Contacts of the helix formed by residues 839 - 858 (chain B) in PDB entry 2NUP
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 ASP 839 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B PRO* 4.6 0.5 - - - +
368B PRO* 2.9 35.9 - - + +
387B ARG* 3.5 23.7 + - - +
388B CYS 3.6 13.3 - - - +
389B THR 2.9 18.3 + - - +
391B THR* 4.9 1.4 - - + +
837B GLY 3.3 2.2 + - - +
838B ALA* 1.3 70.7 - - - +
840B VAL* 1.3 64.8 + - - +
841B GLN* 3.3 11.1 + - - +
842B ALA* 3.0 25.9 + - + -
843B ILE* 3.0 25.0 + - - +
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Residues in contact with VAL 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 5.0 5.6 - - + -
838B ALA* 3.7 5.1 + - - +
839B ASP* 1.3 72.7 + - - +
841B GLN* 1.3 63.1 + - + +
843B ILE* 3.4 9.6 + - - +
844B SER* 2.7 33.1 + - - +
895B SER 3.7 20.3 + - - +
896B LEU* 5.0 3.1 - - + -
898B LEU* 3.8 13.7 - - + -
899B PHE* 3.7 44.5 - - + +
902B PHE* 3.8 22.0 - - + -
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Residues in contact with GLN 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 3.9 34.0 - - + +
366B LYS 5.4 1.0 - - - -
367B PRO* 5.3 5.5 - - - +
387B ARG* 4.4 10.4 + - - +
839B ASP* 3.3 6.8 + - - +
840B VAL* 1.3 83.4 - - + +
842B ALA* 1.3 58.9 + - - +
844B SER* 3.1 9.8 + - - -
845B GLY 2.9 25.3 + - - -
902B PHE* 4.1 11.2 - - + -
935B LEU* 3.6 21.1 - - + +
939B MET* 3.3 45.1 - - + +
940B LEU* 6.2 0.2 - - - +
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Residues in contact with ALA 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ARG* 3.9 17.7 - - + -
388B CYS 4.1 1.3 - - - +
389B THR* 3.7 21.6 - - + +
410B LEU* 4.0 6.7 - - + +
839B ASP* 3.0 33.0 + - + +
841B GLN* 1.3 76.8 - - - +
843B ILE* 1.3 58.4 + - - +
845B GLY* 3.2 1.7 + - - -
846B LEU* 2.9 30.3 + - - +
935B LEU* 3.8 12.2 - - + +
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Residues in contact with ILE 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B THR* 3.8 33.0 - - - +
390B LEU* 4.5 2.9 - - + -
405B LEU* 4.0 29.8 - - + -
406B PRO* 3.9 20.4 - - + +
838B ALA* 4.2 6.1 - - + -
839B ASP 3.0 27.7 + - - +
840B VAL* 3.7 6.7 - - - +
842B ALA* 1.3 75.0 - - - +
844B SER* 1.3 57.8 + - - +
846B LEU* 3.2 1.5 + - - +
847B LEU* 2.8 57.4 + - + +
896B LEU* 4.8 4.9 - - + -
899B PHE* 3.8 14.8 - - + -
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Residues in contact with SER 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840B VAL* 2.7 22.4 + - - +
841B GLN* 3.2 11.4 - - - -
843B ILE* 1.3 78.4 - - - +
845B GLY* 1.3 57.3 + - - +
847B LEU* 3.5 9.6 - - - +
848B ALA* 2.9 28.4 + - - +
899B PHE* 4.7 6.0 - - - -
902B PHE* 3.6 23.0 - - - +
903B VAL* 5.2 1.4 + - - +
906B LEU* 3.7 21.9 - - - +
938B LEU* 4.6 1.6 - - - -
939B MET* 4.4 12.3 - - - -
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Residues in contact with GLY 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU* 4.4 7.6 - - - -
841B GLN 2.9 13.7 + - - -
842B ALA 3.6 2.2 - - - -
844B SER* 1.3 77.1 - - - +
846B LEU* 1.3 61.9 + - - +
848B ALA* 3.1 12.3 + - - +
849B ASN* 3.2 20.7 + - - -
935B LEU* 4.3 6.7 - - - -
938B LEU* 3.3 24.6 - - - +
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Residues in contact with LEU 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B THR* 3.7 23.1 - - + -
406B PRO* 3.9 16.8 - - + -
407B LEU 3.9 7.0 - - - +
408B GLY* 3.7 23.1 - - - +
410B LEU* 4.3 9.1 - - + +
763B HIS* 4.2 22.4 - - + +
786B ALA* 4.5 9.0 - - + -
787B VAL 3.9 15.3 - - - +
788B GLN* 4.7 4.5 - - + +
842B ALA 2.9 19.7 + - - +
843B ILE* 3.8 3.4 - - - +
845B GLY* 1.3 71.6 - - - -
847B LEU* 1.3 60.4 + - - +
849B ASN* 3.6 3.7 + - + +
850B MET* 3.0 43.0 + - + +
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Residues in contact with LEU 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B PRO* 3.9 18.8 - - + -
843B ILE* 2.8 49.4 + - + +
844B SER* 3.5 7.2 - - - +
846B LEU* 1.3 70.6 - - - +
848B ALA* 1.3 54.6 + - - +
850B MET* 3.0 19.7 + - + +
851B ALA* 2.6 38.0 + - - +
866B ALA 5.7 0.9 - - - +
867B LEU* 4.1 18.6 - - + +
870B ALA* 4.1 24.0 - - + -
899B PHE* 3.7 22.7 - - + -
903B VAL* 4.8 6.5 - - + -
906B LEU* 5.2 0.9 - - + -
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Residues in contact with ALA 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844B SER 2.9 12.9 + - - +
