Contacts of the helix formed by residues 596 - 614 (chain A) in PDB entry 3S95
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 596 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GOL 4.8 2.2 + - - -
529A LYS* 4.1 14.3 - - - +
532A VAL* 4.8 2.0 - - - -
594A ARG 3.8 1.0 + - - -
595A PRO* 1.3 77.5 - - - +
597A PHE* 1.3 61.1 + - - +
598A VAL* 3.6 9.8 + - - +
599A LYS* 3.0 26.4 + - - +
600A LEU* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ALA* 3.7 15.6 - - + +
448A MET* 3.5 33.9 - - + -
449A ALA* 3.5 23.7 - - - +
452A HIS* 3.4 39.0 + + - +
461A LEU* 4.3 0.9 - - + -
531A ASP* 3.5 30.3 - - + -
532A VAL* 3.6 14.5 - - + +
535A PHE* 3.6 35.4 - + + -
596A SER* 1.3 72.5 - - - +
598A VAL* 1.3 60.3 + - - +
600A LEU* 3.6 13.7 - - + +
601A GLU* 2.8 31.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
449A ALA* 3.6 22.8 - - + +
453A SER* 6.2 2.0 - - - -
596A SER* 3.3 9.4 + - - +
597A PHE* 1.3 77.8 - - - +
599A LYS* 1.3 65.2 + - + +
601A GLU* 3.4 6.6 + - - +
602A HIS* 2.9 35.3 + - + +
551B ASP* 5.0 1.6 - - - +
552B TYR* 3.2 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GOL 3.6 22.0 - - - +
595A PRO* 4.4 3.4 - - + -
596A SER* 3.0 25.5 + - - +
598A VAL* 1.3 78.0 - - + +
600A LEU* 1.3 58.1 + - - +
602A HIS* 3.0 5.0 + - - +
603A TRP* 2.9 59.4 + - + +
620A GLN* 2.7 22.3 + - - +
514B TYR* 3.4 21.8 + - - +
549B ASP* 2.8 33.5 + - - -
551B ASP* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ALA* 4.1 9.4 - - + -
532A VAL* 3.9 4.7 - - + -
535A PHE* 3.9 13.2 - - + -
582A ILE* 3.5 32.5 - - + -
586A CYS* 3.6 25.4 - - - -
595A PRO* 3.7 26.5 - - + +
596A SER 2.9 18.4 + - - +
597A PHE* 3.6 25.6 - - + +
599A LYS* 1.3 76.0 - - - +
601A GLU* 1.3 56.9 + - - +
603A TRP* 4.0 8.3 - - + -
604A LEU* 2.8 41.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
8A GOL 3.7 26.5 + - - +
442A LYS* 2.9 29.2 + - + +
445A ALA* 3.9 12.5 - - + +
446A SER* 2.7 40.4 + - - +
449A ALA* 4.1 10.7 - - - +
597A PHE 2.8 17.1 + - - +
598A VAL* 3.6 7.5 - - - +
600A LEU* 1.3 74.3 - - - +
602A HIS* 1.3 59.0 + - - +
604A LEU* 4.9 1.6 - - - -
605A GLU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GOL 3.5 38.6 + - - -
598A VAL* 2.9 25.8 + - + -
599A LYS 3.0 8.1 + - - +
601A GLU* 1.3 77.4 - - + +
603A TRP* 1.3 63.5 + - - +
605A GLU* 3.4 2.3 + - - +
606A THR* 2.9 30.7 + - - +
551B ASP* 3.6 47.0 + - + +
552B TYR* 3.6 32.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GOL 4.1 17.9 - - - -
582A ILE* 3.8 28.0 - - + -
585A ARG* 5.0 1.8 - - + -
595A PRO* 3.9 26.5 - - + -
599A LYS* 2.9 39.2 + - + +
600A LEU* 3.6 19.7 - - + +
602A HIS* 1.3 73.4 - - - +
604A LEU* 1.3 59.9 + - + +
606A THR* 3.3 6.8 + - - -
607A LEU* 2.9 24.4 + - - +
620A GLN* 3.0 41.7 + - + +
621A LEU* 3.6 33.5 - - + +
624A LEU* 3.9 33.0 - - + -
551B ASP* 4.3 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A VAL* 3.3 16.9 - - + +
441A ALA* 3.6 31.6 - - + +
442A LYS* 3.9 20.1 - - + +
445A ALA* 4.1 4.5 - - + -
535A PHE* 3.7 22.7 - - + -
539A LEU* 5.2 0.2 - - + -
