Contacts of the helix formed by residues 599 - 620 (chain B) in PDB entry 2PWL
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 599 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B GLN 4.5 5.8 - - - +
598B MET* 1.3 77.5 - - - +
600B PHE* 1.3 65.1 + - - +
601B LYS* 3.4 8.8 + - - +
602B ASP* 2.9 46.1 + - - +
603B LEU* 3.2 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B THR* 1.3 74.1 - - - +
601B LYS* 1.3 65.6 + - - +
603B LEU* 3.1 20.3 + - + +
604B VAL* 3.1 24.4 + - + +
697B PHE* 4.0 9.2 - + - -
727B ASN 3.7 24.7 - - - -
728B CYS* 4.4 0.4 - - - -
729B THR* 4.0 21.8 - - + -
732B LEU* 3.6 32.5 - - + -
760B ILE* 5.1 3.8 - - + -
764B THR* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B THR* 3.2 7.7 + - - +
600B PHE* 1.3 85.9 - - - +
602B ASP* 1.3 53.4 + - - +
604B VAL* 3.2 5.5 + - - +
605B SER* 2.8 35.6 + - - -
761B LEU* 3.6 23.6 - - + -
764B THR* 4.0 19.5 - - + +
765B THR* 2.6 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B GLN 4.3 2.4 - - - +
598B MET* 3.6 28.3 - - + +
599B THR* 2.9 50.0 + - - +
601B LYS* 1.3 77.0 - - - +
603B LEU* 1.3 59.1 + - - +
605B SER* 3.7 6.6 - - - -
606B CYS* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B LEU* 4.3 2.5 - - + -
598B MET* 3.9 23.8 - - + +
599B THR 3.5 13.0 - - - +
600B PHE* 3.1 13.6 + - - +
602B ASP* 1.3 76.0 - - - +
604B VAL* 1.3 63.1 + - - +
606B CYS* 3.4 5.3 + - - +
607B THR* 2.8 29.5 + - - -
696B ILE* 3.7 29.6 - - + +
697B PHE* 3.6 34.1 - - + -
699B LEU* 3.8 23.1 - - + -
727B ASN* 4.4 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B PHE* 3.1 44.5 + - + +
601B LYS* 3.2 6.7 + - - +
603B LEU* 1.3 72.3 - - - +
605B SER* 1.3 61.1 + - - +
607B THR* 3.2 7.1 + - - -
608B TYR* 2.8 28.1 + - - +
697B PHE* 4.3 2.9 - - + -
732B LEU* 4.1 13.7 - - + -
757B LEU* 4.0 15.7 - - + +
760B ILE* 4.3 9.9 - - + -
761B LEU* 3.7 38.8 - - + +
764B THR* 5.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B LYS* 2.8 24.0 + - - -
602B ASP* 3.7 9.0 - - - -
604B VAL* 1.3 74.4 - - - +
606B CYS* 1.3 56.3 + - - +
608B TYR* 3.2 2.9 + - - +
609B GLN* 2.9 51.9 + - - +
761B LEU* 3.9 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B LEU* 3.8 17.7 - - - -
576B LEU* 5.5 2.2 - - - -
598B MET* 5.2 5.6 - - + -
602B ASP 3.0 19.5 + - - +
603B LEU* 3.5 7.6 - - - +
605B SER* 1.3 77.9 - - - +
607B THR* 1.3 60.6 + - - +
609B GLN* 3.3 5.3 + - - +
610B LEU* 3.2 28.8 + - - +
640B MET* 3.7 37.4 - - + +
696B ILE* 3.6 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU 2.8 14.5 + - - -
604B VAL* 3.5 8.3 - - - -
606B CYS* 1.3 76.9 - - - +
608B TYR* 1.3 64.1 + - - +
610B LEU* 3.3 3.4 + - - -
611B ALA* 3.0 19.9 + - - +
689B PHE* 3.5 11.0 - - + -
693B MET* 3.6 32.9 - - + +
696B ILE* 3.9 16.9 - - + +
697B PHE* 3.4 16.1 - - - -
757B LEU* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B LYS* 5.2 8.1 - - - -
604B VAL 2.8 17.2 + - - +
605B SER* 3.2 8.3 + - - +
607B THR* 1.3 77.2 - - - +
609B GLN* 1.3 72.1 + - + +
611B ALA* 3.2 3.6 + - - +
612B ARG* 3.1 57.3 + - + +
754B VAL* 3.9 22.0 - - + -
757B LEU* 3.9 18.1 - - + +
758B ASP* 3.8 48.9 + - + -
761B LEU* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B LYS* 3.9 17.8 - - - +
546B ASN* 3.1 34.9 + - - +
605B SER* 2.9 38.3 + - - +
606B CYS* 3.6 5.9 - - - +
607B THR 3.3 0.2 - - - -
608B TYR* 1.3 85.2 - - + +
610B LEU* 1.3 57.7 + - - +
612B ARG* 3.4 3.9 + - - +
613B GLY 3.1 21.1 + - - -
638B ASN 3.7 14.8 + - - -
639B VAL* 3.5 9.2 - - - +
640B MET* 3.0 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ASN 5.1 0.4 - - - +
