Contacts of the helix formed by residues 665 - 685 (chain A) in PDB entry 6FWF
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 ASP 665 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A ARG* 3.0 37.0 + - - -
592A TRP* 3.2 29.5 - - + -
663A PHE 4.0 7.0 - - - +
664A ASP* 1.3 76.9 + - - +
666A LYS* 1.3 61.2 + - - +
667A LEU 3.6 0.4 - - - -
668A MET* 3.5 27.0 - - + +
669A THR* 3.9 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ASP* 3.9 13.8 + - - +
665A ASP* 1.3 74.4 - - - +
667A LEU* 1.3 59.4 + - + +
668A MET 3.1 1.6 - - - -
669A THR* 2.7 26.9 + - - +
670A TRP* 2.8 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ASP* 4.1 12.3 - - - +
665A ASP* 4.4 0.2 - - - +
666A LYS* 1.3 80.5 - - + +
668A MET* 1.3 53.7 + - - +
670A TRP* 3.5 22.1 - - + +
671A GLY* 2.8 29.2 + - - -
737A CYS* 3.9 21.5 - - + +
738A VAL* 4.3 4.0 - - - +
740A ILE* 4.1 12.3 - - + -
741A GLN* 3.5 45.1 - - + +
744A LYS* 4.0 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A TRP* 3.6 34.5 - - + +
651A LEU* 3.6 24.5 - - + -
663A PHE* 4.1 9.9 - - - -
664A ASP 4.2 1.1 - - - +
665A ASP* 3.5 32.8 - - + +
667A LEU* 1.3 77.7 - - - +
669A THR* 1.3 54.6 + - + +
671A GLY* 3.3 2.5 + - - -
672A PHE* 2.8 54.7 + - + -
738A VAL* 4.9 15.9 - - + +
741A GLN* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A ARG* 5.7 6.3 - - - +
665A ASP 3.9 11.4 - - - +
666A LYS* 2.7 30.0 + - - +
668A MET* 1.3 75.2 - - + +
670A TRP* 1.3 56.3 + - - +
672A PHE* 3.6 11.8 - - + +
673A TRP* 2.8 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A LYS* 2.8 54.9 + - + +
667A LEU* 3.5 20.6 - - + +
669A THR* 1.3 73.4 + - - +
671A GLY* 1.3 54.1 + - - +
673A TRP* 3.9 4.4 - - + +
674A LEU* 2.8 77.4 + - + +
737A CYS* 3.7 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A LEU 2.8 21.9 + - - -
668A MET 3.6 1.8 - - - -
670A TRP* 1.3 71.5 - - - +
672A PHE* 1.3 56.6 - - - +
675A LEU* 2.8 41.2 + - - +
734A GLY* 3.9 12.1 - - - -
737A CYS* 4.0 2.6 - - - +
738A VAL* 3.7 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A TRP* 3.6 44.9 - + + -
595A MET* 4.0 16.6 - - + -
596A CYS* 3.5 39.7 - - - -
599A ALA* 6.0 0.2 - - + -
644A PHE* 4.9 10.1 - + - -
668A MET* 2.8 39.8 + - + +
669A THR* 3.3 11.9 + - + +
671A GLY* 1.3 72.3 - - - +
673A TRP* 1.3 58.7 + - + +
675A LEU* 5.0 0.9 - - + -
676A ASN* 2.8 55.4 + - - +
738A VAL* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A THR* 2.8 33.3 + - - +
670A TRP* 4.0 5.8 - - + +
672A PHE* 1.3 74.3 - - + +
674A LEU* 1.3 60.6 + - + +
676A ASN* 5.1 1.3 - - - -
677A GLY* 2.8 33.3 + - - +
730A ILE* 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A TRP* 2.8 56.5 + - + +
673A TRP* 1.3 72.7 - - + +
675A LEU* 1.3 59.1 + - - +
678A GLY* 2.8 27.0 + - - -
730A ILE* 3.3 40.6 - - + +
733A GLY* 3.8 5.4 - - - -
734A GLY* 3.3 18.6 - - - +
737A CYS* 3.5 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 4.0 1.1 - - + -
639A PHE* 3.8 18.8 - - + -
644A PHE* 4.1 18.4 - - + -
647A LEU* 4.1 16.6 - - + -
671A GLY 2.8 29.6 + - - +
672A PHE* 4.2 0.4 - - + +
674A LEU* 1.3 72.4 - - - +
676A ASN* 1.3 56.9 + - - +
679A LEU* 2.8 30.7 + - - +
731A PHE* 3.2 43.9 - - + +
734A GLY 3.6 15.3 - - - +
735A ALA* 3.3 23.6 - - - +
