Contacts of the helix formed by residues 824 - 843 (chain B) in PDB entry 6MZL
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 PRO 824 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B LYS* 4.9 8.3 - - - +
823B ASN* 1.3 92.4 - - + +
825B ASP* 1.3 81.4 + - + +
826B VAL* 3.4 1.8 - - + -
827B ARG* 3.5 20.0 + - + +
828B LEU* 3.7 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 825 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B LYS* 2.6 43.0 + - - +
772B LEU* 3.4 23.5 - - + +
824B PRO* 1.3 86.5 - - + +
826B VAL* 1.3 60.3 + - + +
827B ARG 3.1 1.8 - - - -
828B LEU* 3.0 24.4 + - + +
829B ILE* 2.9 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 826 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B THR* 4.9 12.6 - - + +
810B VAL* 4.8 11.7 - - + -
822B LEU* 4.4 9.0 - - + +
823B ASN 3.9 19.7 - - - +
825B ASP* 1.3 78.5 - - + +
827B ARG* 1.3 55.6 + - - +
829B ILE* 3.2 16.2 + - + +
830B LEU* 2.9 43.7 + - + +
861B LEU* 4.7 13.9 - - + -
866B HIS* 4.1 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 827 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B ASP 4.9 2.4 + - - -
821B ASN* 3.6 36.5 + - - +
822B LEU 3.7 14.5 + - - +
823B ASN* 6.0 0.2 - - - +
824B PRO* 3.5 14.0 + - + +
825B ASP 3.1 0.2 - - - -
826B VAL* 1.3 78.1 - - - +
828B LEU* 1.3 60.5 + - + +
830B LEU* 3.2 12.5 + - + +
831B GLU* 2.9 40.9 + - - +
210K THR* 3.4 29.0 - - - +
211K PHE* 3.8 23.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 828 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B LEU* 4.2 30.5 - - + -
824B PRO 3.8 9.2 - - - +
825B ASP* 3.0 31.5 + - + +
827B ARG* 1.3 73.7 - - + +
829B ILE* 1.3 67.4 + - - +
831B GLU* 3.1 26.7 + - - +
832B GLU* 3.0 27.1 + - - +
184K ARG* 5.3 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 829 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772B LEU* 4.4 13.2 - - + -
776B LEU* 5.0 4.5 - - + -
802B LEU* 3.8 41.1 - - + +
805B SER* 3.4 28.5 - - - +
807B THR* 6.0 0.7 - - - +
825B ASP* 2.9 17.0 + - + +
826B VAL* 3.4 18.2 - - + +
828B LEU* 1.3 77.0 - - + +
830B LEU* 1.3 56.9 + - - +
832B GLU* 3.3 8.6 + - - +
833B ILE* 2.9 39.0 + - + +
857B ALA* 6.4 1.3 - - + -
861B LEU* 5.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 830 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B LEU* 5.3 3.8 - - + +
826B VAL* 2.9 28.2 + - + +
827B ARG* 3.3 16.8 - - + +
829B ILE* 1.3 77.8 - - - +
831B GLU* 1.3 52.7 + - - +
833B ILE* 3.2 21.6 - - + +
834B THR* 2.3 40.1 + - - -
858B ILE* 6.1 1.3 - - + -
861B LEU* 3.8 19.1 - - + -
866B HIS* 6.3 0.2 - - + -
867B VAL* 4.1 21.3 - - + -
203K LEU* 4.1 18.2 - - + -
204K PHE* 5.4 8.7 - - + -
211K PHE* 3.6 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 831 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B ARG* 2.9 29.5 + - - +
828B LEU* 3.1 27.7 + - - +
830B LEU* 1.3 76.1 - - - +
832B GLU* 1.3 58.8 + - + +
834B THR* 3.4 3.4 + - - -
835B ARG* 3.0 40.4 + - - +
184K ARG* 4.2 11.2 + - - +
188K ARG* 2.7 46.3 + - - +
211K PHE* 3.5 20.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 832 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B LEU* 3.3 51.3 - - - +
779B ILE* 3.2 33.8 - - + +
802B LEU* 3.3 15.7 - - + +
828B LEU 3.0 11.8 + - - +
829B ILE* 3.3 6.7 + - - +
831B GLU* 1.3 77.9 - - + +
833B ILE* 1.3 59.3 + - - +
835B ARG* 3.2 22.9 + - - +
836B PHE* 2.9 40.8 + - + -
184K ARG* 5.4 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 833 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B ILE* 4.9 15.3 - - + -
802B LEU* 5.0 8.3 - - + -
829B ILE* 2.9 29.0 + - + +
830B LEU* 3.2 31.2 - - + +
832B GLU* 1.3 77.0 - - + +
834B THR* 1.3 61.4 + - - +
836B PHE* 3.3 3.3 + - - +
837B LEU* 2.9 36.9 + - + +
854B CYS* 4.1 14.3 - - + -
857B ALA* 4.8 15.9 - - + -
858B ILE* 3.9 27.1 - - + -
861B LEU* 4.1 11.7 - - + -
203K LEU* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 834 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830B LEU* 2.3 26.1 + - - -
831B GLU* 3.6 4.7 - - - -
