Contacts of the helix formed by residues 855 - 877 (chain A) in PDB entry 5XA0
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 SER 855 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854A PHE* 1.3 79.0 - - - +
856A ASP* 1.3 58.5 + - - +
857A LYS 3.1 3.9 - - - +
858A GLU* 3.3 10.3 + - - +
859A LYS* 3.0 34.4 + - - +
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Residues in contact with ASP 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A PHE* 6.1 0.9 - - - -
853A PRO 3.9 14.1 - - - +
854A PHE 2.8 4.8 + - - +
855A SER* 1.3 77.6 - - - +
857A LYS* 1.3 48.9 - - - +
859A LYS* 4.8 2.7 - - - -
860A ASN* 2.1 49.0 - - + +
969A ASP* 5.8 0.2 - - - +
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Residues in contact with LYS 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A SER* 3.1 1.4 - - - +
856A ASP* 1.3 76.0 - - - +
858A GLU* 1.3 54.9 + - - +
860A ASN* 4.1 1.6 - - - -
861A LYS* 2.1 43.8 - - + +
969A ASP* 5.8 8.1 - - + -
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Residues in contact with GLU 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A GLN* 6.2 2.2 - - + -
724A LYS* 4.7 9.8 + - - +
855A SER* 3.3 13.3 + - - +
857A LYS* 1.3 77.0 - - - +
859A LYS* 1.3 61.2 + - - +
861A LYS* 4.0 2.2 - - - -
862A LEU* 2.9 30.8 + - - +
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Residues in contact with LYS 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A ASP* 6.1 4.9 - - + -
855A SER* 3.0 18.5 + - - +
856A ASP* 4.7 1.8 - - - +
858A GLU* 1.3 78.1 - - - +
860A ASN* 1.3 49.8 + - - +
862A LEU* 3.9 3.4 - - - +
863A THR* 2.7 38.2 + - - -
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Residues in contact with ASN 860 (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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856A ASP* 2.1 37.2 + - + +
857A LYS* 4.1 2.5 - - - -
859A LYS* 1.3 72.0 - - - +
861A LYS* 1.3 59.3 - - - +
863A THR* 4.0 6.3 - - - -
864A PHE* 2.9 28.4 + - - +
969A ASP* 5.4 17.2 - - + +
973A LYS* 5.6 10.0 - - + +
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Residues in contact with LYS 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A LYS* 4.9 9.0 - - - +
725A GLU* 2.9 17.9 - - + +
857A LYS* 2.1 34.2 + - + +
858A GLU* 3.9 4.0 - - - +
860A ASN* 1.3 75.1 - - - +
862A LEU* 1.3 68.6 + - - +
863A THR 3.0 0.7 - - - -
864A PHE* 2.9 13.5 + - - +
865A GLU 3.0 6.4 + - - -
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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
----------------------------------------------------------
723A GLN* 4.9 4.9 - - - -
724A LYS 4.3 5.6 - - - +
725A GLU* 3.1 29.7 - - - +
728A ASP* 5.1 0.2 - - - +
858A GLU 2.9 21.7 + - - +
859A LYS* 4.0 4.5 - - - +
861A LYS* 1.3 71.9 - - - +
863A THR* 1.3 57.7 + - - +
866A VAL* 2.8 31.5 + - - +
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Residues in contact with THR 863 (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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859A LYS 2.7 24.3 + - - -
860A ASN* 4.0 5.2 - - - -
862A LEU* 1.3 75.0 - - - +
864A PHE* 1.3 60.2 + - - +
866A VAL* 3.6 7.6 - - - -
867A VAL* 2.7 36.8 + - - +
973A LYS* 6.4 2.0 - - - -
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Residues in contact with PHE 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A ASN 2.9 23.4 + - - +
861A LYS* 2.9 6.7 + - - +
863A THR* 1.3 73.2 - - - +
865A GLU* 1.3 67.9 + - - +
867A VAL* 2.9 13.8 + - - +
868A ASN* 3.2 14.6 + - - +
969A ASP* 5.6 1.1 - - - +
972A LEU* 4.4 28.5 - - + -
973A LYS* 5.4 4.5 - - + +
976A GLU* 4.6 1.0 - - - +
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Residues in contact with GLU 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A GLU* 3.0 40.8 - - + +
728A ASP* 3.5 13.2 - - + +
729A ILE* 4.9 3.6 - - + +
861A LYS 3.0 4.6 + - - -
864A PHE* 1.3 77.1 - - - +
866A VAL* 1.3 64.6 + - - +
868A ASN* 3.7 3.9 + - - +
869A LEU* 3.1 20.3 + - - +
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Residues in contact with VAL 866 (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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728A ASP* 3.8 12.8 - - + -
862A LEU 2.8 21.8 + - - +
863A THR* 3.8 8.5 - - - +
865A GLU* 1.3 77.9 - - - +
867A VAL* 1.3 53.3 + - - +
869A LEU* 3.3 4.5 - - - +
870A ALA* 2.7 33.0 + - - +