579A PHE* 3.8 31.0 - - + -
582A ILE* 3.9 25.4 - - + -
600A LEU* 2.8 28.1 + - + +
603A TRP* 1.3 71.5 - - + +
605A GLU* 1.3 60.1 + - - +
607A LEU* 3.3 2.9 + - + -
608A ARG* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GOL 4.0 22.9 - - - +
442A LYS* 3.6 30.2 - - + +
601A GLU 3.0 19.8 + - - +
602A HIS 3.9 3.1 - - - +
604A LEU* 1.3 73.4 - - - +
606A THR* 1.3 66.1 + - - +
608A ARG* 2.8 46.5 + - - +
609A MET* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A HIS* 2.9 16.4 + - - +
603A TRP* 3.4 10.0 - - - -
605A GLU* 1.3 76.3 - - - +
607A LEU* 1.3 58.6 + - - +
609A MET* 3.3 3.3 + - - +
610A HIS* 2.8 28.4 + - - +
615A LEU* 4.1 17.0 - - + +
616A PRO 3.6 15.9 - - - +
617A LEU* 3.2 30.3 - - - +
618A GLY* 5.3 0.7 - - - -
621A LEU* 4.1 5.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
438A VAL* 3.8 29.4 - - + -
576A PRO* 4.2 15.3 - - + -
577A PRO 3.5 19.7 - - - +
578A SER* 4.0 8.1 - - - +
579A PHE* 3.8 32.3 - - + -
582A ILE* 4.6 5.4 - - + -
603A TRP 2.9 16.8 + - - +
604A LEU* 3.6 6.3 - - + +
606A THR* 1.3 75.3 - - - +
608A ARG* 1.3 64.7 + - - +
610A HIS* 3.2 11.2 + - + +
611A LEU* 3.0 22.3 + - + +
617A LEU* 3.8 19.1 - - + -
621A LEU* 4.4 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A SER* 4.1 19.6 - - - +
438A VAL* 3.7 12.9 - - + +
439A SER* 3.9 28.0 - - - +
442A LYS* 5.3 2.7 - - + -
604A LEU 2.8 17.3 + - - +
605A GLU* 2.8 45.5 + - - +
607A LEU* 1.3 77.5 - - - +
609A MET* 1.3 79.3 + - - +
611A LEU* 3.2 7.0 + - - +
612A ALA* 2.9 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A GLU* 3.0 32.8 + - + +
608A ARG* 1.3 99.8 - - - +
610A HIS* 1.3 61.7 + - - +
612A ALA* 4.3 5.8 - - + +
613A GLY* 2.8 34.0 + - - +
614A HIS 3.1 5.7 + - - -
615A LEU* 3.2 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A PRO* 4.7 13.4 - - + +
606A THR 2.8 14.5 + - - +
607A LEU* 3.3 13.5 - - + +
609A MET* 1.3 77.2 - - - +
611A LEU* 1.3 75.6 + - + +
614A HIS* 3.0 32.0 + - - -
615A LEU* 3.0 30.0 + - - +
616A PRO* 4.7 1.3 - - + +
617A LEU* 3.7 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A TRP* 4.1 7.6 - - + -
435A SER* 4.0 33.0 - - - +
438A VAL* 4.0 22.9 - - + -
576A PRO* 4.0 26.2 - - + -
577A PRO* 5.4 1.6 - - + -
607A LEU* 3.0 19.7 + - + +
608A ARG* 3.6 6.3 - - - +
610A HIS* 1.3 94.0 - - + +
612A ALA* 1.3 61.6 + - - +
614A HIS* 4.5 9.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
435A SER* 5.1 10.8 - - - -
608A ARG* 2.9 33.3 + - + +
609A MET* 4.5 6.5 - - + -
611A LEU* 1.3 78.8 - - - +
613A GLY* 1.3 58.8 + - - +
614A HIS* 3.8 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A MET* 2.8 17.3 + - - +
612A ALA* 1.3 78.3 - - - +
614A HIS* 1.3 78.6 + - - +
615A LEU* 3.1 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A HIS* 3.0 24.3 + - - -
611A LEU 4.5 8.3 + - - -
612A ALA 5.2 2.6 + - - -
613A GLY* 1.3 82.3 - - - +
615A LEU* 1.3 66.8 + - - +
616A PRO* 3.5 4.7 - - - +
----------------------------------------------------------
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