Contacts of the helix formed by residues 854 - 875 (chain A) in PDB entry 6UZA
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 GLN 854 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLU* 3.7 19.4 - - - +
351A GLU* 4.3 17.8 + - - +
853A ARG* 1.3 76.8 - - - +
855A TYR* 1.3 62.0 + - - +
857A LYS* 3.3 27.7 + - - +
858A ILE* 3.0 45.1 + - + +
861A ARG* 4.9 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 855 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU 6.1 0.4 - - - -
292A ASP* 2.9 38.4 + - + -
344A ALA* 3.6 37.0 + - + -
348A GLY 3.9 16.4 - - - -
349A ASP* 3.3 44.4 - - + +
350A VAL 5.5 0.2 - - - +
351A GLU* 4.7 3.8 + - - +
365A ARG* 3.5 11.6 + - - -
853A ARG* 3.5 14.1 - - - +
854A GLN* 1.3 79.9 - - - +
856A GLN* 1.3 63.5 + - - +
858A ILE* 3.5 4.0 + - - -
859A MET* 2.9 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 856 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 3.5 33.9 + - - +
853A ARG* 3.1 60.5 + - + +
854A GLN 3.3 0.2 - - - -
855A TYR* 1.3 86.0 - - - +
857A LYS* 1.3 57.4 + - + +
859A MET* 3.9 5.3 - - - +
860A LYS* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 857 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A ARG 3.4 16.9 + - - +
854A GLN* 3.3 30.3 + - - +
855A TYR 3.3 0.4 - - - -
856A GLN* 1.3 77.6 - - + +
858A ILE* 1.3 57.9 + - + +
860A LYS* 3.3 6.9 + - - +
861A ARG* 3.0 40.3 + - - +
212B ASP* 3.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 858 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLU* 3.6 42.8 - - + +
341A GLU* 4.0 15.5 - - + -
344A ALA* 3.7 26.9 - - + -
854A GLN* 3.0 35.0 + - + +
855A TYR* 4.0 4.5 - - - +
857A LYS* 1.3 75.4 - - - +
859A MET* 1.3 58.2 + - - +
861A ARG* 3.4 20.6 + - - +
862A LEU* 3.0 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 859 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU 4.9 10.3 - - - +
292A ASP* 3.9 9.0 - - - +
293A PRO* 3.8 33.0 - - + -
294A VAL* 4.2 14.6 - - + -
332A LEU* 4.7 4.5 - - + -
344A ALA* 4.4 4.9 - - - +
345A ILE* 4.0 22.7 - - + -
855A TYR* 2.9 54.4 + - + +
856A GLN* 4.1 5.8 - - - +
858A ILE* 1.3 75.3 - - - +
860A LYS* 1.3 58.3 + - - +
862A LEU* 3.8 8.8 - - + +
863A ILE* 2.9 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 860 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A GLN 2.9 20.3 + - - +
857A LYS* 3.7 6.7 - - - +
859A MET* 1.3 77.2 - - - +
861A ARG* 1.3 57.6 + - - +
863A ILE* 3.4 5.5 + - - +
864A LYS* 3.0 28.1 + - - +
86B TYR* 5.3 10.5 - - - +
88B PHE* 3.7 23.0 - - + -
89B SER 3.2 28.5 + - - +
90B ASP* 4.2 15.8 + - - +
91B ARG* 5.7 0.6 - - - +
92B SER* 5.4 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 861 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ASN* 4.0 5.7 - - - +
340A GLU* 3.9 18.5 + - - -
341A GLU* 3.6 17.6 + - - +
854A GLN* 4.9 5.3 + - - +
857A LYS* 3.0 23.3 + - - +
858A ILE* 3.4 27.1 - - - +
860A LYS* 1.3 76.1 - - - +
862A LEU* 1.3 64.2 + - + +
864A LYS* 3.4 6.8 + - - +
865A ARG* 3.0 57.8 + - - +
209B TYR* 5.5 0.3 + - - -
210B ASP* 5.6 4.7 - - - +
212B ASP* 3.0 50.6 + - - +
213B GLY* 5.4 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 862 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 3.9 17.6 - - + +
335A LEU* 4.3 14.6 - - + +
336A CYS* 4.2 13.9 - - - -
341A GLU* 3.6 14.4 - - + +
344A ALA* 5.2 0.2 - - + -
345A ILE* 3.8 30.7 - - + -
858A ILE* 3.0 39.6 + - + +
859A MET* 3.9 10.1 - - + +
861A ARG* 1.3 79.4 - - + +
863A ILE* 1.3 59.5 + - - +
865A ARG* 3.4 29.8 + - - +
866A TYR* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 863 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A SER* 3.4 34.1 - - - +
290A SER 4.9 4.7 - - - +
291A GLU 4.6 6.7 - - - +
293A PRO* 3.8 37.7 - - + -
328A PHE* 6.1 0.2 - - + -
332A LEU* 5.1 4.9 - - + -
859A MET* 2.9 29.9 + - + +
860A LYS* 3.9 5.2 - - - +
862A LEU* 1.3 74.9 - - + +
864A LYS* 1.3 59.9 + - - +
866A TYR* 3.2 6.4 + - - +
867A VAL* 3.0 31.4 + - + +
86B TYR* 6.0 3.6 - - + -
88B PHE* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 864 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A LYS 3.0 18.6 + - - +
861A ARG* 3.8 6.7 - - - +
863A ILE* 1.3 77.4 - - - +
865A ARG* 1.3 61.6 + - - +
867A VAL* 3.4 2.7 + - - +