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Residues in contact with VAL 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A THR* 2.7 25.6 + - - +
864A PHE* 2.9 2.4 + - - +
866A VAL* 1.3 70.7 - - - +
868A ASN* 1.3 69.9 + - - +
869A LEU 3.0 0.7 - - - -
870A ALA* 2.9 17.1 + - - +
871A ARG* 3.0 10.9 + - - +
973A LYS* 5.6 2.5 - - - +
976A GLU* 3.1 32.6 - - + +
977A ILE 5.0 0.4 - - - +
980A PHE* 4.8 0.7 - - - +
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Residues in contact with ASN 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A PHE 3.2 11.4 + - - +
865A GLU* 4.1 3.4 - - - +
867A VAL* 1.3 78.8 - - - +
869A LEU* 1.3 64.7 + - - +
871A ARG* 3.0 16.3 + - - +
872A ASN* 3.1 11.6 + - - +
976A GLU* 3.3 14.8 - - + +
979A GLN* 4.8 4.3 - - + -
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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
----------------------------------------------------------
728A ASP* 4.2 18.4 - - + +
731A SER* 6.2 1.8 - - - -
865A GLU 3.1 14.0 + - - +
866A VAL* 3.3 14.1 - - - +
867A VAL 3.0 0.6 - - - -
868A ASN* 1.3 79.6 - - - +
870A ALA* 1.3 48.6 + - - +
872A ASN* 3.1 9.5 + - - +
873A LEU* 2.7 36.2 + - - +
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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
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866A VAL 2.7 17.5 + - - +
867A VAL* 2.9 12.0 + - - +
869A LEU* 1.3 70.5 - - - +
871A ARG* 1.3 73.0 + - - +
873A LEU* 2.9 7.8 + - - -
874A ILE* 2.8 24.9 + - - +
980A PHE* 4.7 8.5 - - + -
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Residues in contact with ARG 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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867A VAL 3.0 6.8 + - - +
868A ASN 3.1 10.5 - - - +
870A ALA* 1.3 78.7 - - - +
872A ASN* 1.3 62.5 + - - +
873A LEU 3.0 0.3 + - - -
874A ILE* 3.3 3.4 + - - +
875A TYR* 3.1 21.1 + - - +
979A GLN* 2.9 46.2 - - + +
980A PHE* 3.1 17.0 - - - +
983A ASN* 3.8 9.3 - - + +
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Residues in contact with ASN 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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868A ASN 3.1 8.9 + - - +
869A LEU* 3.5 11.9 - - - +
871A ARG* 1.3 81.3 - - + +
873A LEU* 1.3 56.2 + - - +
875A TYR* 4.3 4.4 - - - +
876A PHE* 2.9 33.5 + - + +
983A ASN* 5.5 0.7 - - - -
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Residues in contact with LEU 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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833A PHE* 6.4 2.2 - - + -
869A LEU* 2.7 20.4 + - + +
870A ALA* 3.5 9.2 - - - +
872A ASN* 1.3 72.1 - - - +
874A ILE* 1.3 66.9 + - - +
876A PHE* 4.6 2.9 - - - -
877A GLY* 3.0 24.3 + - - +
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Residues in contact with ILE 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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870A ALA 2.8 15.3 + - - +
871A ARG* 3.7 4.0 - - - +
873A LEU* 1.3 77.4 - - - +
875A TYR* 1.4 58.7 + - - +
877A GLY 2.8 22.2 - - - +
878A PHE* 3.6 10.7 - - - +
980A PHE* 5.6 2.0 - - + +
984A VAL* 4.6 21.3 - - + +
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Residues in contact with TYR 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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741A ALA* 5.7 3.1 - - - +
871A ARG 3.1 15.8 + - - +
872A ASN* 4.3 3.8 - - - +
874A ILE* 1.4 76.8 - - - +
876A PHE* 1.3 62.1 + - - +
877A GLY* 4.6 0.9 - - - -
878A PHE* 5.4 2.0 - - - +
983A ASN* 3.8 27.1 - - + +
984A VAL* 5.6 0.6 - - - +
987A ASP* 4.9 7.4 - - + -
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Residues in contact with PHE 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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739A LEU* 5.3 17.5 - - + +
741A ALA* 5.8 6.5 - - - -
872A ASN 2.9 25.1 + - - +
873A LEU* 4.3 3.6 - - - +
875A TYR* 1.3 74.1 - - - +
877A GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 877 (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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826A LYS* 5.3 9.4 - - - -
873A LEU 3.0 15.8 + - - +
874A ILE* 2.8 17.3 - - - +
875A TYR 4.8 0.4 - - - -
876A PHE* 1.3 78.5 - - - +
878A PHE* 1.3 60.0 + - - -
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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