Contacts of the helix formed by residues 606 - 623 (chain C) in PDB entry 4OQB
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 SER 606 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C MET* 3.3 15.0 - - - +
605C PRO* 1.3 80.2 - - - +
607C LYS* 1.3 75.3 + - - +
608C GLU* 3.5 8.2 + - - +
609C ASP* 3.5 19.1 + - - +
610C ALA* 3.4 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 607 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C LEU* 5.0 21.3 - - + -
574C LEU* 5.7 0.3 - - - +
575C LEU 4.7 7.4 + - - -
584C TRP* 3.5 39.9 - - - +
604C MET* 6.5 0.2 - - + -
606C SER* 1.3 82.4 + - - +
608C GLU* 1.3 62.6 + - + +
609C ASP 3.3 0.4 - - - -
610C ALA* 3.3 21.5 - - + +
611C ILE* 3.7 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 608 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C SER* 3.5 5.9 + - - +
607C LYS* 1.3 76.2 - - + +
609C ASP* 1.3 67.0 + - - +
610C ALA 3.2 0.4 - - - -
611C ILE* 3.6 25.5 + - - +
612C GLU* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 609 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C MET* 4.0 3.0 - - - +
605C PRO* 3.6 24.8 - - + +
606C SER* 3.5 35.5 + - - +
607C LYS 3.3 0.2 - - - -
608C GLU* 1.3 77.1 - - - +
610C ALA* 1.3 59.8 + - - +
612C GLU* 3.4 10.4 + - + +
613C HIS* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 610 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C LEU* 3.4 31.4 - - + -
584C TRP 5.6 1.6 - - - +
585C ILE* 4.1 1.7 - - - +
604C MET* 4.0 19.3 - - + -
606C SER 3.4 10.3 + - - +
607C LYS* 3.3 19.5 - - + +
608C GLU 3.2 0.2 - - - -
609C ASP* 1.3 76.0 - - - +
611C ILE* 1.3 55.6 + - - +
613C HIS* 3.2 1.4 + - - +
614C PHE* 2.7 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 611 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C LEU* 6.4 1.6 - - + -
548C LYS* 5.8 11.2 - - + -
553C PHE* 3.9 24.7 - - + -
574C LEU* 5.0 3.8 - - + -
607C LYS 3.7 9.4 + - - +
608C GLU* 3.6 28.8 + - - +
609C ASP 3.4 0.2 - - - -
610C ALA* 1.3 75.8 - - - +
612C GLU* 1.3 59.9 + - - +
614C PHE* 4.4 4.7 - - - -
615C MET* 3.0 59.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 612 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C GLU 3.4 10.8 + - - +
609C ASP* 3.4 14.3 + - - +
610C ALA 3.2 0.2 - - - -
611C ILE* 1.3 82.6 - - - +
613C HIS* 1.3 57.8 + - - +
615C MET* 4.8 1.2 - - - +
616C LYS* 3.1 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 613 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C ILE* 3.8 20.9 - - + -
587C ARG* 3.9 8.8 + - - -
602C GLU* 3.9 17.2 + - - -
604C MET* 3.8 21.3 - - + +
609C ASP 2.9 17.5 + - - +
610C ALA 3.8 1.3 - - - +
612C GLU* 1.3 75.0 - - - +
614C PHE* 1.3 60.2 + - - +
616C LYS* 4.0 5.9 - - - +
617C LEU* 3.1 69.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 614 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C PHE* 3.5 50.3 - + + -
554C SER* 3.9 4.0 - - - -
555C ALA* 5.0 0.7 - - + -
572C LEU* 3.6 35.4 - - + +
573C GLN* 4.1 7.6 - - - -
574C LEU* 4.1 16.2 - - + -
585C ILE* 3.5 14.8 - - + +
610C ALA 2.7 23.1 + - - +
611C ILE* 3.9 4.5 - - - +
613C HIS* 1.3 71.5 - - - +
615C MET* 1.3 67.3 + - + +
617C LEU* 3.3 3.9 + - - +
