Contacts of the helix formed by residues 609 - 631 (chain F) in PDB entry 6V3O
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 GLY 609 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605F GLY* 2.8 18.6 + - - -
608F ALA* 1.3 81.2 - - - +
610F ARG* 1.3 65.2 + - - -
611F LEU 3.5 1.8 - - - -
612F SER* 4.3 1.3 - - - -
613F ALA* 3.2 22.2 + - - +
724F ALA* 5.5 1.8 - - - -
728F TYR* 3.5 28.7 - - - -
789F PRO 5.4 0.2 - - - -
792F LEU 4.3 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 610 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601F TYR* 4.0 25.3 + - - +
602F SER* 5.4 0.6 - - - +
605F GLY* 4.1 10.9 + - - -
609F GLY* 1.3 71.8 - - - -
611F LEU* 1.3 61.1 + - - +
613F ALA* 3.3 2.3 + - + +
614F ALA* 2.9 36.2 + - + +
642F GLY* 2.5 37.0 + - - -
644F THR* 4.9 6.7 - - - +
789F PRO 4.3 6.7 + - - +
790F VAL* 3.3 50.5 - - - +
792F LEU 4.6 5.5 + - - -
794F VAL* 5.5 2.0 - - + -
825F THR* 5.6 9.7 + - + +
828F LEU* 4.1 20.9 - - - +
829F LEU* 4.3 8.7 - - + -
970F GLY* 4.3 15.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
609F GLY 3.5 0.2 - - - -
610F ARG* 1.3 78.5 - - - +
612F SER* 1.3 64.7 + - - +
614F ALA* 3.4 3.5 + - + +
615F TRP* 3.2 21.5 + - - +
717F MET* 4.2 19.1 - - + -
720F MET* 4.4 17.7 - - + +
721F ALA* 5.6 1.6 - - - -
724F ALA* 4.6 10.1 - - + +
792F LEU 5.8 0.2 + - - -
794F VAL* 4.0 26.7 - - + +
797F ALA* 3.9 27.6 - - + -
798F PHE* 4.7 15.9 - - + -
821F PHE* 5.9 0.7 - - + -
822F PHE* 5.1 10.1 - - + -
825F THR* 4.5 20.9 - - + -
826F LEU* 5.3 6.5 - - + -
829F LEU* 6.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 612 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568F LEU* 3.9 13.3 - - - +
608F ALA* 3.3 15.3 + - - -
609F GLY 3.8 1.0 + - - -
610F ARG 3.4 0.2 - - - -
611F LEU* 1.3 76.4 - - - +
613F ALA* 1.3 62.6 + - - +
615F TRP* 3.3 1.1 + - - +
616F GLN* 3.0 26.9 + - - +
721F ALA* 3.1 29.1 + - - +
724F ALA* 3.6 5.9 - - - +
725F THR* 2.7 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 613 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568F LEU* 3.9 11.2 - - - +
571F LEU* 4.5 3.3 - - - +
601F TYR* 4.8 3.4 - - - +
604F SER* 3.6 17.2 - - - +
605F GLY* 3.6 24.9 - - - +
609F GLY 3.2 18.0 + - - +
610F ARG* 3.7 4.5 - - + +
611F LEU 3.3 0.2 - - - -
612F SER* 1.3 79.8 - - - +
614F ALA* 1.3 63.1 + - - +
616F GLN* 3.9 1.0 - - - +
617F LEU* 3.0 25.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
601F TYR* 6.0 4.3 - - + -
610F ARG* 2.9 24.3 + - - +
611F LEU* 3.8 4.9 - - + +
612F SER 3.3 0.2 - - - -
613F ALA* 1.3 77.7 - - - +
615F TRP* 1.3 62.1 + - - +
617F LEU* 3.2 12.1 + - - +
618F TYR 3.0 18.7 + - - -
821F PHE* 3.8 24.4 - - + -
825F THR* 4.2 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 615 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611F LEU 3.2 13.4 + - - +
612F SER* 4.0 4.5 - - - +
614F ALA* 1.3 73.7 - - - +
616F GLN* 1.3 68.8 + - - +
617F LEU 3.3 0.2 + - - -
618F TYR* 3.3 22.7 + + + -
619F ARG* 3.1 42.3 + - + +
714F ARG* 4.0 39.3 - - + -
717F MET* 3.4 52.7 - - + +
718F ASP* 2.7 26.9 + - - -