845B GLY 3.1 10.0 + - - +
847B LEU* 1.3 76.5 - - - +
849B ASN* 1.3 57.8 + - - +
851B ALA* 3.1 8.1 + - - +
852B VAL* 2.9 32.9 + - - +
867B LEU* 5.1 0.4 - - - -
906B LEU* 4.4 17.9 - - + +
912B PHE* 3.6 8.4 - - + -
930B VAL* 3.5 22.0 - - + -
938B LEU* 4.2 12.6 - - + -
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Residues in contact with ASN 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU* 6.1 1.2 - - - +
763B HIS* 3.0 44.0 - - + +
786B ALA* 4.3 10.7 - - - +
845B GLY* 3.2 16.2 + - - -
846B LEU* 3.8 7.9 - - - +
847B LEU 3.3 0.2 - - - -
848B ALA* 1.3 77.9 - - - +
850B MET* 1.3 63.8 + - - +
852B VAL* 3.3 6.5 + - - +
853B ASP* 3.2 25.8 + - - +
930B VAL* 3.4 27.1 + - - +
931B LYS* 3.5 24.6 - - + +
938B LEU* 5.5 2.0 - - - +
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Residues in contact with MET 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B PRO* 4.0 11.2 - - + -
763B HIS* 4.5 10.8 - - + +
788B GLN* 3.5 39.5 - - - +
846B LEU* 3.0 38.3 + - + +
847B LEU* 3.0 24.1 + - + +
849B ASN* 1.3 79.9 - - - +
851B ALA* 1.3 56.6 + - - +
853B ASP* 3.3 6.4 + - - +
854B ARG* 2.9 28.5 + - - +
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Residues in contact with ALA 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847B LEU 2.6 19.7 + - - +
848B ALA 3.4 0.7 - - - +
850B MET* 1.3 70.5 - - - +
852B VAL* 1.3 62.1 + - - +
854B ARG* 3.3 7.0 + - - -
855B SER* 2.8 27.7 + - - -
863B ALA* 3.3 10.9 - - + +
866B ALA* 6.3 1.8 - - - -
867B LEU* 3.9 27.4 - - + -
912B PHE* 3.4 26.9 - - + -
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Residues in contact with VAL 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B ARG* 4.5 10.1 - - - +
848B ALA 2.9 20.7 + - - +
849B ASN* 3.3 7.6 + - - +
851B ALA* 1.3 76.2 - - - +
853B ASP* 1.3 62.5 + - - +
855B SER* 3.1 16.5 + - - -
856B MET* 3.2 18.2 + - + +
912B PHE* 3.8 16.4 - - + -
927B MET* 3.8 38.1 - - + +
930B VAL* 3.9 20.2 - - + -
931B LYS* 4.2 21.5 - - + -
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Residues in contact with ASP 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761B THR* 4.5 6.4 - - - +
762B PHE 5.0 0.9 - - - +
763B HIS* 3.3 21.5 - - - -
849B ASN 3.2 6.5 + - - +
850B MET* 3.3 8.7 + - - +
852B VAL* 1.3 74.4 - - - +
854B ARG* 1.3 67.1 + - - +
856B MET* 3.4 7.0 + - - +
857B THR* 2.9 28.6 + - - -
931B LYS* 3.0 30.7 + - - -
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Residues in contact with ARG 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850B MET 2.9 13.6 + - - +
851B ALA* 3.3 13.2 - - - +
853B ASP* 1.3 76.9 - - - +
855B SER* 1.3 51.1 + - - +
857B THR* 4.3 8.9 - - - +
858B ALA* 2.6 52.6 + - - +
862B ASP* 3.4 11.0 + - + +
863B ALA* 3.4 25.1 - - - +
866B ALA* 2.8 38.4 - - + +
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Residues in contact with SER 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666B MET* 3.5 32.3 - - - +
667B THR* 5.0 2.1 - - - +
851B ALA 2.8 16.0 + - - -
852B VAL 3.3 7.4 + - - -
854B ARG* 1.3 77.7 - - - +
856B MET* 1.3 66.1 + - - +
857B THR 3.1 1.0 + - - -
858B ALA 3.2 17.7 - - - +
859B SER* 3.4 18.8 + - - -
860B LEU* 4.3 2.5 - - - +
863B ALA* 3.1 13.0 - - - +
912B PHE* 4.2 1.0 - - - -
927B MET* 3.7 11.3 - - - +
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Residues in contact with MET 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666B MET* 3.2 70.4 - - + +
667B THR* 3.4 28.1 - - + +
668B PRO* 5.1 4.5 - - + -
707B ARG* 5.1 11.9 - - - +
852B VAL* 3.2 17.3 + - + +
853B ASP* 3.8 9.6 - - - +
855B SER* 1.3 79.9 - - - +
857B THR* 1.3 60.1 + - - +
858B ALA 4.8 0.9 - - - +
924B ILE* 4.6 2.2 - - + -
927B MET* 4.0 14.6 - - - -
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Residues in contact with THR 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853B ASP* 2.9 15.7 + - - +
854B ARG* 3.6 16.6 - - - +
856B MET* 1.3 80.4 - - - +
858B ALA* 1.3 67.6 + - + +
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Residues in contact with ALA 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B THR* 6.2 0.2 - - - +
854B ARG* 2.6 23.7 + - - +
855B SER 3.2 7.1 - - - +
856B MET 4.8 0.9 - - - +
857B THR* 1.3 79.2 - - + +
859B SER* 1.3 66.2 + - - +
862B ASP* 3.3 26.5 - - + +
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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