Contacts of the helix formed by residues 844 - 865 (chain S) in PDB entry 1NVU
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 ASN 844 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842S THR* 3.4 1.3 - - - +
843S GLU* 1.3 76.8 - - - +
845S LEU* 1.3 64.8 + - - +
846S GLU* 3.2 14.9 + - - +
847S GLU* 3.0 42.9 + - - +
848S ARG* 2.9 23.5 + - - +
1027S PHE* 2.8 30.0 + - - +
1028S PRO 3.6 17.7 + - - +
1029S LYS* 4.0 20.1 - - - +
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Residues in contact with LEU 845 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843S GLU 3.2 4.4 + - - -
844S ASN* 1.3 72.2 - - - +
846S GLU* 1.3 60.1 + - - +
848S ARG* 3.0 29.9 + - - +
849S VAL* 2.9 35.8 + - + +
888S HIS* 3.7 26.9 - - + +
889S THR* 3.8 13.0 - - - +
892S GLN* 3.4 27.8 - - - +
1017S GLU* 4.1 0.7 - - - +
1024S LEU* 4.4 21.8 - - + -
1027S PHE* 5.6 1.2 - - - +
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Residues in contact with GLU 846 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844S ASN* 3.2 11.2 + - - +
845S LEU* 1.3 80.3 - - - +
847S GLU* 1.3 64.1 + - + +
849S VAL* 3.4 8.7 + - - +
850S ALA* 3.2 19.6 + - - +
892S GLN* 5.0 7.4 - - - +
1029S LYS* 5.4 10.3 - - - +
1035S LEU* 5.0 4.2 - - + +
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Residues in contact with GLU 847 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777S LEU* 5.4 0.2 - - - +
842S THR* 3.4 14.3 - - + +
844S ASN* 3.0 24.9 + - - +
846S GLU* 1.3 77.4 - - + +
848S ARG* 1.3 57.1 + - - +
850S ALA* 3.1 4.7 + - - +
851S VAL* 2.9 29.5 + - - +
1028S PRO 4.3 0.2 - - - +
1029S LYS* 2.8 35.1 + - + +
1030S LYS* 2.8 33.0 + - - +
1031S TYR* 2.8 38.2 + - + +
1035S LEU* 3.6 20.8 - - + +
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Residues in contact with ARG 848 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839S ILE* 3.3 44.2 - - + +
842S THR* 2.9 23.6 + - - +
843S GLU* 2.8 30.3 + - - +
844S ASN 2.9 9.1 + - - +
845S LEU* 3.4 24.1 - - - +
847S GLU* 1.3 73.8 - - - +
849S VAL* 1.3 61.9 + - - +
851S VAL* 3.0 3.6 + - - +
852S VAL* 2.8 29.5 + - - +
886S LEU* 4.1 2.8 - - - +
889S THR* 2.9 22.4 + - + -
1016S ILE* 3.7 28.1 + - - +
1017S GLU* 2.9 34.6 + - - +
1024S LEU* 5.4 1.6 - - - +
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Residues in contact with VAL 849 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845S LEU* 2.9 26.4 + - + +
846S GLU* 3.5 9.6 - - - +
847S GLU 3.3 0.2 - - - -
848S ARG* 1.3 75.3 - - - +
850S ALA* 1.3 62.7 + - - +
852S VAL 3.4 0.2 + - - -
853S SER* 2.9 31.8 + - - +
889S THR* 3.8 29.8 - - + +
892S GLN* 3.8 43.5 - - + +
893S ILE* 3.8 12.8 - - + +
894S PRO* 5.6 0.9 - - + -
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Residues in contact with ALA 850 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777S LEU* 4.2 6.2 - - + +
846S GLU 3.2 12.8 + - - +
847S GLU 3.1 10.6 + - - +
849S VAL* 1.3 78.4 - - - +
851S VAL* 1.3 61.1 + - + +
853S SER* 3.9 6.5 - - - -
854S ARG* 3.0 26.3 + - - +
1035S LEU* 4.1 36.6 - - + +
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Residues in contact with VAL 851 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776S LEU* 3.8 19.9 - - + +
777S LEU* 4.0 24.9 - - + -
838S CYS* 3.9 13.0 - - + +
839S ILE* 3.9 24.9 - - + -
842S THR* 3.6 19.7 - - - +
847S GLU 2.9 17.2 + - - +
848S ARG* 3.0 9.4 + - - +
