Contacts of the helix formed by residues 609 - 632 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B GLY* 2.8 17.2 + - - -
608B ALA* 1.3 82.4 - - - +
610B ARG* 1.3 65.3 + - - -
611B LEU 3.5 1.6 - - - -
612B SER 4.4 0.2 - - - -
613B ALA* 3.2 19.2 + - - +
724B ALA* 5.5 2.2 - - - -
728B TYR* 3.4 29.3 - - - -
792B LEU 4.3 5.4 - - - -
793B GLY* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B TYR* 4.0 18.6 + - - +
602B SER* 4.5 5.3 - - - +
605B GLY* 4.1 11.2 + - - -
609B GLY* 1.3 70.9 - - - -
611B LEU* 1.3 62.2 + - - +
613B ALA* 3.0 4.6 + - + +
614B ALA* 2.8 34.1 + - + +
642B GLY* 2.6 35.4 + - - -
644B THR* 4.6 8.5 - - - +
789B PRO 4.4 6.7 + - - +
790B VAL* 3.3 45.5 - - - +
792B LEU 4.6 6.0 + - - +
794B VAL* 5.5 2.5 - - + -
825B THR* 5.5 3.7 + - - +
828B LEU* 3.6 31.1 - - - +
829B LEU* 4.3 10.5 - - + -
970B GLY* 4.1 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B GLY 3.5 0.8 - - - -
610B ARG* 1.3 79.6 - - - +
612B SER* 1.3 63.5 + - - +
614B ALA* 3.3 8.5 + - + +
615B TRP* 3.2 20.6 + - - +
717B MET* 4.4 20.0 - - + -
720B MET* 4.4 17.5 - - + +
721B ALA* 5.7 0.7 - - - -
724B ALA* 4.4 11.4 - - + +
792B LEU 5.7 0.2 + - - -
793B GLY 5.6 0.2 - - - -
794B VAL* 3.9 27.6 - - + +
797B ALA* 3.8 29.2 - - + -
798B PHE* 4.7 14.1 - - + -
821B PHE* 5.9 1.1 - - + -
822B PHE* 5.2 10.1 - - + -
825B THR* 5.5 5.6 - - - +
826B LEU* 5.2 10.3 - - + -
829B LEU* 6.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU* 4.2 11.8 - - - +
608B ALA 3.6 9.3 + - - -
609B GLY 3.9 1.6 + - - -
610B ARG 3.3 0.2 - - - -
611B LEU* 1.3 75.0 - - - +
613B ALA* 1.3 67.1 + - - +
615B TRP* 3.3 1.7 + - - +
616B GLN* 2.9 26.3 + - - +
721B ALA* 2.8 45.8 + - - +
724B ALA* 3.6 10.3 - - - +
725B THR* 2.9 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU* 4.0 12.5 - - + +
571B LEU* 4.6 2.9 - - - +
601B TYR* 4.7 3.4 - - - +
604B SER* 3.6 17.2 - - - +
605B GLY* 3.6 24.5 - - - +
609B GLY 3.2 18.3 + - - +
610B ARG* 3.0 5.7 + - + +
612B SER* 1.3 78.4 - - - +
614B ALA* 1.3 62.7 + - - +
616B GLN* 4.0 0.9 - - - +
617B LEU* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B TYR* 6.1 7.0 - - + -
610B ARG* 2.8 24.8 + - + +
611B LEU* 3.6 9.9 - - + +
612B SER 3.2 0.2 - - - -
613B ALA* 1.3 74.3 - - - +
615B TRP* 1.3 60.7 + - - +
617B LEU* 3.4 5.6 + - - +
618B TYR 3.1 17.5 + - - -
821B PHE* 3.7 14.9 - - + -
825B THR* 4.2 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B LEU 3.2 12.1 + - - +
612B SER* 4.0 4.3 - - - +
614B ALA* 1.3 73.6 - - - +
616B GLN* 1.3 65.8 + - - +
618B TYR* 3.4 23.2 + + + -
619B ARG* 3.2 52.9 + - + +
714B ARG* 4.0 42.0 - - + -
717B MET* 3.4 53.1 - - + +
718B ASP* 2.8 25.8 + - - +
721B ALA* 4.3 9.0 - - + -
819B TRP* 3.6 28.5 - + - -
821B PHE* 4.0 16.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU* 3.6 24.6 - - + +
571B LEU* 3.7 38.4 + - + -
572B GLN* 3.5 32.0 + - + +
612B SER 2.9 17.9 + - - +
613B ALA 4.1 0.9 - - - +
615B TRP* 1.3 77.9 - - - +
617B LEU* 1.3 57.5 + - - +
