Contacts of the helix formed by residues 606 - 627 (chain F) in PDB entry 6OD3
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 THR 606 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604F PRO* 3.0 21.6 + - + +
605F GLN* 1.3 73.9 - - - +
607F LYS* 1.3 66.0 + - - +
608F LEU* 3.7 7.3 + - - +
609F LEU* 3.2 23.2 + - - +
610F ILE* 3.0 26.6 + - - +
4Y A 3.9 37.7 - - - +
5Y C 3.4 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 607 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580E ARG* 4.8 2.8 - - - +
584E ILE* 4.0 21.5 - - + -
701E CL 3.4 25.0 - - + +
581F VAL* 5.4 2.8 + - - +
584F ILE* 4.1 9.8 - - - +
585F ASN* 5.3 6.5 - - - +
588F PHE* 3.5 50.0 - - + -
606F THR* 1.3 72.3 - - - +
608F LEU* 1.3 62.9 + - - +
610F ILE* 3.3 2.3 + - + -
611F LEU* 3.2 29.4 + - - +
5Y C 2.7 33.0 + - - +
6Y A 3.0 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ARG* 5.7 0.4 - - - +
580E ARG* 6.4 0.7 - - + -
583E ASP* 3.5 51.8 - - + +
584E ILE* 4.1 13.0 - - + +
587E ALA* 4.0 7.6 - - + -
606F THR* 3.3 7.2 + - - +
607F LYS* 1.3 79.0 - - - +
609F LEU* 1.3 60.5 + - - +
611F LEU* 3.4 5.8 + - - +
612F HIS* 2.7 60.4 + - + -
605G GLN* 5.9 3.4 - - - +
578H ARG* 5.6 6.1 - - - +
5Y C 5.2 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601F SER* 5.5 0.2 - - - +
603F LYS* 4.1 20.0 - - + +
604F PRO 3.2 24.2 - - - +
605F GLN* 4.4 4.3 - - - -
606F THR* 3.2 22.4 + - - +
608F LEU* 1.3 76.9 - - - +
610F ILE* 1.3 54.6 + - - +
612F HIS* 3.1 10.5 + - + +
613F GLN* 2.7 64.5 + - + +
573H ASN* 3.8 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 610 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588F PHE* 3.5 40.2 - - + +
589F LYS* 5.5 2.5 - - + +
591F LEU* 3.8 31.6 - - + +
592F GLY* 4.0 9.9 - - - +
595F VAL* 4.7 2.0 - - + +
605F GLN* 3.5 43.7 - - + +
606F THR 3.0 18.8 + - - +
607F LYS* 3.3 4.7 + - + +
609F LEU* 1.3 75.8 - - - +
611F LEU* 1.3 56.8 + - - +
613F GLN* 3.7 9.8 - - - +
614F ALA* 2.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 611 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B MET* 3.4 11.3 - - + +
584E ILE* 3.9 13.0 - - + +
587E ALA* 3.6 31.2 - - + +
588E PHE* 3.8 34.5 - - + +
591E LEU* 3.7 26.9 - - + +
611E LEU* 4.1 11.4 - - + -
588F PHE* 3.8 18.8 - - + -
591F LEU* 4.7 1.3 - - + -
607F LYS 3.2 17.0 + - - +
608F LEU* 3.7 7.0 - - - +
609F LEU 3.2 0.2 - - - -
610F ILE* 1.3 76.3 - - - +
612F HIS* 1.3 62.3 + - - +
614F ALA* 3.5 5.5 + - - +
615F VAL* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 612 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ARG* 3.1 37.3 + - - -
571B MET* 3.6 30.5 - - + +
574B ASN* 6.1 2.7 - - - -
587E ALA* 4.4 2.0 - - + +
608F LEU* 2.7 57.9 + - + +
609F LEU* 3.5 15.5 - - + +
611F LEU* 1.3 74.2 - - - +
613F GLN* 1.3 65.1 + - - +
615F VAL* 3.3 5.2 + - - +
616F ALA* 3.2 20.8 + - - +
578H ARG* 4.7 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 613 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595F VAL* 3.3 28.3 - - + +
596F GLN* 6.4 0.2 - - - -
599F LEU* 3.5 30.6 - - + +
601F SER* 4.3 17.4 - - - -
605F GLN* 4.2 9.6 + - - +
609F LEU* 2.7 55.5 + - + +
610F ILE* 3.7 18.3 - - - +
612F HIS* 1.3 71.9 - - - +
614F ALA* 1.3 57.4 + - - +
616F ALA* 3.3 5.2 + - - +
617F VAL* 2.9 34.0 + - - +
573H ASN* 4.6 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 614 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591E LEU* 4.2 15.3 - - + -
614E ALA* 4.8 2.0 - - + -
618E ILE* 4.5 3.8 - - + -
591F LEU* 4.0 32.1 - - + -
595F VAL* 3.7 10.7 - - + +
610F ILE 2.8 16.6 + - - +
611F LEU 3.8 5.6 - - - +
612F HIS 3.2 0.2 - - - -
613F GLN* 1.3 77.7 - - - +
615F VAL* 1.3 62.0 + - - +
617F VAL* 3.4 1.2 + - - +
618F ILE* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 615 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B MET* 3.7 28.5 - - + +
572B ALA* 3.9 26.7 - - - +
590E GLU* 5.1 0.7 - - + -
591E LEU* 3.8 24.9 - - + +
594E MET* 3.6 33.0 - - + -
611F LEU 3.3 12.5 + - - +
612F HIS 3.3 7.8 + - - +
613F GLN 3.3 0.4 - - - -
614F ALA* 1.3 77.2 - - - +
616F ALA* 1.3 63.6 + - - +
618F ILE* 3.4 2.3 + - - +
619F LEU* 3.1 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 616 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B ALA* 3.8 23.2 - - + +
