Contacts of the helix formed by residues 859 - 880 (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 SER 859 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661B ALA 4.5 7.9 - - - -
666B MET* 6.1 1.6 - - - -
854B ARG 3.5 0.2 + - - -
855B SER* 3.4 13.9 + - - -
858B ALA* 1.3 85.1 - - - +
860B LEU* 1.3 60.2 + - - +
861B SER* 3.3 19.4 + - - -
862B ASP* 3.0 19.6 + - - +
863B ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 860 (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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661B ALA* 4.2 21.2 + - + +
666B MET* 4.5 22.6 - - + +
855B SER* 4.3 9.2 - - - +
859B SER* 1.3 75.0 - - - +
861B SER* 1.3 57.8 + - - +
863B ALA* 3.3 4.1 - - - +
864B ARG* 2.8 39.3 + - - +
911B SER 4.1 7.9 - - - +
912B PHE* 4.0 35.9 - - + +
913B GLN 4.2 0.4 - - - +
914B THR* 3.9 21.1 - - + -
923B ARG* 3.5 28.3 - - - +
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Residues in contact with SER 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B ALA* 3.1 32.9 + - - +
859B SER* 3.2 8.5 + - - -
860B LEU* 1.3 76.6 - - - +
862B ASP* 1.3 59.2 + - - +
864B ARG* 3.2 8.8 + - - +
865B ASP* 2.9 41.5 + - - +
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Residues in contact with ASP 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B ARG* 3.4 20.1 + - - +
858B ALA* 3.3 27.1 - - + +
859B SER* 3.0 24.4 + - - +
861B SER* 1.3 81.3 - - - +
863B ALA* 1.3 63.0 + - - +
865B ASP* 3.4 9.3 + - - +
866B ALA 2.9 20.4 + - - -
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Residues in contact with ALA 863 (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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851B ALA* 3.3 18.6 - - + +
854B ARG* 3.4 14.3 - - + +
855B SER* 3.1 28.5 - - - +
859B SER 2.9 9.6 + - - +
860B LEU* 3.3 9.6 - - - +
862B ASP* 1.3 77.7 - - - +
864B ARG* 1.3 63.3 + - - +
866B ALA* 3.4 2.4 + - - +
867B LEU* 3.2 28.6 + - - +
912B PHE* 4.6 7.2 - - + -
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Residues in contact with ARG 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B ALA* 5.6 1.3 - - - -
860B LEU* 2.8 29.8 + - + +
861B SER* 3.6 7.4 - - - +
863B ALA* 1.3 74.1 - - - +
865B ASP* 1.3 61.0 + - - +
867B LEU* 3.3 6.6 - - - +
868B VAL* 3.0 31.4 + - + +
907B LEU* 3.2 50.4 + - + +
912B PHE* 2.7 41.7 + - + +
914B THR* 3.3 42.0 + - - +
1077B ALA* 6.3 1.0 - - - +
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Residues in contact with ASP 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861B SER* 2.9 27.6 + - - +
862B ASP* 3.8 9.5 - - - +
864B ARG* 1.3 74.6 - - - +
866B ALA* 1.3 55.0 + - - +
867B LEU 3.0 1.3 - - - -
868B VAL* 2.9 9.8 + - - +
869B ASN* 2.6 50.7 + - - +
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Residues in contact with ALA 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847B LEU* 5.7 1.0 - - - +
851B ALA* 6.3 1.6 - - - -
854B ARG* 2.8 39.3 - - + +
862B ASP 2.9 8.7 + - - +
863B ALA 3.8 4.0 - - - +
865B ASP* 1.3 76.8 - - - +
867B LEU* 1.3 62.1 + - + +
869B ASN* 3.3 13.0 + - - +
870B ALA* 2.9 23.2 + - - +
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Residues in contact with LEU 867 (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* 4.1 30.1 - - + +