618C TYR* 2.8 31.1 + + + +
626C TRP* 3.6 46.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 615 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C PHE* 3.8 14.6 - - + -
611C ILE* 3.0 43.5 + - + +
612C GLU* 4.8 1.6 - - - +
614C PHE* 1.3 85.0 - - + +
616C LYS* 1.3 56.6 + - - +
618C TYR* 3.7 8.2 - - - +
619C GLU* 3.2 29.3 + - - +
626C TRP* 3.8 43.9 + - + +
627C HIS* 4.2 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 616 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C GLU* 3.1 26.4 + - + +
613C HIS* 4.0 6.3 - - - +
614C PHE 3.2 0.6 - - - -
615C MET* 1.3 75.4 - - - +
617C LEU* 1.3 59.7 + - + +
619C GLU* 3.5 3.4 + - - +
620C GLU* 2.9 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 617 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C TYR* 4.2 9.0 + - - +
572C LEU* 4.4 10.5 - - + -
585C ILE* 4.2 10.8 - - + -
587C ARG* 3.5 48.0 - - + +
613C HIS* 3.1 53.1 + - + +
614C PHE 3.7 2.9 - - - +
616C LYS* 1.3 72.6 - - + +
618C TYR* 1.3 69.3 + - - +
620C GLU* 3.4 17.4 + - - +
621C LYS* 3.1 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 618 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C LYS* 5.9 0.9 + - - -
555C ALA* 4.0 17.8 - - + +
557C LEU* 4.3 14.5 - - + +
572C LEU* 4.0 18.3 - - + +
614C PHE* 2.8 19.0 + - + +
615C MET* 3.7 9.0 - - - +
616C LYS 3.3 0.2 - - - -
617C LEU* 1.3 74.8 - - - +
619C GLU* 1.3 54.5 + - - +
621C LYS* 2.9 7.2 + - - +
622C THR* 2.7 62.6 + - + +
624C ASN* 3.8 6.5 - - + -
625C ALA 3.5 21.3 + - - -
626C TRP* 3.5 50.3 + + + -
631C PHE* 4.4 5.7 - - - -
640C PRO* 4.0 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 619 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615C MET 3.2 15.1 + - - +
616C LYS* 4.1 2.9 - - - +
618C TYR* 1.3 79.8 - - - +
620C GLU* 1.3 59.2 + - - +
623C GLY* 2.8 41.3 + - - +
624C ASN 3.3 24.6 - - - +
625C ALA* 4.3 13.5 - - - +
637C LYS* 4.9 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 620 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616C LYS* 2.9 29.5 + - + +
617C LEU* 3.6 16.7 - - - +
619C GLU* 1.3 77.7 - - - +
621C LYS* 1.3 84.7 + - - +
637C LYS* 4.1 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 621 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C LEU* 4.1 9.4 - - + -
570C TYR* 3.8 44.4 - - + -
617C LEU* 3.1 24.2 + - - +
618C TYR* 2.9 3.4 + - - +
620C GLU* 1.3 109.1 + - - +
622C THR* 1.3 59.9 + - - +
637C LYS* 3.3 10.5 - - - +
638C PHE* 2.8 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C LEU* 4.2 15.0 - - - -
618C TYR* 2.7 62.0 + - + +
621C LYS* 1.3 74.2 - - - +
623C GLY* 1.3 57.1 + - - +
624C ASN* 3.4 23.3 - - + +
631C PHE* 3.2 23.6 - - + -
634C TYR* 4.1 4.7 + - - +
637C LYS* 3.5 9.2 - - - +
638C PHE* 3.3 21.6 + - - +
640C PRO* 3.6 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 623 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619C GLU* 2.8 28.7 + - - +
621C LYS 3.6 1.0 - - - -
622C THR* 1.3 76.9 - - - +
624C ASN* 1.3 63.2 + - - +
634C TYR* 3.8 20.9 - - - -
637C LYS* 3.8 15.2 - - - +
----------------------------------------------------------
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