738A VAL* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A ALA* 4.5 10.1 - - - +
603A TRP* 3.7 18.9 + - + +
644A PHE* 3.1 32.9 - - - -
672A PHE* 2.8 51.7 + - - +
673A TRP* 4.5 1.1 - - - +
675A LEU* 1.3 70.3 - - - +
677A GLY* 1.3 54.4 + - - +
679A LEU* 3.7 4.9 - - - +
680A VAL* 2.8 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A TRP* 2.8 29.2 + - - -
676A ASN* 1.3 71.7 - - - +
678A GLY* 1.3 54.2 + - - +
680A VAL* 3.5 10.0 - - - +
681A GLY* 2.8 30.7 + - - -
727A ALA* 5.0 0.5 - - - +
730A ILE* 4.5 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A LEU 2.8 22.1 + - - -
675A LEU 3.7 0.9 - - - -
677A GLY* 1.3 72.6 - - - +
679A LEU* 1.3 52.1 + - - +
682A MET* 2.8 36.0 + - - +
727A ALA* 3.3 29.7 - - - +
730A ILE* 3.8 5.8 - - - +
731A PHE* 3.9 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 679 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A TRP* 3.7 34.1 - - + -
635A HIS* 3.8 36.6 - - + +
636A ALA 4.4 0.7 - - - +
639A PHE* 4.4 5.8 - - + -
640A GLY* 4.0 21.1 - - - +
644A PHE* 4.1 15.0 - - + -
675A LEU 2.8 21.5 + - - +
676A ASN* 3.7 5.2 - - - +
678A GLY* 1.3 69.6 - - - +
680A VAL* 1.3 62.3 + - - +
681A GLY 3.1 1.1 - - - -
682A MET* 3.2 7.3 + - + +
683A ILE* 2.8 41.5 + - + +
731A PHE* 3.6 15.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 680 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A TRP* 4.4 13.6 - - + -
676A ASN 2.8 25.8 + - - +
677A GLY* 3.5 12.1 - - - +
679A LEU* 1.3 75.2 - - - +
681A GLY* 1.3 57.8 + - - +
683A ILE* 3.6 16.1 - - + +
684A ALA* 2.8 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 681 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A GLY 2.8 22.6 + - - -
678A GLY 3.7 0.7 - - - -
679A LEU 3.1 0.2 - - - -
680A VAL* 1.3 77.9 - - - +
682A MET* 1.3 57.0 + - - +
684A ALA* 4.8 0.9 - - - -
685A ILE* 2.8 50.2 + - - +
727A ALA* 3.6 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A HIS* 3.8 28.9 - - + -
678A GLY 2.8 19.8 + - - +
679A LEU* 3.7 15.3 - - + +
681A GLY* 1.3 71.8 - - - +
683A ILE* 1.3 65.4 + - + +
686A SER* 3.8 10.0 - - - -
687A LEU* 3.4 30.5 + - + +
724A ARG* 3.6 24.9 - - + +
727A ALA* 3.3 10.9 - - + +
728A ASP* 3.3 26.5 - - - +
731A PHE* 4.6 9.2 - - + -
1002A HEM 3.5 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A TRP* 3.6 28.3 - - + -
606A ILE* 5.8 3.8 - - + -
611A PHE* 5.5 5.8 - - + -
632A VAL* 4.0 45.0 - - + +
635A HIS* 4.4 6.7 - - + -
636A ALA* 4.6 2.7 - - + -
679A LEU* 2.8 41.5 + - + +
680A VAL* 3.6 17.7 - - + +
682A MET* 1.3 80.0 - - + +
684A ALA* 1.3 57.1 + - + +
687A LEU* 4.4 7.0 - - + -
688A LEU* 3.6 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A VAL* 2.8 30.5 + - + +
681A GLY* 4.1 1.3 - - - +
683A ILE* 1.3 76.2 - - + +
685A ILE* 1.3 67.5 + - + +
686A SER 3.3 1.1 - - - -
688A LEU* 3.9 9.9 - - + +
689A PRO* 3.1 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A GLY* 2.8 33.8 + - - +
684A ALA* 1.3 77.0 - - + +
686A SER* 1.3 65.9 + - - +
689A PRO* 3.1 17.0 - - - +
720A LEU* 3.3 13.7 - - + +
723A VAL* 4.2 31.0 - - + +
726A ALA* 5.9 3.4 - - + -
727A ALA* 5.0 10.1 - - + +
----------------------------------------------------------
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