848B ALA* 4.8 0.7 - - - +
851B ALA* 3.9 26.9 - - + -
863B ALA 3.2 18.0 + - - +
864B ARG* 3.3 10.1 - - - +
865B ASP 3.0 0.2 - - - -
866B ALA* 1.3 76.5 - - - +
868B VAL* 1.3 65.3 + - - +
870B ALA* 2.9 22.4 + - - +
871B VAL 3.6 3.1 + - - -
903B VAL* 4.1 19.5 - - + +
906B LEU* 4.6 18.4 - - + -
907B LEU* 3.8 25.6 - - + -
912B PHE* 4.1 20.4 - - + -
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Residues in contact with VAL 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864B ARG* 3.0 15.0 + - + +
865B ASP* 2.9 11.5 + - - +
867B LEU* 1.3 79.0 - - - +
869B ASN* 1.3 65.7 + - - +
871B VAL* 3.4 5.4 + - - +
872B ILE* 3.2 38.6 + - + +
903B VAL* 4.6 5.6 - - - +
907B LEU* 3.6 25.8 - - + -
1083B PHE* 4.1 18.2 - - + -
1086B HIS* 4.1 17.7 - - + +
1087B ILE* 5.6 1.1 - - + -
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Residues in contact with ASN 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865B ASP* 2.6 39.1 + - - +
866B ALA* 3.6 10.7 - - - +
867B LEU 3.1 0.2 - - - -
868B VAL* 1.3 75.9 - - - +
870B ALA* 1.3 55.9 + - - +
872B ILE* 4.2 15.3 - - - +
873B ASP* 2.8 49.0 + - - +
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Residues in contact with ALA 870 (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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404B LYS 4.1 8.7 - - - +
405B LEU* 6.2 0.2 - - + -
406B PRO* 5.8 2.5 - - + -
847B LEU* 4.1 35.2 - - + -
866B ALA 2.9 10.9 + - - +
867B LEU* 2.9 13.4 + - - +
869B ASN* 1.3 76.8 - - - +
871B VAL* 1.3 51.4 + - - +
873B ASP* 4.3 2.2 - - - -
874B SER* 2.6 36.2 + - - -
899B PHE* 3.8 6.9 - - + -
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Residues in contact with VAL 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B LEU 4.1 2.2 - - - +
868B VAL* 3.4 8.2 + - - +
869B ASN 3.3 0.2 - - - -
870B ALA* 1.3 75.3 - - - +
872B ILE* 1.3 63.1 + - - +
874B SER* 2.8 17.7 + - - -
875B LEU* 3.0 23.4 + - + +
899B PHE* 3.7 15.0 - - + +
900B PRO* 3.7 20.6 - - + -
903B VAL* 3.4 45.1 - - + -
1083B PHE* 5.0 1.6 - - + -
1087B ILE* 3.3 32.8 - - + -
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Residues in contact with ILE 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868B VAL* 3.2 37.6 + - + +
869B ASN* 3.8 15.7 - - - +
871B VAL* 1.3 76.7 - - - +
873B ASP* 1.3 65.0 + - - +
875B LEU* 3.7 0.7 - - - +
876B SER* 2.7 37.0 + - - -
1086B HIS* 4.4 2.9 - - + -
1087B ILE* 4.6 15.9 - - + -
1090B GLN* 3.7 55.0 - - + +
1091B VAL* 4.2 10.4 - - - +
1093B LYS* 6.3 0.2 - - - -
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Residues in contact with ASP 873 (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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404B LYS* 3.2 33.3 - - + +
869B ASN* 2.8 37.3 + - - +
870B ALA* 4.6 2.9 - - - +
872B ILE* 1.3 80.6 - - - +
874B SER* 1.3 55.9 + - - +
876B SER* 4.1 5.5 - - - -
877B ALA* 3.1 26.1 + - - +
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Residues in contact with SER 874 (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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403B ALA 3.8 11.7 - - - -
404B LYS* 3.7 13.9 - - - +
405B LEU* 3.8 16.8 - - - -
835B PHE* 3.7 10.6 - - - -
870B ALA 2.6 25.6 + - - -
871B VAL 2.8 11.4 + - - -
873B ASP* 1.3 74.1 - - - +