832B GLU 3.2 0.2 - - - -
833B ILE* 1.3 79.8 - - - +
835B ARG* 1.3 62.0 + - - +
837B LEU* 3.4 2.2 + - - +
838B ASN* 2.8 38.7 + - - +
191K THR* 4.6 7.9 - - + -
203K LEU* 4.4 7.3 - - - +
211K PHE* 3.4 32.3 - - + +
212K PRO* 5.3 2.2 - - + -
213K LEU* 3.6 31.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 835 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B ILE* 6.2 1.4 - - - +
831B GLU* 3.0 22.8 + - - +
832B GLU* 3.3 23.3 - - - +
834B THR* 1.3 77.4 - - - +
836B PHE* 1.3 63.3 + - + +
838B ASN* 3.2 2.4 + - - +
839B MET* 2.8 41.5 + - - +
184K ARG* 3.0 58.2 + - - +
187K GLU* 3.8 20.7 + - + -
188K ARG* 3.3 52.3 - - + +
191K THR* 4.1 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 836 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B ILE* 3.6 34.1 - - + -
782B ASN* 4.9 6.5 - - - -
795B ARG* 3.9 33.2 - - + -
799B ILE* 3.7 26.2 - - + -
832B GLU* 2.9 35.1 + - + +
833B ILE* 3.3 3.3 + - - +
835B ARG* 1.3 81.2 - - + +
837B LEU* 1.3 58.9 + - - +
839B MET* 3.7 28.2 - - + +
840B GLU* 2.9 34.8 + - + +
850B ILE* 3.9 24.6 - - + +
854B CYS* 4.1 4.3 - - - -
187K GLU* 5.2 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 837 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B ILE* 2.9 24.1 + - + +
834B THR 3.8 3.8 - - - +
836B PHE* 1.3 78.1 - - - +
838B ASN* 1.3 59.9 + - - +
840B GLU* 3.6 1.2 + - - +
841B LYS* 2.9 26.3 + - - +
851B THR* 3.7 34.2 + - + +
854B CYS* 3.6 25.1 - - + -
855B LEU* 5.3 3.1 - - + -
858B ILE* 3.7 29.4 - - + -
877B TYR* 5.1 12.6 - - + +
213K LEU* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 838 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B THR* 2.8 27.0 + - - +
835B ARG 4.0 2.2 - - - +
837B LEU* 1.3 77.0 - - - +
839B MET* 1.3 60.0 + - - +
841B LYS* 3.2 7.3 + - - +
842B LEU* 3.0 34.8 + - + +
191K THR* 3.4 36.1 + - + +
212K PRO 4.8 2.6 + - - -
213K LEU* 3.5 21.1 - - - +
214K ILE* 3.3 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 839 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B ARG* 4.7 12.6 - - - +
835B ARG* 2.8 25.8 + - + +
836B PHE* 3.7 33.4 - - + +
838B ASN* 1.3 76.4 - - - +
840B GLU* 1.3 55.3 + - + +
842B LEU* 2.8 6.6 + - - -
843B LEU* 2.4 58.1 + - + +
219H GLU* 3.3 26.5 - - - +
187K GLU* 4.0 35.4 - - + +
191K THR* 5.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 840 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B ARG* 3.6 6.6 + - - -
836B PHE* 2.9 18.2 + - + +
837B LEU 3.8 0.7 - - - +
839B MET* 1.3 74.0 - - + +
841B LYS* 1.3 64.6 + - - +
843B LEU* 4.3 6.8 - - - +
844B PRO* 3.2 28.0 - - - +
845B SER* 2.5 57.9 + - - +
848B HIS* 3.9 15.5 + - - +
850B ILE* 3.3 34.9 - - + +
851B THR* 3.4 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 841 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837B LEU 2.9 16.4 + - - +
838B ASN* 3.4 13.7 - - - +
839B MET 3.1 0.4 - - - -
840B GLU* 1.3 79.3 - - - +
842B LEU* 1.3 62.6 + - + +
844B PRO* 4.0 5.9 - - - +
877B TYR* 5.2 10.1 + - - +
882B HIS* 4.5 9.1 + - - -
194K MET* 6.6 0.2 - - + -
214K ILE* 4.3 25.1 - - + +
215K ALA 3.9 12.3 - - - +
216K ALA* 3.9 4.9 - - - +
217K ARG* 3.0 46.4 - - - +
219K PHE* 4.9 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 842 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B ASN* 3.0 16.6 + - + +
839B MET* 2.8 10.1 + - - +
841B LYS* 1.3 80.1 - - + +
843B LEU* 1.3 65.8 + - + +
844B PRO* 3.2 8.5 - - - +
222H LEU* 5.2 20.2 - - + +
226H GLU* 4.7 6.1 - - - +
190K LEU* 3.8 33.0 - - + +
191K THR* 6.2 0.4 - - - -
194K MET* 3.6 41.1 - - + -
214K ILE* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 843 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B ARG* 4.6 14.8 - - - +
839B MET* 2.4 49.9 + - + +
840B GLU* 4.3 9.4 - - - +
842B LEU* 1.3 66.0 - - + +
844B PRO* 1.3 72.6 - - + +
845B SER* 4.5 3.5 - - - +
218H VAL* 4.0 19.5 - - + -
219H GLU* 4.2 21.3 - - + +
222H LEU* 3.9 25.4 - - + -
183K ARG* 6.2 0.2 - - - +
----------------------------------------------------------
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