850S ALA* 1.3 74.9 - - - +
852S VAL* 1.3 66.3 + - - +
854S ARG* 3.2 3.6 + - - +
855S ILE* 3.1 23.7 + - + +
1031S TYR* 3.8 12.8 - - + +
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Residues in contact with VAL 852 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839S ILE* 3.9 31.9 - - + -
848S ARG 2.8 21.0 + - - +
849S VAL 3.8 3.8 - - - +
851S VAL* 1.3 73.1 - - - +
853S SER* 1.3 63.0 + - - +
855S ILE* 3.2 9.4 + - - +
856S ILE* 3.0 29.0 + - + +
878S MET* 4.2 7.4 - - + -
889S THR* 3.8 17.5 - - + -
890S PHE* 3.9 29.6 - - + -
893S ILE* 3.6 19.7 - - + -
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Residues in contact with SER 853 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849S VAL* 2.9 23.4 + - - +
850S ALA* 3.9 7.0 - - - -
851S VAL 3.3 0.2 - - - -
852S VAL* 1.3 74.0 - - - +
854S ARG* 1.3 65.6 + - - +
856S ILE* 3.2 2.5 + - - -
857S GLU* 3.0 22.7 + - - +
893S ILE* 3.2 13.5 - - - +
894S PRO* 4.2 5.9 - - - +
897S GLN* 3.0 37.2 + - - +
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Residues in contact with ARG 854 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764S HIS* 4.1 11.7 + - - -
776S LEU* 4.2 15.3 - - + +
777S LEU* 3.0 58.8 + - + +
779S LEU 4.3 5.1 + - - -
781S PRO* 4.0 18.3 - - + +
850S ALA 3.0 18.9 + - - +
851S VAL 3.2 4.7 + - - +
853S SER* 1.3 76.0 - - - +
855S ILE* 1.3 57.9 + - - +
857S GLU* 3.1 22.3 + - - +
858S ILE* 3.0 34.3 + - + +
1034S PRO 4.9 1.0 + - - -
1035S LEU* 2.9 35.0 + - - +
1036S LYS 3.8 2.6 + - - -
1037S SER* 3.4 24.9 - - - +
1038S PRO* 4.2 3.2 - - - +
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Residues in contact with ILE 855 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776S LEU* 3.9 17.7 - - + -
835S PHE* 3.9 42.0 - - + +
839S ILE* 3.7 34.8 - - + -
851S VAL* 3.1 23.3 + - + +
852S VAL 3.2 6.5 + - - +
854S ARG* 1.3 76.3 - - - +
856S ILE* 1.3 62.5 + - - +
858S ILE* 3.2 9.7 + - - +
859S LEU* 3.1 19.9 + - - +
874S VAL* 3.8 18.1 - - + +
878S MET* 3.5 18.4 - - + -
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Residues in contact with ILE 856 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852S VAL* 3.0 31.3 + - + +
853S SER* 3.2 7.8 + - - +
855S ILE* 1.3 75.3 - - - +
857S GLU* 1.3 60.5 + - - +
859S LEU* 3.3 9.6 + - + +
860S GLN* 3.0 25.0 + - - +
874S VAL* 5.1 1.6 - - + -
878S MET* 4.3 11.4 - - + -
890S PHE* 5.0 0.9 - - + -
893S ILE* 4.1 22.0 - - + -
897S GLN* 3.8 39.3 - - + +
898S LYS* 5.6 0.2 - - - -
900S ILE* 3.9 18.4 - - + -
901S LEU* 4.3 27.1 - - + +
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Residues in contact with GLU 857 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781S PRO* 4.3 6.8 - - + +
853S SER* 3.0 19.7 + - - +
854S ARG* 3.1 18.4 + - - +
856S ILE* 1.3 75.0 - - - +
858S ILE* 1.3 63.8 + - - +
860S GLN* 3.1 14.5 + - - +
861S VAL* 3.1 25.3 + - - +
897S GLN* 3.4 15.4 + - - +
1037S SER* 2.5 38.1 + - - -
1039S GLY* 4.2 9.5 - - - -
1040S VAL* 3.5 25.6 + - + +
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Residues in contact with ILE 858 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776S LEU* 3.8 27.8 - - + -
781S PRO* 3.9 27.4 - - + +
784S ILE* 3.6 31.4 - - + -
785S ALA* 3.9 9.8 - - + +
835S PHE* 4.6 13.2 - - + -
854S ARG* 3.0 19.7 + - + +
855S ILE* 3.5 11.2 - - - +
856S ILE 3.2 0.2 - - - -
857S GLU* 1.3 76.7 - - - +
859S LEU* 1.3 62.6 + - - +