619B ARG* 2.9 34.8 + - - +
620B ALA* 3.0 26.1 + - - +
623B GLU* 5.6 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B LEU* 4.4 17.2 - - + +
599B VAL* 3.5 35.7 - - + -
600B GLY 3.9 18.8 - - - +
601B TYR* 4.1 26.7 - - + +
613B ALA 3.1 19.5 + - - +
614B ALA* 3.7 6.7 - - - +
615B TRP 3.2 0.2 - - - -
616B GLN* 1.3 73.9 - - - +
618B TYR* 1.3 66.4 + - - +
620B ALA* 3.2 4.5 + - + +
621B GLN* 2.9 68.2 + - + +
659B GLN* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B ALA 3.1 14.3 + - - +
615B TRP* 3.4 31.4 + + + +
617B LEU* 1.3 77.1 - - - +
619B ARG* 1.3 58.9 + - - +
621B GLN* 3.4 11.6 + - - +
622B GLU* 3.0 51.5 + - - +
658B SER 4.2 10.8 - - - -
660B PRO* 3.6 31.7 - - + +
661B PRO* 3.8 18.4 - - - +
706B PRO* 5.7 1.6 - - + +
707B VAL 4.8 1.7 + - - -
709B PRO* 3.6 33.9 - - + +
714B ARG* 4.9 0.4 - - - -
819B TRP* 4.5 5.6 + + - -
821B PHE* 3.9 32.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B TRP* 3.2 61.9 + - + +
616B GLN* 2.9 39.6 + - - +
617B LEU 3.2 0.6 - - - -
618B TYR* 1.3 75.6 - - - +
620B ALA* 1.3 59.9 + - - +
622B GLU* 3.1 20.2 + - - +
623B GLU* 2.8 48.9 + - - +
714B ARG* 4.4 6.5 - - - +
718B ASP* 3.1 20.0 + - - -
721B ALA* 5.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B LEU* 3.7 40.2 - - + +
574B ALA* 5.0 0.9 - - + -
575B PRO* 4.2 8.9 - - - +
616B GLN* 3.0 21.6 + - - +
617B LEU* 3.6 4.0 - - + +
619B ARG* 1.3 76.5 - - - +
621B GLN* 1.3 56.5 + - - +
623B GLU* 4.1 1.3 - - - +
624B MET* 2.9 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 621 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B VAL* 4.8 6.0 - - + +
617B LEU* 2.9 43.1 + - + +
618B TYR* 3.6 7.2 - - - +
620B ALA* 1.3 76.1 - - - +
622B GLU* 1.3 62.7 + - - +
624B MET* 3.9 11.8 - - + +
625B ALA* 3.0 26.0 + - - +
635B LEU* 5.3 0.9 - - - +
637B LEU* 4.6 14.0 - - + +
639B HIS* 3.4 19.4 + - - -
659B GLN* 3.0 23.5 + - - +
660B PRO* 3.3 23.9 - - + +
663B THR* 3.9 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 622 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B TYR* 3.0 35.9 + - + +
619B ARG* 3.1 17.9 + - - +
621B GLN* 1.3 78.3 - - - +
623B GLU* 1.3 65.0 + - + +
625B ALA* 3.4 3.4 + - - -
626B GLN* 3.1 37.7 + - + +
660B PRO* 4.5 12.5 - - + +
661B PRO* 5.6 4.8 - - + +
709B PRO* 4.6 2.4 - - - +
714B ARG* 2.7 41.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 623 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B GLN 4.9 3.3 - - - +
575B PRO* 3.3 32.2 - - + +
616B GLN* 5.6 2.5 + - - -
619B ARG* 2.8 39.2 + - - +
620B ALA* 4.9 0.8 - - - -
622B GLU* 1.3 71.7 - - + +
624B MET* 1.3 66.8 + - - +
625B ALA 3.1 1.5 + - - -
626B GLN* 3.4 6.1 + - - +
627B VAL* 3.1 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 624 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 4.9 2.9 - - + -
571B LEU* 5.3 1.1 - - + -
574B ALA* 4.3 14.8 - - + -
575B PRO* 4.1 24.2 - - + +
578B VAL* 4.1 13.3 - - + +
582B PHE* 5.6 0.3 - - - -
597B VAL* 3.9 40.8 - - + -