721F ALA* 4.2 12.1 - - + -
819F TRP* 3.6 28.9 - + - -
821F PHE* 4.1 16.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 616 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568F LEU* 3.5 32.1 - - + +
571F LEU* 3.8 20.6 - - + +
572F GLN* 3.4 40.6 + - - +
612F SER 3.0 17.7 + - - +
613F ALA 4.0 1.3 - - - +
615F TRP* 1.3 79.9 - - - +
617F LEU* 1.3 57.0 + - - +
619F ARG* 3.4 29.1 + - - +
620F ALA* 2.9 29.9 + - - +
623F GLU* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 617 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571F LEU* 4.4 17.4 - - + +
599F VAL* 3.5 38.4 - - + -
600F GLY 5.1 5.4 - - - +
601F TYR* 3.3 48.7 - - + +
613F ALA 3.0 19.3 + - - +
614F ALA* 3.4 8.7 - - - +
615F TRP 3.1 0.4 - - - -
616F GLN* 1.3 74.0 - - - +
618F TYR* 1.3 67.4 + - - +
620F ALA* 3.1 5.6 + - + +
621F GLN* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 618 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614F ALA 3.0 12.8 + - - +
615F TRP* 3.3 30.3 + + + +
617F LEU* 1.3 76.0 - - - +
619F ARG* 1.3 58.9 + - - +
621F GLN* 3.4 12.6 + - - +
622F GLU* 3.0 53.5 + - - +
658F SER 4.2 5.6 - - - -
660F PRO* 3.7 40.1 - - + +
661F PRO* 4.0 8.7 - - - +
706F PRO* 5.6 2.0 - - + +
707F VAL 4.7 2.4 + - - -
709F PRO* 3.5 33.2 - - + +
714F ARG* 4.8 0.4 - - - -
819F TRP* 4.3 6.0 + + - -
821F PHE* 3.8 39.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 619 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572F GLN* 5.3 9.1 - - - +
615F TRP* 3.1 57.8 + - + +
616F GLN* 3.8 27.6 + - - +
618F TYR* 1.3 75.6 - - - +
620F ALA* 1.3 62.7 + - - +
622F GLU* 3.2 16.1 + - - +
623F GLU* 2.9 62.5 + - - +
714F ARG* 4.7 6.0 - - - +
718F ASP* 4.3 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 620 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571F LEU* 3.7 40.2 - - + +
574F ALA* 4.9 3.4 - - + -
575F PRO* 4.6 8.5 - - - -
616F GLN* 2.9 20.6 + - - +
617F LEU* 3.1 4.5 + - + +
619F ARG* 1.3 76.6 - - - +
621F GLN* 1.3 56.6 + - - +
623F GLU* 3.3 1.6 + - - +
624F MET* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 621 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599F VAL* 4.8 2.3 - - + +
601F TYR* 4.6 1.0 + - - -
617F LEU* 2.9 37.4 + - + +
618F TYR* 3.6 14.6 + - - +
620F ALA* 1.3 77.1 - - - +
622F GLU* 1.3 63.4 + - - +
624F MET* 3.8 12.0 - - + +
625F ALA* 3.0 25.6 + - - +
635F LEU* 5.3 1.1 - - - +
637F LEU* 3.2 33.4 - - + +
639F HIS* 3.5 12.7 - - - -
659F GLN* 3.0 22.9 + - - +
660F PRO* 3.3 27.8 - - + +
663F THR* 4.0 7.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
618F TYR* 3.0 35.7 + - + +
619F ARG* 3.2 15.6 + - - +
621F GLN* 1.3 77.9 - - - +
623F GLU* 1.3 64.1 + - + +
625F ALA* 3.5 5.9 + - - +
626F GLN* 3.3 23.8 + - - +
660F PRO* 4.5 13.6 - - + +
661F PRO* 5.7 4.5 - - + +
663F THR* 4.8 0.9 - - - -
709F PRO* 4.7 2.3 - - - +
714F ARG* 2.6 40.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 623 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572F GLN 4.8 4.0 - - - +
575F PRO* 3.3 31.5 - - + +
616F GLN* 6.1 0.2 - - - -