861S VAL* 3.1 5.6 + - - +
862S PHE* 2.9 48.7 + - + -
874S VAL* 5.1 0.2 - - + -
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Residues in contact with LEU 859 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855S ILE 3.1 12.5 + - - +
856S ILE* 3.4 10.3 - - - +
857S GLU 3.2 0.2 - - - -
858S ILE* 1.3 76.5 - - - +
860S GLN* 1.3 60.6 + - - +
862S PHE* 3.0 14.9 + - - +
863S GLN* 2.9 40.4 + - + +
871S VAL* 4.3 16.2 - - + +
874S VAL* 3.6 32.7 - - + +
875S VAL* 4.3 0.4 - - + -
900S ILE* 3.5 26.9 - - + -
901S LEU* 4.2 15.9 - - + -
904S ALA* 3.8 26.0 - - + -
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Residues in contact with GLN 860 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856S ILE 3.0 11.8 + - - +
857S GLU* 3.1 22.4 + - - +
859S LEU* 1.3 83.5 - - - +
861S VAL* 1.3 60.2 + - - +
863S GLN* 3.4 6.8 + - - +
864S GLU* 3.2 34.1 + - + +
897S GLN* 5.4 3.2 - - - +
900S ILE* 3.7 33.0 - - + +
1040S VAL* 3.8 27.9 - - + +
1041S ARG* 5.0 5.2 + - - -
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Residues in contact with VAL 861 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781S PRO 4.6 1.3 - - - +
782S ILE* 4.2 32.5 - - + +
785S ALA* 3.4 26.2 - - + -
786S ARG* 5.1 1.3 - - + -
857S GLU 3.1 13.8 + - - +
858S ILE 3.1 3.6 + - - +
860S GLN* 1.3 73.2 - - - +
862S PHE* 1.3 66.9 + - - +
864S GLU* 3.1 17.8 + - - +
865S LEU* 2.9 33.9 + - + +
1040S VAL* 3.8 27.8 - - + +
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Residues in contact with PHE 862 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785S ALA* 3.5 30.7 - - + -
788S LEU* 4.0 26.2 - - + -
789S THR* 3.6 11.9 - - - -
835S PHE* 4.9 4.0 - + - -
858S ILE* 2.9 32.5 + - + -
859S LEU* 3.0 16.1 + - - +
861S VAL* 1.3 76.5 - - - +
863S GLN* 1.3 60.3 + - - +
865S LEU* 3.2 3.6 + - - +
866S ASN 3.0 3.5 + - - -
867S ASN* 2.9 48.2 + - - +
870S GLY* 3.3 35.7 - - - -
871S VAL* 3.8 13.5 - - + -
873S GLU* 4.3 7.2 - - - -
874S VAL* 4.2 8.3 - - + -
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Residues in contact with GLN 863 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859S LEU* 2.9 28.5 + - + +
860S GLN* 3.6 9.2 - - - +
861S VAL 3.2 0.2 - - - -
862S PHE* 1.3 73.3 - - - +
864S GLU* 1.3 67.5 + - + +
866S ASN* 3.1 20.7 + - - +
868S PHE* 4.6 5.5 - - - -
871S VAL* 3.5 21.8 - - + +
900S ILE* 4.9 3.2 + - - +
903S GLU* 5.1 4.2 - - - +
904S ALA* 4.1 27.9 - - - +
907S LEU* 4.2 10.7 - - - +
918S LYS* 2.6 37.0 + - - +
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Residues in contact with GLU 864 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860S GLN* 3.2 29.1 + - + +
861S VAL* 3.1 21.4 + - - +
863S GLN* 1.3 78.0 - - + +
865S LEU* 1.3 63.4 + - + +
866S ASN* 3.2 8.2 + - - +
1040S VAL* 4.6 8.9 - - - +
1041S ARG* 3.2 35.1 + - - -
1042S PRO* 5.6 1.7 - - - +
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Residues in contact with LEU 865 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785S ALA* 4.0 8.5 - - + +
786S ARG* 4.0 15.9 - - + -
789S THR* 3.4 32.5 - - + +
861S VAL* 2.9 32.8 + - + +
862S PHE* 3.7 4.5 - - - +
863S GLN 3.1 0.4 - - - -
864S GLU* 1.3 79.0 - - + +
866S ASN* 1.3 62.5 + - - +
867S ASN 3.1 1.1 - - - +
925S PRO 3.7 1.7 - - - +
979S TYR* 2.7 44.5 + - + -
981S LEU* 4.2 24.2 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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