599B VAL* 4.6 13.2 - - + -
620B ALA* 2.9 41.0 + - + +
621B GLN* 3.9 8.7 - - + +
623B GLU* 1.3 76.0 - - - +
625B ALA* 1.3 56.4 + - - +
627B VAL* 3.5 8.7 + - - +
628B ALA* 2.8 29.5 + - - +
635B LEU* 3.8 18.0 - - + +
637B LEU* 4.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 625 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B GLN 3.0 18.2 + - - +
622B GLU* 3.6 7.4 - - - +
623B GLU 3.1 0.2 - - - -
624B MET* 1.3 77.7 - - - +
626B GLN* 1.3 70.5 + - - +
628B ALA* 3.2 5.1 + - - +
629B LYS* 2.8 26.5 + - - +
635B LEU* 4.2 10.3 - - + -
661B PRO 5.1 0.7 - - - +
662B ASP* 3.8 27.5 - - - +
663B THR* 4.9 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 626 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B GLU* 3.1 32.0 + - + +
623B GLU* 3.4 5.7 + - - +
625B ALA* 1.3 84.2 - - - +
627B VAL* 1.3 61.1 + - - +
629B LYS* 3.7 14.2 - - + +
630B ARG* 2.9 43.9 + - + +
661B PRO 4.6 9.5 + - - -
662B ASP* 4.5 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 627 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B PRO* 4.0 19.1 - - + +
578B VAL* 4.1 7.2 - - + -
579B GLU* 3.8 38.8 - - + +
582B PHE* 4.1 11.7 - - + -
623B GLU* 3.1 17.7 + - + +
624B MET* 3.5 9.4 - - - +
626B GLN* 1.3 75.6 - - - +
628B ALA* 1.3 63.4 + - - +
630B ARG* 3.2 31.3 + - - +
631B TYR* 3.3 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 628 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B PHE* 4.0 7.0 - - + -
624B MET 2.8 18.7 + - - +
625B ALA* 3.4 5.6 - - - +
627B VAL* 1.3 76.9 - - - +
629B LYS* 1.3 63.2 + - - +
631B TYR 3.3 0.7 + - - -
632B GLY 3.0 18.5 + - - -
633B VAL* 3.0 43.9 + - + +
635B LEU* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 629 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B ALA 2.8 19.2 + - - +
626B GLN* 3.3 15.9 + - - +
628B ALA* 1.3 72.5 - - - +
630B ARG* 1.3 64.5 + - + +
632B GLY* 3.2 12.5 + - - +
633B VAL 5.0 2.0 - - - -
662B ASP* 3.4 33.9 + - - +
665B ASN* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 630 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B GLU* 3.0 40.0 + - - -
626B GLN* 2.9 30.2 + - + +
627B VAL* 3.5 23.6 - - - +
628B ALA 3.2 0.4 - - - -
629B LYS* 1.3 79.3 - - + +
631B TYR* 1.3 68.4 + - + +
632B GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 631 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B GLU* 3.1 47.8 + - + +
582B PHE* 3.5 55.2 - + + -
583B SER* 4.1 11.7 - - - -
588B MET* 3.6 25.3 - - + +
627B VAL* 3.3 18.5 + - + +
628B ALA 3.3 1.1 + - - +
630B ARG* 1.3 88.3 - - + +
632B GLY* 1.3 62.5 + - - +
633B VAL* 3.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 632 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B GLY* 4.3 8.1 - - - +
628B ALA 3.0 5.8 + - - -
629B LYS* 3.2 13.0 + - - -
630B ARG 3.3 1.2 + - - -
631B TYR* 1.3 78.3 - - - +
633B VAL* 1.3 61.4 + - - +
----------------------------------------------------------
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