Contacts of the helix formed by residues 595 - 616 (chain A) in PDB entry 1Q6X
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 SER 595 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ASP* 3.9 9.5 + - - -
570A TYR* 2.9 15.3 + - - -
587A SER* 4.1 0.4 + - - -
594A THR* 1.3 76.4 - - - +
596A SER* 1.3 64.2 + - - +
597A VAL* 3.8 6.9 + - - +
598A GLU* 3.5 36.0 + - - +
599A PHE* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ASP* 2.8 42.4 + - - -
403A PHE 4.6 0.2 - - - -
404A ILE* 3.9 9.8 - - - +
570A TYR* 4.3 1.8 - - - -
585A ILE* 3.8 28.0 - - - +
586A SER 3.3 4.7 - - - -
587A SER* 2.7 28.6 + - - -
595A SER* 1.3 72.1 - - - +
597A VAL* 1.3 61.8 + - - +
599A PHE 3.7 0.2 + - - -
600A ALA* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ASP* 4.7 11.4 - - - +
403A PHE 6.1 0.2 - - - +
404A ILE* 4.4 25.8 - - + -
595A SER* 3.3 6.4 + - - +
596A SER* 1.3 73.9 - - - +
598A GLU* 1.3 65.5 + - - +
600A ALA* 3.3 6.2 + - + +
601A GLU* 3.1 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 4.1 26.2 - - + +
570A TYR* 5.8 0.4 - - - +
595A SER* 3.4 28.2 + - - +
597A VAL* 1.3 78.0 - - - +
599A PHE* 1.3 58.6 + - - +
601A GLU* 3.4 11.4 + - - +
602A ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 4.1 25.1 - - + -
434A ALA* 4.0 3.8 - - + -
435A TYR* 3.9 37.2 - + - -
438A LEU* 3.8 19.9 - - + +
439A TYR* 5.2 0.2 - + - -
547A LEU* 4.4 20.2 - - + -
570A TYR* 3.6 32.5 - + + +
572A ALA* 4.8 7.4 - - + -
585A ILE* 3.8 24.2 - - + -
595A SER 3.1 16.4 + - - +
596A SER 4.0 2.7 - - - +
598A GLU* 1.3 74.0 - - - +
600A ALA* 1.3 60.6 + - - +
602A ALA* 3.1 2.6 + - - +
603A VAL* 2.9 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ILE* 4.4 8.5 - - + -
406A TYR* 3.7 37.5 - - + -
585A ILE* 3.5 23.0 - - + +
596A SER 3.1 19.2 + - - +
597A VAL* 3.6 6.3 - - + +
599A PHE* 1.3 76.9 - - - +
601A GLU* 1.3 57.9 + - + +
603A VAL* 3.0 6.7 + - - +
604A GLY 2.9 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 4.6 15.0 - - + -
597A VAL* 3.1 32.4 + - + +
598A GLU* 3.8 11.4 - - - +
600A ALA* 1.3 78.1 - - + +
602A ALA* 1.3 57.3 + - - +
604A GLY* 3.3 1.0 + - - +
605A ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ALA* 3.7 25.8 - - + +
437A ARG* 3.9 9.9 - - + +
438A LEU* 3.8 17.3 - - + -
598A GLU 2.9 15.2 + - - +
599A PHE 3.1 8.7 + - - +
601A GLU* 1.3 74.6 - - - +
603A VAL* 1.3 62.5 + - - +
605A ALA* 3.5 6.3 + - - +
606A SER* 2.9 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 5.4 2.0 - - + -
430A ALA* 5.2 5.8 - - + -
431A LEU* 3.8 12.8 - - + -
434A ALA* 3.7 18.8 - - + -
583A PHE* 3.8 40.4 - - + -
585A ILE* 4.5 5.2 - - + -
599A PHE* 2.9 41.2 + - + +
600A ALA* 3.4 9.9 - - - +
602A ALA* 1.3 76.0 - - - +
604A GLY* 1.3 65.0 + - - +
606A SER* 3.3 4.1 + - - -
607A LEU* 3.1 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 3.5 28.9 - - - -
408A PHE* 4.0 11.6 - - - -
600A ALA 2.9 10.3 + - - -
601A GLU 3.3 2.0 + - - -
603A VAL* 1.3 77.1 - - - +
605A ALA* 1.3 62.2 + - - +
607A LEU* 3.0 14.1 + - - +
608A VAL* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 3.7 23.6 - - - +
601A GLU 2.9 16.8 + - - +
602A ALA* 3.8 7.0 - - - +
604A GLY* 1.3 73.9 - - - +
606A SER* 1.3 58.1 + - - +
608A VAL* 3.2 8.1 + - - +
609A ASP* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ALA* 3.8 20.2 - - - -
433A LEU* 3.2 24.6 - - - +
434A ALA* 3.3 9.9 + - - -
437A ARG* 3.2 17.0 + - - +
