Contacts of the helix formed by residues 668 - 687 (chain B) in PDB entry 6AHU
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 668 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 4.1 18.3 - - - +
335B LEU* 3.8 25.1 - - + -
338B ASP* 4.4 6.5 - - - +
660B PRO 4.5 8.7 - - - +
663B PHE* 5.6 1.3 - - + -
665B ASP* 3.4 18.8 + - - +
666B CYS 3.5 0.2 - - - -
667B PRO* 1.3 81.4 - - - +
669B GLY* 1.3 64.9 + - - +
670B MET 3.3 1.8 - - - -
671B LEU* 3.3 14.5 + - - +
672B PHE* 3.4 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B GLY* 3.9 23.4 - - - +
663B PHE 4.0 7.4 - - - -
664B PRO* 4.8 3.6 - - - -
665B ASP* 2.5 27.1 + - - -
668B ALA* 1.3 74.2 - - - +
670B MET* 1.3 61.1 + - - +
671B LEU 3.3 0.2 - - - -
672B PHE 4.0 0.2 - - - -
673B ALA* 3.1 31.2 + - - +
708B TRP* 5.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 670 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B PRO* 6.1 1.6 - - - -
665B ASP 3.7 10.2 + - - +
666B CYS* 3.6 24.4 + - - +
668B ALA 3.3 0.8 - - - -
669B GLY* 1.3 80.7 - - - +
671B LEU* 1.3 65.2 + - + +
673B ALA* 4.2 4.8 - - - +
674B GLU* 3.5 22.2 + - - +
706B CYS* 5.6 10.8 - - + -
708B TRP* 4.3 18.8 - - - +
709B GLU* 3.5 34.5 - - + +
803B LEU* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 671 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 6.0 3.4 - - - +
337B GLN* 6.1 1.6 - - - +
667B PRO 3.4 22.2 - - - +
668B ALA* 3.3 7.7 + - - +
669B GLY 3.3 0.6 - - - -
670B MET* 1.3 83.2 - - + +
672B PHE* 1.3 58.0 + - - +
674B GLU* 3.8 4.8 + - + +
675B GLU* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 672 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LYS* 4.8 8.5 - - - -
218B TRP* 3.7 38.6 - + + -
334B THR* 5.9 5.4 - - + -
660B PRO* 4.8 8.5 - - + +
661B GLY* 3.6 41.1 - - - -
662B ASP* 4.0 18.2 - - - -
668B ALA 3.4 8.3 + - - +
669B GLY 3.7 0.9 + - - +
671B LEU* 1.3 77.8 - - - +
673B ALA* 1.3 57.6 + - - +
674B GLU 3.3 0.2 - - - -
675B GLU* 3.2 14.1 + - + +
676B GLN* 2.6 59.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 673 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B GLY 5.3 3.4 - - - +
669B GLY 3.1 20.2 + - - +
670B MET* 4.6 5.2 - - - +
672B PHE* 1.3 76.4 - - - +
674B GLU* 1.3 61.3 + - - +
676B GLN* 3.5 9.1 - - - +
677B ALA* 2.8 27.5 + - - +
705B CYS* 4.3 29.1 - - - +
706B CYS* 5.8 6.3 - - + -
708B TRP* 5.1 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 674 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B MET 3.5 19.6 + - - +
671B LEU* 4.0 6.1 - - + +
672B PHE 3.3 0.4 - - - -
673B ALA* 1.3 76.6 - - - +
675B GLU* 1.3 59.0 + - - +
677B ALA* 3.2 12.8 + - - +
678B LYS* 3.0 52.9 + - - +
706B CYS* 5.4 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 675 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LYS* 6.2 4.0 - - - -
218B TRP* 6.2 5.4 - - + +
671B LEU 3.1 20.3 + - - +
672B PHE* 3.5 18.4 - - + +
674B GLU* 1.3 74.8 - - - +
676B GLN* 1.3 61.2 + - - +
678B LYS* 3.4 29.2 + - - +
679B ASN* 3.1 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 676 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B PHE* 2.6 47.4 + - + +
673B ALA* 3.5 11.4 - - - +
674B GLU 3.3 0.2 - - - -
675B GLU* 1.3 73.9 - - - +
677B ALA* 1.3 59.3 + - - +
679B ASN* 3.5 17.9 + - - +
680B LEU* 3.5 44.6 + - + +
703B PRO 6.0 0.2 - - - +
705B CYS* 5.4 3.8 - - - -
872B HIS* 4.3 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 677 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B ALA 2.8 16.8 + - - +
674B GLU* 3.2 18.8 + - - +
676B GLN* 1.3 75.8 - - - +