875B LEU* 1.3 62.5 + - - +
876B SER 3.2 1.1 - - - -
877B ALA* 3.4 2.9 + - - +
878B TYR* 2.9 26.9 + - - +
896B LEU* 5.3 1.1 - - - -
899B PHE* 3.3 15.5 - - - -
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Residues in contact with LEU 875 (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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353B LEU* 4.7 0.4 - - + -
871B VAL* 3.0 34.4 + - + +
874B SER* 1.3 78.1 + - - +
876B SER* 1.3 61.3 + - - +
878B TYR* 3.3 5.1 - - + +
879B ARG* 3.0 27.0 + - - +
890B LEU* 4.5 6.7 - - + -
891B MET 4.6 5.6 - - - +
892B VAL* 3.2 46.0 - - + -
893B PRO* 4.6 2.2 - - + -
896B LEU* 4.2 23.1 - - + -
899B PHE* 5.1 2.5 - - + -
900B PRO* 4.1 14.1 - - + -
1087B ILE* 4.4 10.1 - - + -
1091B VAL* 4.0 17.1 - - + +
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Residues in contact with SER 876 (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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872B ILE* 2.7 25.0 + - - -
873B ASP* 4.1 5.6 - - - -
875B LEU* 1.3 77.0 - - - +
877B ALA* 1.3 66.1 + - - +
879B ARG* 3.2 3.3 + - - +
880B SER* 3.0 30.2 + - - -
1090B GLN 5.0 0.5 + - - -
1091B VAL* 3.2 36.5 + - - +
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Residues in contact with ALA 877 (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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402B LYS 3.2 27.4 - - - +
403B ALA* 4.4 4.0 - - - +
404B LYS* 4.0 5.4 - - + -
831B LEU* 4.5 7.2 - - + +
835B PHE* 4.8 3.6 - - + -
873B ASP 3.1 19.6 + - - +
874B SER* 3.6 5.8 - - - +
875B LEU 3.3 0.2 - - - -
876B SER* 1.3 81.2 - - - +
878B TYR* 1.3 63.4 + - - +
880B SER* 3.5 13.7 + - - -
881B SER* 3.6 11.4 + - - -
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Residues in contact with TYR 878 (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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350B VAL* 3.6 25.9 - - + +
832B ASN* 4.5 17.1 + - - -
835B PHE* 3.7 34.7 - + + -
874B SER 2.9 15.0 + - - +
875B LEU* 3.3 12.8 - - - +
876B SER 3.1 0.2 - - - -
877B ALA* 1.3 77.4 - - - +
879B ARG* 1.3 60.5 + - - +
881B SER* 2.9 20.8 + - - -
882B VAL* 3.2 40.7 - - + +
891B MET* 3.7 17.0 - - + -
892B VAL* 3.7 7.6 - - - -
893B PRO* 3.4 53.4 - - + +
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Residues in contact with ARG 879 (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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875B LEU 3.0 13.2 + - - +
876B SER 3.6 4.5 - - - +
878B TYR* 1.3 77.3 - - + +
880B SER* 1.3 56.7 + - - +
881B SER 2.7 16.0 + - - -
882B VAL* 3.0 30.9 + - + +
888B PRO* 4.3 20.2 + - - +
889B GLY 4.2 13.9 + - - -
890B LEU* 6.0 1.0 - - - +
891B MET* 5.5 8.7 - - + +
1091B VAL* 3.7 21.7 - - + +
1092B ASN* 2.4 50.6 - - - +
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Residues in contact with SER 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876B SER* 3.0 20.4 + - - -
877B ALA* 3.8 8.9 - - - -
878B TYR 3.3 0.2 - - - -
879B ARG* 1.3 75.1 - - - +
881B SER* 1.3 57.0 + - - +
882B VAL 3.7 0.9 - - - -
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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
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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