 + - - +
654A CYS* 3.1 22.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 4.0 14.3 - - + +
647A SER 2.8 21.5 + - - +
648A GLU* 3.8 2.4 - - - +
650A VAL* 1.3 72.8 - - - +
652A ALA* 1.3 62.7 + - - +
654A CYS* 3.1 4.0 + - - +
655A MET* 3.0 53.0 + - + +
673B HIS* 2.7 41.2 + - - -
677B MET* 3.5 11.9 - - - +
682B TYR* 3.7 38.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A GLU 2.8 22.1 + - - +
649A ALA* 3.7 6.5 - - - +
651A GLN* 1.3 72.9 - - - +
653A ALA* 1.3 57.1 + - - +
655A MET* 3.2 16.9 + - + +
656A LEU* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 4.2 17.8 - - + +
585A VAL* 3.7 20.9 - - + -
586A ALA 4.3 7.4 - - - +
587A PRO 4.5 3.8 - - - +
590A LEU* 4.7 2.5 - - + -
606A VAL* 4.1 14.0 - - + +
649A ALA 3.0 17.8 + - - +
650A VAL* 3.6 6.7 - - - +
652A ALA* 1.3 73.4 - - - +
654A CYS* 1.3 58.4 + - - +
656A LEU* 3.8 4.0 - - - +
657A ARG* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A VAL* 3.9 15.3 - - - -
609A LEU* 4.3 9.0 - - - -
612A LEU* 4.1 18.6 - - - -
650A VAL* 3.1 23.4 + - - -
651A GLN 3.1 7.1 + - - +
653A ALA* 1.3 75.9 - - - +
655A MET* 1.3 62.0 + - - +
658A TYR* 3.1 10.4 + - - +
682B TYR* 3.6 15.5 - - + -
684B ASN* 3.3 35.9 - - - +
685B PRO* 4.7 0.2 - - - +
686B THR* 3.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A GLN* 3.0 38.4 + - - +
652A ALA* 3.2 22.2 + - + +
654A CYS* 1.3 77.5 - - - +
656A LEU* 1.3 61.8 + - - +
658A TYR* 3.6 8.1 + - - +
659A GLN* 3.3 20.1 + - - +
673B HIS* 6.0 0.2 - - - +
682B TYR* 3.0 24.9 - - + +
685B PRO* 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 4.5 24.2 - - + -
587A PRO* 6.0 0.9 - - + -
652A ALA 2.9 18.4 + - - +
653A ALA* 3.8 4.3 - - - +
655A MET* 1.3 74.1 - - - +
657A ARG* 1.3 57.8 + - - +
659A GLN* 3.3 8.6 + - + +
660A LYS* 3.0 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A PRO* 3.6 21.2 + - - +
588A ALA* 3.8 31.1 + - - +
605A ARG* 5.5 5.1 - - - +
606A VAL* 3.7 17.2 - - + +
607A ARG* 4.8 20.2 - - - +
653A ALA 3.0 19.5 + - - +
656A LEU* 1.3 73.1 - - - +
658A TYR* 1.3 65.8 + - - +
660A LYS* 3.4 16.8 + - - +
661A CYS* 2.9 44.6 + - - -
686B THR* 3.6 26.2 - - + +
690B PHE* 5.7 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A CYS 3.1 13.6 + - - +
655A MET* 3.8 5.8 - - - +
656A LEU 3.4 0.2 - - - -
657A ARG* 1.3 74.8 - - - +
659A GLN* 1.3 67.9 + - + +
661A CYS* 3.3 3.7 + - - +
662A LEU* 3.0 58.0 + - + +
685B PRO* 3.7 44.6 - - + -
686B THR* 3.1 17.5 + - - +
689B PHE* 3.7 30.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A MET 3.3 9.7 + - - +
656A LEU* 3.3 14.3 + - + +
658A TYR* 1.3 81.2 - - + +
660A LYS* 1.3 64.1 + - + +
662A LEU* 3.3 21.4 + - - +
663A ASP* 2.9 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 5.3 2.4 - - - +
587A PRO* 4.4 20.7 - - + +
656A LEU* 3.0 59.0 + - + +
657A ARG* 3.4 18.8 + - - +
659A GLN* 1.3 76.0 - - + +
661A CYS* 1.3 59.0 + - - +
663A ASP* 3.9 5.0 - - - +
664A ALA* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ARG* 2.9 47.3 + - - +
658A TYR* 3.7 5.4 - - - +
660A LYS* 1.3 75.2 - - - +
662A LEU* 1.3 65.3 + - - +
664A ALA* 3.3 5.8 + - - +
665A ARG* 3.0 28.8 + - - +
686B THR* 4.3 1.1 - - + -
689B PHE* 3.5 26.9 - - + -
690B PHE* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A TYR* 3.0 54.3 + - + +
659A GLN* 3.7 22.4 - - - +
661A CYS* 1.3 72.8 - - - +
663A ASP* 1.3 57.7 + - - +
665A ARG* 3.4 2.6 + - - +
666A SER* 3.1 28.8 + - - -
689B PHE* 3.7 28.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A GLN* 2.9 34.1 + - + +
660A LYS* 3.9 6.3 - - - +
662A LEU* 1.3 74.9 - - - +
664A ALA* 1.3 64.4 + - - +
666A SER* 3.1 22.8 + - - -
667A GLN* 3.7 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A LYS 3.0 18.6 + - - +
661A CYS* 3.7 6.7 - - - +
663A ASP* 1.3 76.0 - - - +
665A ARG* 1.3 62.6 + - + +
666A SER 3.3 0.7 + - - -
667A GLN* 3.4 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A ARG* 4.8 3.0 - - - +
661A CYS* 3.0 17.8 + - - +
662A LEU* 3.8 3.8 - - + +
664A ALA* 1.3 78.0 - - + +
666A SER* 1.3 57.0 + - - +
667A GLN 3.3 3.8 + - - -
689B PHE* 3.5 28.5 - - + -
690B PHE* 3.4 22.8 - - - -
693B MET* 3.4 33.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU 3.1 14.1 + - - -
663A ASP* 3.1 19.1 + - - -
664A ALA 3.2 0.4 - - - -
665A ARG* 1.3 78.1 - - - +
667A GLN* 1.3 69.9 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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