Contacts of the helix formed by residues 856 - 878 (chain A) in PDB entry 5QSY
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 856 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855A GLU* 1.3 89.3 - - + +
857A ASN* 1.3 63.9 + - - +
858A LYS 3.1 1.8 + - - -
859A ILE* 3.4 29.0 + - + +
860A GLU* 3.5 8.1 + - - +
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Residues in contact with ASN 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A GLU 2.8 9.9 + - - +
856A ALA* 1.3 75.6 - - - +
858A LYS* 1.3 54.7 + - - +
860A GLU* 3.7 10.9 + - - +
861A ALA* 2.9 28.9 + - - +
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Residues in contact with LYS 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A GLU* 2.8 47.9 + - - +
857A ASN* 1.3 70.8 - - - +
859A ILE* 1.3 69.1 + - + +
860A GLU 3.2 1.1 - - - -
861A ALA* 3.9 5.8 - - - +
862A LEU* 3.1 22.3 + - - +
865A ARG* 5.0 2.1 + - - -
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Residues in contact with ILE 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A GLU* 3.6 16.4 - - - +
856A ALA* 3.4 22.4 - - + +
858A LYS* 1.3 84.4 - - + +
860A GLU* 1.3 70.5 + - + +
862A LEU* 3.6 14.0 + - + +
863A HIS* 3.3 38.4 + - + +
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Residues in contact with GLU 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A ALA 3.5 13.0 + - - +
857A ASN* 4.0 11.8 - - - +
858A LYS 3.2 0.4 - - - -
859A ILE* 1.3 86.0 - - + +
861A ALA* 1.3 63.7 + - - +
862A LEU 3.2 1.3 - - - -
863A HIS* 3.4 8.7 + - + +
864A LYS* 3.2 21.8 + - - +
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Residues in contact with ALA 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A ASN 2.9 20.8 + - - +
858A LYS* 4.1 6.3 - - - +
860A GLU* 1.3 77.3 - - - +
862A LEU* 1.3 59.3 + - - +
864A LYS* 3.6 23.7 - - - +
865A ARG* 3.2 41.5 + - - +
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Residues in contact with LEU 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A LYS 3.1 18.3 + - - +
859A ILE* 3.6 16.2 - - + +
860A GLU 3.2 0.2 - - - -
861A ALA* 1.3 74.1 - - - +
863A HIS* 1.3 67.7 + - + +
865A ARG* 3.3 29.5 + - + +
866A ARG* 2.8 46.0 + - + +
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Residues in contact with HIS 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A ILE* 3.3 30.5 + - + +
860A GLU* 3.4 9.1 + - + +
862A LEU* 1.3 82.6 - - + +
864A LYS* 1.3 52.6 + - - +
866A ARG* 3.1 26.4 + - - +
867A ASN* 2.8 45.5 + - - +
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Residues in contact with LYS 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A GLU* 2.8 36.0 + - + +
860A GLU 3.2 13.9 + - - +
861A ALA* 3.6 29.9 - - - +
862A LEU 3.2 0.2 - - - -
863A HIS* 1.3 75.6 - - - +
865A ARG* 1.3 66.6 + - - +
867A ASN* 3.1 9.6 + - - +
868A LEU* 2.9 42.1 + - + +
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Residues in contact with ARG 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789A GLU* 5.3 0.7 - - - +
836A HIS 3.3 17.7 - - - +
837A VAL* 3.3 39.3 + - + +
839A ILE* 3.8 28.9 - - - +
858A LYS 5.0 2.0 + - - -
861A ALA* 3.2 41.6 + - - +
862A LEU* 3.6 32.8 - - + +
864A LYS* 1.3 85.0 - - - +
866A ARG* 1.3 65.8 + - - +
868A LEU* 3.4 11.6 + - + +
869A LEU* 3.0 24.1 + - - +
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Residues in contact with ARG 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A LEU* 2.8 34.8 + - + +
863A HIS* 3.1 34.7 + - - +
865A ARG* 1.3 76.9 - - - +
867A ASN* 1.3 52.2 + - - +
869A LEU* 3.1 8.5 + - - +
870A ALA* 2.8 36.2 + - - +
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Residues in contact with ASN 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A MET* 4.4 6.4 - - - +
863A HIS* 2.8 31.9 + - - +
864A LYS* 3.1 9.3 + - - +
866A ARG* 1.3 72.7 - - - +
868A LEU* 1.3 58.7 + - + +
870A ALA* 3.5 8.6 - - - +
871A ALA* 2.8 36.7 + - - +
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Residues in contact with LEU 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789A GLU* 4.1 27.4 - - + +
792A PHE* 3.4 31.7 - - + -
793A MET* 3.4 33.9 - - + -
832A PHE* 4.1 20.0 - - + -
836A HIS 5.2 2.7 - - - +
837A VAL* 4.3 9.9 - - + -
864A LYS* 2.9 30.7 + - + +
