Contacts of the helix formed by residues 606 - 627 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B PRO* 3.1 17.7 + - + +
605B GLN* 1.3 74.1 - - - +
607B LYS* 1.3 65.7 + - - +
608B LEU 3.7 2.0 + - - -
609B LEU* 3.2 13.2 + - - +
610B ILE* 2.9 26.0 + - - +
701B EDO 2.5 36.4 + - - +
702B EDO 4.2 2.2 - - - -
4X A 3.7 36.3 - - - +
5X C 3.3 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ARG* 4.6 3.7 - - - +
584A ILE* 3.9 20.9 - - + -
581B VAL* 5.5 2.8 + - - +
584B ILE* 4.4 8.0 - - - +
585B ASN* 5.2 4.7 - - - +
588B PHE* 3.4 36.5 - - + -
606B THR* 1.3 72.5 - - - +
608B LEU* 1.3 62.8 + - - +
610B ILE 3.4 0.2 + - - -
611B LEU* 3.1 30.3 + - - +
702B EDO 3.5 18.4 - - - +
703B CL 3.4 30.4 - - + +
5X C 2.7 30.7 + - - +
6X A 2.7 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ARG* 5.8 1.1 - - + +
583A ASP* 3.4 51.1 - - + +
584A ILE* 4.0 14.0 - - + +
587A ALA* 4.1 5.6 - - + -
606B THR* 3.3 1.8 + - - -
607B LYS* 1.3 78.0 - - - +
609B LEU* 1.3 62.9 + - - +
611B LEU* 3.3 4.1 + - - +
612B HIS* 3.0 60.4 + - + +
701B EDO 3.6 37.4 + - - +
5X C 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LYS* 4.1 41.3 - - + +
604B PRO 3.4 23.3 - - - +
605B GLN* 4.1 6.3 - - - -
606B THR* 3.2 21.7 + - - +
608B LEU* 1.3 79.6 - - - +
610B ILE* 1.3 52.0 + - - +
612B HIS* 3.2 10.7 + - + +
613B GLN* 2.7 70.5 + - + +
701B EDO 3.8 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B PHE* 3.6 26.7 - - + +
589B LYS* 5.2 0.9 - - - -
591B LEU* 3.8 20.0 - - + +
592B GLY* 3.7 30.7 - - - +
595B VAL* 4.7 1.2 - - + +
605B GLN* 3.8 31.4 - - + +
606B THR 2.9 20.3 + - - +
607B LYS 3.8 4.0 - - - +
609B LEU* 1.3 74.4 - - - +
611B LEU* 1.3 59.1 + - - +
613B GLN* 3.3 7.8 + - - +
614B ALA* 2.8 29.3 + - - +
702B EDO 3.4 26.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
584A ILE* 3.6 22.9 - - + +
587A ALA* 3.7 23.1 - - + +
588A PHE* 3.6 47.3 - - + +
591A LEU* 3.7 24.2 - - + +
611A LEU* 4.0 4.5 - - + -
588B PHE* 3.7 17.3 - - + -
591B LEU* 4.8 1.1 - - + -
607B LYS 3.1 18.8 + - - +
608B LEU* 3.7 2.9 - - - +
609B LEU 3.3 0.2 - - - -
610B ILE* 1.3 76.9 - - - +
612B HIS* 1.3 63.4 + - - +
614B ALA* 3.3 4.8 + - - +
615B VAL* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ASP* 4.9 1.0 + - + -
587A ALA* 3.7 22.4 - - + +
608B LEU* 3.0 50.5 + - + +
609B LEU* 3.7 12.0 - - + +
611B LEU* 1.3 75.5 - - - +
613B GLN* 1.3 63.3 + - + +
615B VAL* 3.4 8.7 + - + +
616B ALA* 3.0 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B VAL* 3.4 27.0 - - + +
596B GLN* 5.4 0.4 + - - -
599B LEU* 3.6 27.1 - - + +
601B SER* 3.7 26.5 + - - -
603B LYS 5.6 0.2 + - - -
605B GLN* 3.4 19.3 + - - +
609B LEU* 2.7 55.8 + - + +
610B ILE* 3.7 9.8 - - - +
612B HIS* 1.3 71.4 - - + +
614B ALA* 1.3 59.9 + - - +
616B ALA* 3.2 3.5 + - - +
617B VAL* 2.8 34.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
591A LEU* 4.2 15.3 - - + -
614A ALA* 4.8 0.7 - - + -
618A ILE* 4.6 3.6 - - + -
591B LEU* 3.8 35.4 - - + -
595B VAL* 3.7 10.5 - - + +
610B ILE 2.8 21.2 + - - +
611B LEU 3.3 4.2 + - - +
613B GLN* 1.3 72.8 - - - +
615B VAL* 1.3 62.4 + - - +
617B VAL* 3.9 1.4 - - - +
618B ILE* 3.1 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ALA* 4.7 4.0 - - - +
590A GLU* 4.5 16.6 - - + +
591A LEU* 3.9 29.8 - - + +
594A MET* 3.6 30.7 - - - +
611B LEU 3.0 18.1 + - - +
612B HIS* 3.7 10.3 - - + +
614B ALA* 1.3 77.2 - - - +
616B ALA* 1.3 62.5 + - - +
618B ILE 3.5 0.2 + - - -
619B LEU* 3.0 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B LEU* 4.7 13.7 - - + -