579B LEU* 5.4 1.0 - - - +
599F LEU* 5.4 3.4 - - + -
612F HIS 3.2 12.8 + - - +
613F GLN* 3.3 9.2 + - - +
615F VAL* 1.3 79.7 - - - +
617F VAL* 1.3 56.0 + - - +
619F LEU* 3.5 1.6 + - - +
620F SER* 2.9 31.0 + - - -
571H MET* 3.6 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 617 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618E ILE* 3.9 19.7 - - + -
594F MET 4.9 0.4 - - - +
595F VAL* 3.9 24.7 - - + +
598F HIS* 3.7 30.5 - - + -
599F LEU* 4.8 2.7 - - + -
613F GLN 2.9 21.0 + - - +
614F ALA 3.9 3.8 - - - +
616F ALA* 1.3 76.2 - - - +
618F ILE* 1.3 55.6 + - - +
620F SER* 3.3 1.0 + - - -
621F LEU* 2.9 45.8 + - + +
571H MET* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 618 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591E LEU* 4.1 22.0 - - + -
594E MET* 4.0 17.7 - - + -
595E VAL* 4.2 13.2 - - + -
598E HIS* 3.6 29.4 - - + +
614E ALA* 4.7 3.8 - - + +
617E VAL* 4.0 17.5 - - + -
618E ILE* 3.7 23.3 - - + -
621E LEU* 3.7 16.7 - - + +
614F ALA 3.0 18.5 + - - +
615F VAL 3.9 3.6 - - - +
617F VAL* 1.3 77.0 - - - +
619F LEU* 1.3 60.1 + - + +
621F LEU* 3.4 0.4 + - - -
622F GLU* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B ARG* 5.6 3.1 - - - +
572B ALA* 3.5 44.9 - - + +
575B ALA* 3.7 13.9 - - + -
576B ARG* 4.3 14.1 - - + +
579B LEU* 3.9 14.2 - - + +
594E MET* 4.4 17.0 - - + -
598E HIS* 5.7 0.7 - - - +
615F VAL* 3.1 18.3 + - + +
616F ALA 4.0 2.7 - - - +
618F ILE* 1.3 77.4 - - + +
620F SER* 1.3 61.8 + - - +
622F GLU* 3.4 22.7 + - - +
623F GLN* 3.1 22.3 + - - +
626F ARG* 5.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 620 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B LEU* 4.0 24.2 - - - +
582B ARG* 4.3 1.0 + - - -
616F ALA 2.9 20.1 + - - -
617F VAL 3.7 0.9 - - - -
619F LEU* 1.3 77.1 - - - +
621F LEU* 1.3 63.3 + - - +
623F GLN* 3.2 13.6 + - - +
624F GLN* 3.3 16.8 + - - +
570H ARG* 4.0 16.5 + - - +
571H MET* 3.5 34.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618E ILE* 3.8 16.8 - - + +
621E LEU* 3.7 24.5 - - + -
622E GLU* 3.7 28.9 - - + -
625E VAL* 4.1 11.7 - - + +
598F HIS* 3.6 23.6 - - + +
617F VAL* 2.9 36.5 + - + +
620F SER* 1.3 74.4 - - - +
622F GLU* 1.3 64.7 + - - +
624F GLN* 3.2 25.5 + - - +
625F VAL* 3.2 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 622 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598E HIS* 4.0 29.2 + - + -
621E LEU* 4.3 6.2 - - + +
618F ILE 2.9 18.6 + - - +
619F LEU* 3.5 27.9 - - - +
620F SER 3.3 0.2 - - - -
621F LEU* 1.3 75.7 - - - +
623F GLN* 1.3 62.0 + - - +
625F VAL* 3.4 10.2 + - + +
626F ARG* 3.4 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 623 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B LEU* 3.8 22.3 - - + +
582B ARG* 2.6 26.9 + - - -
583B ASP* 2.7 27.3 + - - -
619F LEU 3.1 14.1 + - - +
620F SER* 3.4 9.6 + - - +
621F LEU 3.2 0.4 - - - -
622F GLU* 1.3 75.6 - - - +
624F GLN* 1.3 64.8 + - + +
626F ARG* 3.3 40.4 + - - +
627F GLU* 3.3 12.3 + - - +
570H ARG* 5.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 624 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625E VAL* 3.8 31.6 - - + +
598F HIS* 5.6 1.4 + - - -
620F SER* 3.3 11.5 + - - +
621F LEU* 3.2 34.1 + - - +
623F GLN* 1.3 77.5 - - + +
625F VAL* 1.3 61.7 + - - +
627F GLU* 3.2 25.6 + - - +
570H ARG* 3.2 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 625 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621E LEU* 4.2 15.0 - - + +
624E GLN* 3.8 32.8 - - + +
625E VAL* 3.9 17.9 - - + +
621F LEU 3.2 15.4 + - - +
622F GLU* 3.7 8.5 - - + +
623F GLN 3.2 0.4 - - - -
624F GLN* 1.3 77.3 - - - +
626F ARG* 1.3 62.6 + - + +
627F GLU 3.3 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 626 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B LEU* 6.1 0.6 - - - +
619F LEU 5.0 1.2 + - - -
622F GLU* 3.4 43.3 + - + +
623F GLN* 3.3 42.4 + - - +
624F GLN 3.3 0.4 - - - -
625F VAL* 1.3 79.0 - - + +
627F GLU* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 627 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623F GLN 3.3 11.2 + - - +
624F GLN* 3.2 20.9 + - - +
625F VAL 3.2 5.9 - - - +
626F ARG* 1.3 81.2 - - - +
----------------------------------------------------------
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