868A LEU* 3.0 31.3 + - + +
88B PHE* 3.7 24.0 - - + -
90B ASP* 4.8 3.5 - - + +
132B MET* 2.7 37.1 + - - +
133B GLY* 4.0 6.5 + - - -
134B GLN* 4.3 5.1 - - - +
209B TYR* 3.6 36.4 + - - +
210B ASP* 2.5 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 865 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.0 38.7 + - + -
337A ARG* 3.7 43.4 - - - +
338A ASN* 5.3 0.4 - - - +
341A GLU* 2.4 47.3 + - - -
861A ARG* 3.0 39.1 + - - +
862A LEU* 3.5 15.7 - - - +
863A ILE 3.4 0.2 - - - -
864A LYS* 1.3 74.8 - - - +
866A TYR* 1.3 57.5 + - - +
868A LEU* 3.9 5.0 - - - +
869A GLN* 2.9 33.4 + - - +
209B TYR* 4.7 10.5 - - - +
214B THR 5.1 2.1 + - - +
215B ARG 5.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 866 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TYR* 4.0 11.4 - - - -
283A PRO* 3.7 23.2 - - + +
287A SER* 4.3 14.1 - - - -
327A ASP 5.1 0.9 + - - -
328A PHE* 3.5 44.9 - + - -
331A GLY* 4.1 21.7 - - - -
332A LEU* 3.8 17.9 - - + -
335A LEU* 3.7 20.1 - - + +
862A LEU 2.9 17.1 + - - +
863A ILE* 3.2 7.4 + - - +
865A ARG* 1.3 76.5 - - - +
867A VAL* 1.3 59.0 + - - +
869A GLN* 4.0 2.5 - - + +
870A ALA* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 867 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TYR* 4.0 28.5 - - + -
287A SER* 4.4 9.2 - - - +
288A LEU* 4.3 18.8 - - + -
863A ILE* 3.0 25.8 + - + +
864A LYS* 3.9 5.4 - - - +
865A ARG 3.3 0.2 - - - -
866A TYR* 1.3 77.3 - - - +
868A LEU* 1.3 57.6 + - + +
870A ALA* 3.4 4.9 + - - +
871A GLN* 3.0 51.4 + - - +
88B PHE* 5.0 0.7 - - + -
132B MET* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 868 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A LYS* 3.0 26.9 + - + +
865A ARG* 4.1 4.3 - - - +
867A VAL* 1.3 78.1 - - - +
869A GLN* 1.3 56.1 + - - +
871A GLN* 3.4 17.7 + - - +
872A ILE* 3.0 37.8 + - + +
132B MET* 3.8 28.0 - - + -
134B GLN* 4.5 8.3 - - - +
209B TYR* 3.8 36.6 - - + +
215B ARG* 4.1 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 869 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 4.2 23.6 - - + +
865A ARG 2.9 19.2 + - - +
866A TYR* 4.1 3.4 - - + +
868A LEU* 1.3 77.2 - - - +
870A ALA* 1.3 57.7 + - - +
872A ILE* 3.3 22.7 + - - +
873A ASP* 2.9 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 870 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TYR* 3.3 36.1 - - + +
866A TYR* 2.9 28.7 + - + +
867A VAL 3.7 1.6 - - - +
869A GLN* 1.3 75.2 - - - +
871A GLN* 1.3 58.7 + - - +
873A ASP* 3.4 7.5 + - - +
874A LYS* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TYR* 3.8 28.2 - - + +
233A GLU* 5.0 1.8 - - - +
867A VAL* 3.0 39.7 + - - +
868A LEU* 3.8 17.0 - - - +
870A ALA* 1.3 73.2 - - - +
872A ILE* 1.3 62.0 + - + +
874A LYS* 3.3 12.6 + - - +
875A GLU* 3.0 35.8 + - - +
131B TYR* 4.1 16.2 + - - -
132B MET* 5.2 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A LEU* 3.0 26.4 + - + +
869A GLN* 3.6 23.3 - - - +
870A ALA 3.3 0.2 - - - -
871A GLN* 1.3 77.7 - - + +
873A ASP* 1.3 69.7 + - - +
875A GLU* 3.2 20.8 + - - +
876A SER* 3.5 15.7 + - - +
167B LEU* 6.5 0.7 - - + -
171B LYS* 6.4 0.7 - - - +
215B ARG* 6.1 4.3 - - - +
216B PHE* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A GLN* 2.9 46.6 + - - +
870A ALA* 3.9 6.3 - - - +
871A GLN 3.3 0.2 - - - -
872A ILE* 1.3 79.6 - - - +
874A LYS* 1.3 60.5 + - - +
876A SER* 3.4 17.8 + - - -
877A ASP* 4.0 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A CYS 5.6 2.0 - - - +
230A GLN* 2.6 38.5 + - + +
231A GLU* 4.6 6.1 + - - +
232A TYR* 3.3 29.3 - - - +
870A ALA 2.9 15.8 + - - +
871A GLN* 3.7 14.3 - - - +
873A ASP* 1.3 75.7 - - - +
875A GLU* 1.3 58.9 + - + +
876A SER 3.1 5.6 + - - -
877A ASP* 3.7 17.0 + - - +
881B GLU* 3.1 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 875 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A GLN* 3.0 21.1 + - + +
872A ILE* 3.2 13.8 + - - +
874A LYS* 1.3 77.0 - - + +
876A SER* 1.3 57.8 + - - -
877A ASP 3.7 0.7 - - - -
171B LYS* 4.3 15.8 + - - -
880B ASN* 3.6 8.1 + - - -
881B GLU* 4.4 12.1 - - + +
882B GLY* 3.4 33.2 + - - +
885B LYS* 3.3 30.7 + - - +
----------------------------------------------------------
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