678B LYS* 1.3 60.0 + - - +
679B ASN 3.4 0.2 - - - -
680B LEU 4.4 0.4 - - - -
681B LEU* 3.2 27.9 + - - +
704B PHE* 3.3 33.7 - - + -
705B CYS 6.1 0.4 - - - +
706B CYS* 5.7 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 678 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B GLU* 3.0 41.3 + - - +
675B GLU* 3.8 26.2 + - - +
676B GLN 3.3 0.8 - - - -
677B ALA* 1.3 77.1 - - - +
679B ASN* 1.3 64.6 + - - +
681B LEU* 4.3 4.4 - - - +
682B GLU* 3.6 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 679 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LYS* 6.2 2.4 - - - +
675B GLU* 3.1 34.4 + - - +
676B GLN* 3.5 15.1 + - - +
677B ALA 3.4 0.4 - - - -
678B LYS* 1.3 80.2 - - - +
680B LEU* 1.3 69.2 + - + +
682B GLU* 3.4 7.1 + - - +
683B LYS* 3.1 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 680 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B GLN* 3.5 40.5 + - + +
679B ASN* 1.3 83.8 - - + +
681B LEU* 1.3 60.9 + - - +
683B LYS* 3.5 22.1 - - + +
684B TYR* 2.7 28.6 + - - +
703B PRO* 3.7 34.3 - - + +
704B PHE* 4.3 11.2 - - + -
872B HIS* 4.7 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 681 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B ALA 3.2 21.3 + - - +
678B LYS* 4.7 3.8 - - + +
679B ASN 3.4 0.4 - - - -
680B LEU* 1.3 75.5 - - - +
682B GLU* 1.3 61.8 + - - +
684B TYR* 4.1 9.6 - - + -
685B LYS* 3.0 45.7 + - + +
704B PHE* 3.6 24.7 - - + -
947B LEU* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 682 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B LYS 3.6 14.8 + - - +
679B ASN* 3.4 10.9 + - - +
680B LEU 3.3 0.4 - - - -
681B LEU* 1.3 79.3 - - - +
683B LYS* 1.3 56.1 + - + +
685B LYS* 3.6 5.6 + - - +
686B ARG* 3.1 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B ASN* 3.1 21.6 + - - +
680B LEU* 3.3 24.0 + - + +
681B LEU 3.3 0.2 - - - -
682B GLU* 1.3 75.7 - - + +
684B TYR* 1.3 63.4 + - - +
686B ARG* 3.5 31.5 + - - +
687B ARG* 3.5 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 684 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B LEU 2.7 19.8 + - - +
681B LEU* 3.7 16.4 - - + +
682B GLU 3.3 0.4 - - - -
683B LYS* 1.3 74.6 - - - +
685B LYS* 1.3 80.6 + - + +
686B ARG 3.5 0.2 + - - -
687B ARG* 3.4 3.1 + - - +
692B ARG* 2.4 74.5 + - + +
693B PRO 4.9 3.9 + - - -
694B ASN* 5.1 4.3 - - - -
695B TYR* 4.0 34.0 - + - -
703B PRO* 6.2 0.4 - - + -
704B PHE* 5.2 7.0 - + + -
945B LEU* 2.6 43.1 + - + +
946B GLY* 5.6 0.9 - - - -
947B LEU* 6.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 685 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B LEU* 3.0 37.0 + - + +
682B GLU* 4.3 6.5 - - - +
684B TYR* 1.3 89.9 - - + +
686B ARG* 1.3 63.6 + - - +
687B ARG 3.4 3.8 - - - +
692B ARG* 4.7 4.4 - - - +
942B ALA* 4.9 10.4 + - - +
944B THR* 3.5 37.6 + - - +
945B LEU 4.8 2.6 - - - +
947B LEU* 4.6 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A G 6.1 4.7 - - - +
14A A 3.2 42.5 + - - +
15A A 3.4 33.8 + - - +
682B GLU* 3.1 43.9 + - - +
683B LYS* 3.7 26.7 - - - +
684B TYR 3.2 0.6 - - - -
685B LYS* 1.3 80.4 - - - +
687B ARG* 1.3 61.1 + - - +
688B PRO* 3.6 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A A 3.8 22.8 + - - +
16A G 4.6 12.9 + - - -
683B LYS 3.5 11.7 + - - +
684B TYR* 3.4 2.1 + - - +
685B LYS 3.4 4.5 - - - +
686B ARG* 1.3 78.2 - - - +
688B PRO* 1.3 77.9 - - + +
691B LYS* 3.9 21.0 + - + -
692B ARG* 2.7 63.1 + - + +
693B PRO* 5.2 3.4 - - - +
----------------------------------------------------------
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