Contacts of the helix formed by residues 589 - 613 (chain A) in PDB entry 6R7Y
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 ALA 589 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A SER* 3.2 3.6 - - - -
588A LYS* 1.3 79.6 - - - +
590A ASP* 1.3 70.0 + - - +
591A LEU 3.5 0.2 - - - -
592A ILE* 4.3 2.6 + - - -
593A LEU* 3.9 13.2 + - - +
588B LYS* 4.1 28.3 - - + +
589B ALA* 5.2 0.7 - - + +
592B ILE* 3.4 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A PHE* 5.0 8.5 - - + -
587A SER* 3.8 21.3 + - - +
589A ALA* 1.3 86.8 - - - +
591A LEU* 1.3 59.5 + - - +
592A ILE 3.3 0.4 - - - -
593A LEU* 3.4 12.2 + - - +
594A ILE* 2.9 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A GLY* 4.4 17.3 - - - +
580A VAL* 3.8 25.1 - - + +
581A ASN* 3.9 24.9 - - - +
584A PHE* 3.6 40.5 - - + -
587A SER 4.1 5.2 + - - +
588A LYS* 4.2 20.4 - - + +
589A ALA 3.5 0.2 - - - -
590A ASP* 1.3 76.5 - - - +
592A ILE* 1.3 67.4 + - + +
594A ILE* 3.3 1.4 + - + +
595A VAL* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A LYS* 3.6 20.6 + - + +
589A ALA* 4.3 4.0 + - - +
590A ASP 3.3 0.2 - - - -
591A LEU* 1.3 83.8 - - + +
593A LEU* 1.3 59.3 + - - +
595A VAL* 3.8 6.0 - - + +
596A VAL* 2.9 40.5 + - + +
589B ALA* 3.4 33.7 - - + +
592B ILE* 3.9 24.7 - - + -
593B LEU* 4.3 28.5 - - + -
596B VAL* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A ALA 3.9 16.3 + - - +
590A ASP* 3.4 15.9 + - + +
591A LEU 3.3 0.4 - - - -
592A ILE* 1.3 79.5 - - - +
594A ILE* 1.3 59.3 + - + +
596A VAL* 3.8 11.9 - - + +
597A ALA* 2.9 28.9 + - - +
592B ILE* 4.2 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A PHE* 3.7 34.5 - - + -
590A ASP* 2.9 23.0 + - + +
591A LEU* 3.9 4.9 - - + +
593A LEU* 1.3 75.6 - - + +
595A VAL* 1.3 64.0 + - + +
597A ALA* 3.3 6.7 + - + +
598A VAL* 2.9 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A CYS* 3.5 34.4 - - + +
572A ALA* 5.4 0.9 - - - -
574A ILE* 4.3 14.8 - - + -
575A GLY* 4.3 15.5 - - - +
580A VAL* 5.3 1.3 - - + -
591A LEU* 2.9 37.1 + - + +
592A ILE* 3.9 6.7 - - + +
594A ILE* 1.3 79.6 - - + +
596A VAL* 1.3 59.3 + - + +
598A VAL* 3.2 7.6 + - - +
599A GLU* 2.8 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ILE* 2.9 30.6 + - + +
593A LEU* 3.9 13.2 - - + +
595A VAL* 1.3 79.1 - - + +
597A ALA* 1.3 58.2 + - - +
599A GLU* 3.2 10.9 + - + +
600A HIS* 2.8 52.8 + - + +
592B ILE* 5.5 0.7 - - + -
593B LEU* 6.2 0.7 - - + -
596B VAL* 3.7 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A LEU 2.9 18.6 + - - +
594A ILE* 3.6 8.3 - - + +
596A VAL* 1.3 78.7 - - - +
598A VAL* 1.3 56.9 + - + +
600A HIS* 4.2 4.1 - - - +
601A ALA* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 5.6 15.7 - - + -
248A SER* 6.5 0.2 - - - -
571A CYS* 4.3 14.6 - - - -
574A ILE* 5.3 9.4 - - + -
594A ILE* 2.9 27.3 + - + +
595A VAL* 3.2 6.9 + - - +
597A ALA* 1.3 75.7 - - + +
599A GLU* 1.3 58.2 + - - +
601A ALA* 3.8 5.4 - - - +
602A LEU* 2.9 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A VAL* 3.8 16.7 - - + +
568A VAL* 4.2 12.7 - - + +
571A CYS* 3.7 24.9 - - + -
595A VAL* 2.8 17.7 + - + +
596A VAL* 3.2 15.3 + - + +
598A VAL* 1.3 77.1 - - - +
600A HIS* 1.3 71.9 + - - +
603A LEU* 3.1 48.2 + - - +
600B HIS* 2.6 41.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A VAL* 2.8 36.3 + - + +
597A ALA* 4.2 3.8 - - - +
599A GLU* 1.3 92.9 - - - +
601A ALA* 1.3 61.0 + - - +
603A LEU* 3.8 10.1 - - + +
604A ALA* 2.9 30.8 + - - +
568B VAL* 5.0 20.2 - - + +
596B VAL* 5.6 0.4 - - + -
599B GLU* 2.6 43.7 + - + -
600B HIS* 3.3 8.2 + + - -
603B LEU* 5.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ALA 2.8 19.8 + - - +
598A VAL* 3.9 5.6 - - - +