619F ARG* 2.9 61.6 + - - +
620F ALA* 5.0 0.7 - - - -
622F GLU* 1.3 77.5 - - + +
624F MET* 1.3 65.4 + - - +
626F GLN* 3.2 27.9 + - - +
627F VAL* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 624 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565F PHE* 5.5 0.4 - - + -
571F LEU* 5.9 0.7 - - + -
574F ALA* 4.3 12.1 - - + -
575F PRO* 4.0 23.3 - - + -
578F VAL* 4.0 24.9 - - + +
597F VAL* 4.1 25.6 - - + -
599F VAL* 4.8 10.3 - - + -
620F ALA* 2.8 34.5 + - + +
621F GLN* 3.9 9.4 - - - +
623F GLU* 1.3 76.7 - - - +
625F ALA* 1.3 57.1 + - - +
627F VAL* 3.0 10.4 - - - +
628F ALA* 3.0 29.3 + - - +
635F LEU* 3.7 13.1 - - + +
637F LEU* 4.2 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 625 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621F GLN 3.0 17.9 + - - +
622F GLU* 3.7 5.2 - - - +
623F GLU 3.2 0.4 - - - -
624F MET* 1.3 77.9 - - - +
626F GLN* 1.3 57.1 + - - +
628F ALA* 3.3 3.2 + - - +
629F LYS* 2.9 32.3 + - - +
635F LEU* 4.1 11.4 - - + +
661F PRO 5.0 2.2 - - - +
662F ASP 3.8 22.0 - - - +
663F THR* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 626 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622F GLU* 3.3 15.0 + - - +
623F GLU* 3.2 35.0 + - - +
625F ALA* 1.3 77.6 - - - +
627F VAL* 1.3 69.4 + - + +
629F LYS* 3.5 6.1 + - - +
630F ARG* 3.1 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 627 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575F PRO* 4.3 15.0 - - + +
578F VAL* 4.9 9.4 - - + -
579F GLU* 3.6 37.2 - - + +
582F PHE* 4.5 4.7 - - + -
623F GLU 3.2 11.9 - - - +
624F MET* 3.0 26.7 - - - +
626F GLN* 1.3 83.1 - - + +
628F ALA* 1.3 62.5 + - - +
630F ARG* 3.2 16.5 + - - +
631F TYR* 3.1 38.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 628 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582F PHE* 3.9 22.0 - - + -
624F MET 3.0 19.4 + - - +
625F ALA* 3.7 4.7 - - - +
627F VAL* 1.3 77.8 - - - +
629F LYS* 1.3 63.0 + - - +
631F TYR 3.3 1.9 + - - -
632F GLY 2.9 5.0 + - - -
633F VAL 2.9 42.0 + - - +
635F LEU* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 629 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625F ALA 2.9 18.1 + - - +
626F GLN* 3.8 7.6 - - - +
628F ALA* 1.3 76.2 - - - +
630F ARG* 1.3 63.5 + - + +
632F GLY* 3.2 12.6 + - - +
633F VAL 5.0 1.3 - - - -
662F ASP* 4.1 34.0 + - + +
665F ASN* 4.2 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 630 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579F GLU* 2.8 40.8 + - - -
626F GLN* 3.1 22.8 + - + +
627F VAL* 3.2 20.7 + - - +
629F LYS* 1.3 78.6 - - + +
631F TYR* 1.3 71.3 + - + +
632F GLY 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 631 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579F GLU* 3.3 30.8 + - + +
582F PHE* 3.5 42.2 - - + -
583F SER* 2.6 32.6 + - - -
588F MET* 3.7 16.7 - - + +
627F VAL* 3.1 42.3 + - + +
628F ALA 4.2 1.1 - - - +
630F ARG* 1.3 90.2 + - + +
632F GLY* 1.3 63.1 + - - +
633F VAL* 3.4 9.3 + - + +
----------------------------------------------------------
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