602A ALA 2.9 21.4 + - - -
603A VAL 3.5 6.1 - - - -
604A GLY 3.2 0.2 - - - -
605A ALA* 1.3 77.2 - - - +
607A LEU* 1.3 56.9 + - - +
609A ASP* 3.5 1.5 + - - +
610A MET* 3.0 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 6.1 0.2 - - + -
408A PHE* 3.4 47.1 - - + -
411A TYR* 2.6 37.7 + - + +
426A PHE* 3.9 16.4 - - + -
427A ILE* 5.1 4.7 - - + -
430A ALA* 3.7 24.0 - - + -
581A ILE* 4.4 8.7 - - + -
583A PHE* 3.9 25.1 - - + -
603A VAL* 3.1 19.4 + - + +
604A GLY* 3.0 5.1 + - - +
606A SER* 1.3 73.5 - - - +
608A VAL* 1.3 64.6 + - - +
610A MET* 4.5 1.6 - - - -
611A ARG 3.2 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PHE* 4.2 15.3 - - + -
410A ASN* 4.7 13.2 - - - +
411A TYR* 5.0 1.3 - - - -
604A GLY 3.1 16.0 + - - +
605A ALA* 3.6 8.1 - - - +
607A LEU* 1.3 75.7 - - - +
609A ASP* 1.3 68.7 + - - +
611A ARG* 3.2 19.3 + - - +
612A ASP* 3.1 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LEU* 4.8 3.3 - - + +
437A ARG* 3.0 31.2 + - - +
476A MET* 4.2 21.2 - - + +
477A THR* 5.8 1.6 - - - +
605A ALA* 2.9 20.2 + - - +
606A SER* 3.7 6.3 - - - +
608A VAL* 1.3 82.1 - - - +
610A MET* 1.3 60.9 + - - +
612A ASP* 3.3 10.4 + - - +
613A LEU* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PHE* 3.7 56.1 - - + +
429A VAL* 3.9 20.6 - - + -
430A ALA* 3.6 28.9 - - - -
433A LEU* 4.5 8.1 - - + -
472A PHE* 4.3 24.2 - - + -
476A MET* 4.9 1.1 - - + -
492A LEU* 4.6 11.9 - - + +
496A MET* 5.5 0.7 - - - -
606A SER 3.0 25.6 + - - +
607A LEU* 4.0 3.1 - - - +
608A VAL 3.2 0.2 - - - -
609A ASP* 1.3 76.0 - - - +
611A ARG* 1.3 62.2 + - - +
613A LEU* 3.5 8.7 + - - +
614A CYS* 3.3 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ASN* 3.5 45.9 + - - +
411A TYR* 3.7 28.0 - - + +
415A PHE* 3.3 34.9 - - + -
607A LEU 3.2 16.2 + - - +
608A VAL* 3.2 19.9 + - - +
610A MET* 1.3 74.3 - - - +
612A ASP* 1.3 72.3 + - - +
614A CYS* 3.2 3.8 + - - +
615A SER* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A VAL* 3.1 30.6 + - - +
609A ASP* 3.7 11.9 - - - +
611A ARG* 1.3 85.7 + - - +
613A LEU* 1.3 61.7 + - - +
615A SER* 3.4 8.9 + - - -
616A SER* 3.3 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PHE* 3.9 19.3 - - + -
476A MET* 4.0 13.0 - - + -
485A ALA* 3.9 25.1 - - + +
488A LYS* 3.8 37.7 - - + +
489A LEU* 3.6 17.9 - - + +
492A LEU* 3.8 24.7 - - + -
609A ASP 3.1 12.8 + - - +
610A MET* 3.6 9.6 - - - +
611A ARG 3.1 0.4 - - - -
612A ASP* 1.3 78.9 - - - +
614A CYS* 1.3 59.6 + - - +
616A SER* 3.2 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PHE* 4.4 2.9 - - + -
419A GLN* 3.1 47.2 + - + +
421A TYR* 4.4 16.8 - - - -
426A PHE* 4.6 9.6 - - - -
489A LEU* 4.1 11.9 - - - -
492A LEU* 4.5 12.6 - - - -
610A MET 3.3 14.6 + - - +
611A ARG 3.2 7.6 + - - +
613A LEU* 1.3 79.5 - - - +
615A SER* 1.3 60.8 - - - +
617A ARG* 3.4 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PHE* 4.9 5.5 - - - -
419A GLN* 5.6 0.9 - - - +
611A ARG* 3.0 25.5 + - - +
612A ASP* 3.7 10.6 + - - -
613A LEU 3.2 0.2 - - - -
614A CYS* 1.3 72.4 - - - +
616A SER* 1.3 56.2 + - - +
617A ARG 3.1 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ALA* 3.5 29.0 - - - +
489A LEU* 4.5 5.5 - - - +
612A ASP 3.3 11.8 + - - -
613A LEU* 3.5 15.3 - - - -
614A CYS 3.1 0.8 - - - -
615A SER* 1.3 75.9 - - - +
617A ARG* 1.3 57.3 + - - +
----------------------------------------------------------
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