612B HIS 3.0 16.7 + - - +
613B GLN* 3.7 6.5 - - - +
615B VAL* 1.3 78.7 - - - +
617B VAL* 1.3 57.8 + - - +
619B LEU* 3.6 7.4 + - - +
620B SER* 2.9 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ILE* 4.0 19.3 - - + -
595B VAL* 3.9 16.4 - - + -
598B HIS* 3.7 37.2 - - + -
599B LEU* 3.8 26.9 - - + -
613B GLN 2.8 20.1 + - - +
614B ALA 3.9 3.4 - - - +
615B VAL 3.3 0.2 - - - -
616B ALA* 1.3 74.0 - - - +
618B ILE* 1.3 59.3 + - - +
620B SER* 3.2 5.8 + - - -
621B LEU* 2.8 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A LEU* 3.9 23.8 - - + -
594A MET* 3.7 21.1 - - + -
595A VAL* 4.2 11.7 - - + +
598A HIS* 3.8 15.9 - - + +
614A ALA* 4.6 3.8 - - + +
617A VAL* 4.0 17.3 - - + -
618A ILE* 3.7 24.2 - - + -
621A LEU* 3.9 12.7 - - + +
614B ALA 3.1 18.8 + - - +
617B VAL* 1.3 75.7 - - - +
619B LEU* 1.3 58.0 + - - +
621B LEU* 3.3 2.8 + - - +
622B GLU* 2.9 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A GLU* 5.5 3.4 - - - +
594A MET* 3.7 19.3 - - + -
615B VAL* 3.0 38.3 + - + +
616B ALA* 4.0 6.1 - - - +
618B ILE* 1.3 75.3 - - - +
620B SER* 1.3 61.7 + - - +
622B GLU* 3.5 22.9 + - - +
623B GLN* 3.4 19.6 + - - +
626B ARG* 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B HIS* 6.6 0.4 - - - -
599B LEU* 6.2 3.1 - - - -
616B ALA 2.9 19.7 + - - -
617B VAL* 3.2 6.9 + - - -
619B LEU* 1.3 75.2 - - - +
621B LEU* 1.3 65.0 + - - +
623B GLN* 3.3 6.6 + - - +
624B GLN* 3.2 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ILE* 3.9 20.4 - - + +
621A LEU* 3.7 33.0 - - + +
622A GLU* 3.9 13.7 - - + -
625A VAL* 4.1 11.3 - - + +
598B HIS* 3.6 21.8 - - + +
617B VAL* 2.8 38.3 + - + +
618B ILE 3.9 4.0 - - - +
620B SER* 1.3 69.9 - - - +
622B GLU* 1.3 64.4 + - - +
624B GLN* 3.4 27.9 + - - +
625B VAL* 3.2 27.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
594A MET* 4.8 3.6 - - - +
598A HIS* 2.3 48.2 + - + +
621A LEU* 4.5 2.7 - - + -
618B ILE* 2.9 28.0 + - + +
619B LEU* 3.6 27.6 - - - +
620B SER 3.2 0.2 - - - -
621B LEU* 1.3 77.2 - - - +
623B GLN* 1.3 62.6 + - - +
625B VAL* 3.2 16.9 + - - +
626B ARG* 3.3 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 623 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B LEU 3.4 8.5 + - - +
620B SER* 3.3 9.4 + - - +
622B GLU* 1.3 77.3 - - - +
624B GLN* 1.3 65.7 + - + +
626B ARG* 3.1 39.6 + - - +
627B GLU* 3.1 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 624 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A VAL* 3.4 34.7 - - + +
598B HIS* 5.3 3.8 + - - -
620B SER* 3.2 32.5 + - - +
621B LEU* 3.7 27.3 - - - +
622B GLU 3.3 0.4 - - - -
623B GLN* 1.3 78.0 - - + +
625B VAL* 1.3 60.3 + - - +
627B GLU* 3.5 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 625 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A LEU* 4.6 10.1 - - + +
624A GLN* 4.1 34.5 - - + +
625A VAL* 3.8 18.6 - - + +
621B LEU 3.2 15.7 + - - +
622B GLU* 3.2 8.0 + - - +
623B GLN 3.2 0.6 - - - -
624B GLN* 1.3 77.7 - - - +
626B ARG* 1.3 62.7 + - + +
627B GLU 3.3 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 626 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B LEU 5.4 0.2 + - - -
622B GLU* 3.3 46.5 + - - +
623B GLN* 3.1 42.2 + - - +
625B VAL* 1.3 77.6 - - + +
627B GLU* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 627 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B GLN* 3.1 39.6 + - - +
624B GLN* 3.5 19.3 - - - +
625B VAL 3.2 13.0 - - - +
626B ARG* 1.3 80.2 - - - +
----------------------------------------------------------
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