865A ARG* 3.6 17.3 - - + +
867A ASN* 1.3 76.4 - - + +
869A LEU* 1.3 64.9 + - - +
871A ALA* 3.5 1.2 + - - +
872A PHE* 3.1 16.5 + - - +
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Residues in contact with LEU 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A VAL* 4.2 18.2 - - + -
837A VAL* 3.8 16.5 - - + +
838A PHE* 4.3 16.8 - - + -
865A ARG 3.0 14.5 + - - +
866A ARG* 3.5 9.2 - - - +
868A LEU* 1.3 75.6 - - - +
870A ALA* 1.3 52.1 + - - +
872A PHE* 3.1 12.1 + - + +
873A SER* 2.6 44.6 + - - +
890A PHE* 3.7 34.8 - - + -
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Residues in contact with ALA 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A ARG 2.8 17.1 + - - +
867A ASN* 3.1 14.1 + - - +
869A LEU* 1.3 78.4 - - - +
871A ALA* 1.3 60.5 + - - +
873A SER* 3.3 19.0 + - - -
874A LYS* 3.4 17.5 + - - +
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Residues in contact with ALA 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A MET* 3.7 28.9 - - + -
796A CYS* 3.7 28.8 - - + +
797A ASP* 5.5 0.4 - - - +
867A ASN 2.8 19.7 + - - +
868A LEU 4.0 2.7 - - - +
870A ALA* 1.3 70.0 - - - +
872A PHE* 1.3 63.5 + - - +
874A LYS* 3.7 24.8 + - + +
875A LEU* 4.0 5.7 + - - +
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Residues in contact with PHE 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A PHE* 3.8 22.4 - + + -
796A CYS* 4.1 5.7 - - - -
829A LEU* 3.6 23.8 - - + -
830A LEU* 4.0 20.4 - - + -
833A VAL* 3.7 19.5 - - + -
868A LEU 3.1 13.6 + - - +
869A LEU* 3.1 18.6 + - + +
871A ALA* 1.3 75.8 - - - +
873A SER* 1.3 64.6 + - - +
875A LEU* 3.0 26.4 + - + +
876A ILE* 3.3 37.5 + - + +
881A VAL* 3.8 36.3 - - + -
886A ALA* 4.3 7.4 - - + -
890A PHE* 4.7 4.0 - + - -
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Residues in contact with SER 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869A LEU* 2.6 39.2 + - - +
870A ALA* 3.3 12.5 + - - -
872A PHE* 1.3 72.2 - - - +
874A LYS* 1.3 62.4 + - - +
876A ILE* 3.2 24.9 + - - +
877A ILE* 3.2 25.5 + - - +
890A PHE* 5.2 2.8 - - - -
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Residues in contact with LYS 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796A CYS 5.6 1.8 + - - +
797A ASP* 5.6 5.9 + - - +
800A MET* 3.5 37.2 - - + +
870A ALA 3.4 13.5 + - - +
871A ALA* 3.9 15.9 - - - +
872A PHE 3.2 0.8 - - - -
873A SER* 1.3 77.5 - - - +
875A LEU* 1.3 61.0 + - - +
876A ILE 3.4 0.5 + - - -
877A ILE* 3.5 13.6 + - + +
878A TYR* 3.2 32.0 - - + -
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Residues in contact with LEU 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796A CYS* 3.9 40.4 - - - +
799A LEU* 3.8 39.7 - - + -
800A MET* 3.7 20.2 - - + -
829A LEU* 4.2 10.3 - - + -
871A ALA 4.0 9.0 - - - +
872A PHE* 3.0 15.4 + - + +
874A LYS* 1.3 76.2 - - - +
876A ILE* 1.3 59.5 + - - +
878A TYR 3.7 0.9 + - - -
879A ASP 3.6 1.4 + - - -
880A ILE* 2.8 46.0 + - + +
881A VAL* 3.4 16.0 + - + -
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Residues in contact with ILE 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A PHE* 3.3 38.1 - - + +
873A SER* 3.2 13.8 + - - +
875A LEU* 1.3 75.3 - - - +
877A ILE* 1.3 68.7 + - + +
879A ASP* 3.0 16.3 + - - -
881A VAL* 3.6 24.7 - - + -
883A MET* 3.7 36.0 - - + +
886A ALA* 3.8 13.9 - - + -
890A PHE* 3.8 21.8 - - + -
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Residues in contact with ILE 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A SER* 3.2 22.6 + - - +
874A LYS* 3.8 13.7 - - + +
875A LEU 3.5 0.4 - - - -
876A ILE* 1.3 81.1 - - + +
878A TYR* 1.3 83.1 + - + +
879A ASP 3.6 1.6 + - - -
883A MET* 5.1 5.7 - - - +
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Residues in contact with TYR 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A MET* 4.1 21.1 - - + -
874A LYS* 3.2 32.5 + - + +
875A LEU 3.7 0.2 + - - -
876A ILE 3.2 1.2 - - - -
877A ILE* 1.3 97.1 - - + +
879A ASP* 1.3 69.2 + - - +
880A ILE* 3.1 22.2 + - + +
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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) + - + + + + + -
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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