600A HIS* 1.3 77.3 - - - +
602A LEU* 1.3 59.5 + - + +
604A ALA* 4.0 4.5 - - - +
605A LEU* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA* 4.8 2.0 - - + -
248A SER* 4.0 27.1 - - - +
251A LEU* 4.0 26.7 - - + -
252A ILE* 3.8 34.5 - - + +
567A VAL* 4.3 13.7 - - + -
571A CYS* 5.1 4.9 - - - -
598A VAL* 2.9 35.2 + - + +
599A GLU 4.1 2.2 - - - +
601A ALA* 1.3 75.1 - - + +
603A LEU* 1.3 62.4 + - - +
605A LEU* 3.5 6.7 + - + +
606A LYS* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A VAL* 3.9 37.0 - - + +
567A VAL* 3.9 26.2 - - + -
568A VAL* 4.9 6.5 - - + -
599A GLU* 3.1 40.5 + - - +
600A HIS* 3.9 12.6 - - + +
601A ALA 3.4 0.2 - - - -
602A LEU* 1.3 76.9 - - - +
604A ALA* 1.3 61.9 + - - +
606A LYS* 3.4 5.0 + - + +
607A PHE* 3.1 37.9 + - + +
600B HIS* 4.8 5.2 - - + +
603B LEU* 6.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A HIS 2.9 18.7 + - - +
601A ALA* 4.1 4.5 - - - +
603A LEU* 1.3 76.9 - - - +
605A LEU* 1.3 57.3 + - - +
607A PHE* 3.5 4.6 + - - +
608A ILE* 3.1 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 3.7 30.7 - - + -
601A ALA 3.0 19.0 + - - +
602A LEU* 4.0 8.1 - - + +
604A ALA* 1.3 75.0 - - - +
606A LYS* 1.3 60.4 + - - +
608A ILE* 3.9 14.3 - - + +
609A LEU* 3.0 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 2.7 22.9 + - - +
252A ILE* 5.6 5.4 - - + +
254A SER* 3.4 0.4 + - - -
255A THR* 2.4 46.5 + - + +
560A GLU* 4.4 7.6 - - - +
563A SER* 2.4 42.9 + - - +
564A VAL* 3.8 20.2 - - + -
567A VAL* 3.7 19.7 - - + -
602A LEU* 2.8 17.6 + - - +
603A LEU* 3.8 7.0 - - + +
604A ALA 3.3 0.2 - - - -
605A LEU* 1.3 76.2 - - - +
607A PHE* 1.3 59.4 + - + +
609A LEU* 3.3 8.5 + - - +
610A ALA* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A GLU* 3.8 19.5 - - + -
564A VAL* 3.6 37.7 - - + -
603A LEU* 3.1 28.7 + - + +
604A ALA* 4.2 4.5 - - - +
606A LYS* 1.3 74.7 - - + +
608A ILE* 1.3 61.3 + - + +
610A ALA* 3.3 6.4 + - + +
611A PHE* 3.0 29.2 + - - +
607B PHE* 4.4 26.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ALA* 3.1 29.5 + - + +
605A LEU* 3.9 15.3 - - + +
607A PHE* 1.3 75.9 - - + +
609A LEU* 1.3 54.0 + - + +
611A PHE* 3.1 10.4 + - + +
612A ALA* 2.6 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 4.0 29.6 - - + +
255A THR* 4.6 8.7 - - + -
256A VAL* 4.5 14.8 - - + -
259A GLU* 4.3 1.1 - - - +
605A LEU* 3.0 34.0 + - + +
606A LYS* 3.6 7.4 - - - +
607A PHE 3.3 0.2 - - - -
608A ILE* 1.3 78.8 - - + +
610A ALA* 1.3 59.0 + - - +
612A ALA* 4.4 6.1 - - + +
613A ILE* 3.3 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A THR* 4.5 5.5 - - + +
259A GLU* 2.9 22.8 - - + +
560A GLU* 4.3 17.9 - - - +
606A LYS 3.1 16.0 + - - +
607A PHE* 3.9 8.1 - - + +
608A ILE 3.3 0.2 - - - -
609A LEU* 1.3 77.7 - - - +
611A PHE* 1.3 54.6 + - - +
612A ALA 3.5 0.2 - - - -
613A ILE 3.7 0.2 - - - +
703A CA 2.3 32.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PHE 3.0 17.3 + - - +
608A ILE* 3.6 9.6 - - + +
610A ALA* 1.3 78.0 - - - +
612A ALA* 1.3 64.0 + - - +
613A ILE 3.6 2.8 - - - +
703A CA 4.4 0.9 - - - -
554B VAL* 6.2 0.9 - - + -
557B LEU* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ILE* 2.6 27.9 + - + +
609A LEU* 4.4 7.9 - - + +
610A ALA 3.5 0.2 - - - -
611A PHE* 1.3 77.9 - - + +
613A ILE* 1.3 67.1 + - + +
614A PRO* 3.4 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 5.1 12.6 - - + -
259A GLU* 3.6 25.4 - - + +
260A LEU* 5.1 9.0 - - + -
263A ARG* 3.8 28.7 - - - +
609A LEU* 3.3 40.9 + - + +
611A PHE 4.3 2.0 - - - +
612A ALA* 1.3 77.5 - - + +
614A PRO* 1.3 68.8 - - + +
703A CA 2.6 28.8 - - - -
----------------------------------------------------------
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