572B LEU* 4.1 11.2 - - + -
606B CYS* 3.2 26.0 + - - +
607B THR 3.8 3.8 - - - +
608B TYR 3.3 0.2 - - - -
609B GLN* 1.3 74.6 - - - +
611B ALA* 1.3 65.7 + - - +
613B GLY* 3.3 1.3 + - - +
614B MET* 3.0 28.8 + - + +
632B VAL* 3.8 18.4 - - + -
640B MET* 3.7 23.6 - - + -
642B ILE* 3.7 27.7 - - + +
689B PHE* 3.7 13.9 - - + -
692B LEU* 4.0 14.8 - - + -
696B ILE* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B THR 3.0 13.2 + - - +
608B TYR 3.2 8.9 + - - +
610B LEU* 1.3 77.5 - - - +
612B ARG* 1.3 58.8 + - - +
614B MET* 3.2 5.0 + - - +
615B GLU* 2.8 30.1 + - - +
689B PHE* 3.6 14.3 - - + -
750B PHE* 4.3 5.3 - - + +
753B LEU* 4.4 6.1 - - + -
754B VAL* 3.5 22.2 - - + +
757B LEU* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B HIS* 4.1 11.9 + - + +
545B LYS* 6.3 0.2 - - - +
546B ASN* 4.1 10.3 + - - +
608B TYR* 3.1 49.1 + - + +
609B GLN* 3.6 8.5 - - - +
610B LEU 3.2 0.2 - - - -
611B ALA* 1.3 77.2 - - - +
613B GLY* 1.3 62.7 + - - +
615B GLU* 3.2 13.6 + - - +
616B TYR* 3.0 24.1 + - - +
754B VAL* 3.5 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B HIS* 4.1 9.0 - - - -
546B ASN* 4.0 19.6 - - - +
547B ILE* 3.7 5.5 - - - +
609B GLN 3.1 11.1 + - - -
610B LEU 3.3 3.1 + - - -
611B ALA 3.3 0.2 - - - -
612B ARG* 1.3 78.1 - - - +
614B MET* 1.3 55.6 + - - +
616B TYR* 3.3 4.5 + - - +
617B LEU* 2.9 27.9 + - - +
642B ILE* 3.8 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B LEU* 3.0 19.9 + - + +
611B ALA 3.7 0.2 - - - +
613B GLY* 1.3 73.0 - - - +
615B GLU* 1.3 61.3 + - - +
617B LEU* 3.5 23.0 - - + +
618B ALA* 2.8 33.6 + - + +
622B CYS 5.3 1.1 - - - +
624B HIS* 4.3 3.6 - - + +
627B LEU* 3.7 28.3 - - + -
642B ILE* 3.6 20.9 - - + -
685B ASP* 3.4 33.7 - - + +
689B PHE* 4.4 3.6 - - + -
750B PHE* 3.4 44.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B ALA 2.8 17.2 + - - +
612B ARG* 3.2 17.6 + - - +
614B MET* 1.3 76.5 - - - +
616B TYR* 1.3 63.0 + - - +
618B ALA* 3.5 3.8 + - - +
619B SER* 3.1 23.2 + - - -
750B PHE* 3.7 17.4 - - + +
751B LYS* 3.4 40.9 - - + +
754B VAL* 3.8 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B ILE* 2.7 40.6 + - + -
542B GLY* 3.8 8.1 - - - -
543B LYS 4.0 12.3 + - - -
544B HIS* 3.4 43.5 - + + +
547B ILE* 3.4 20.0 - - + -
612B ARG 3.0 9.8 + - - +
613B GLY 3.5 6.3 - - - +
615B GLU* 1.3 77.0 - - - +
617B LEU* 1.3 64.0 + - - +
619B SER* 2.7 27.2 + - - -
620B GLN* 3.1 34.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
541B ILE* 3.4 36.8 - - + -
547B ILE* 3.4 22.7 - - + -
613B GLY 2.9 14.7 + - - +
614B MET* 3.5 33.2 - - + +
616B TYR* 1.3 76.5 - - - +
618B ALA* 1.3 57.1 + - - +
620B GLN* 2.9 20.7 + - + +
622B CYS* 3.2 36.3 + - + +
624B HIS* 4.3 14.6 - - + -
642B ILE* 4.5 5.2 - - + -
645B PHE* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B MET* 2.8 21.0 + - + +
615B GLU* 3.8 5.4 - - - +
617B LEU* 1.3 73.3 - - - +
619B SER* 1.3 57.3 + - - +
620B GLN 3.1 0.2 - - - -
621B LYS* 3.0 20.6 + - - +
622B CYS 4.0 2.2 + - - -
682B HIS* 3.5 44.7 + - + +
750B PHE* 4.4 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B GLU* 3.1 13.6 + - - -
616B TYR* 2.7 29.4 + - - -
618B ALA* 1.3 76.3 - - - +
620B GLN* 1.3 70.6 + - - +
621B LYS* 3.1 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B MET 4.3 8.8 + - - +
541B ILE* 3.4 27.8 + - + +
616B TYR* 3.1 45.7 + - + +
617B LEU* 2.9 12.1 + - - +
619B SER* 1.3 89.7 + - - +
621B LYS* 1.3 72.9 + - - +
622B CYS* 3.1 9.7 + - + +
650B ASP* 5.0 1.4 - - - +
----------------------------------------------------------
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