Contacts of the helix formed by residues 877 - 892 (chain B) in PDB entry 3ZNS
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 877 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767B PRO* 3.8 33.3 + - + -
768B PRO 3.0 29.8 + - - +
769B MET* 3.5 18.5 - - - +
773B GLU* 2.9 17.8 + - - +
875B LYS 3.6 1.8 + - - -
876B PRO* 1.3 76.7 - - - +
878B LEU* 1.3 63.0 + - - +
879B ASN* 3.2 8.1 + - - +
880B ALA* 2.7 34.0 + - - +
881B ILE* 3.1 16.1 + - - +
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Residues in contact with LEU 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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767B PRO* 5.2 3.6 - - + +
876B PRO 3.9 0.2 + - - -
877B ASN* 1.3 75.1 - - - +
879B ASN* 1.3 56.2 + - - +
881B ILE* 3.3 24.3 + - + -
882B ARG* 2.7 53.1 + - - +
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Residues in contact with ASN 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B ALA 3.6 13.1 - - - +
763B GLY* 3.4 27.5 - - - +
764B GLY 4.7 1.0 - - - +
766B ASP 3.5 20.3 - - - +
767B PRO* 3.7 9.6 - - + +
769B MET* 4.4 7.0 - - + -
877B ASN* 3.2 9.5 + - - +
878B LEU* 1.3 79.4 - - - +
880B ALA* 1.3 57.7 + - - +
882B ARG* 3.3 16.1 + - - +
883B SER* 2.9 34.0 + - - -
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Residues in contact with ALA 880 (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 TRP* 3.5 25.2 - - + -
769B MET* 3.9 3.7 - - - -
773B GLU* 3.4 35.7 - - + +
876B PRO* 4.4 6.7 - - + -
877B ASN* 2.7 17.2 + - - +
879B ASN* 1.3 73.1 - - - +
881B ILE* 1.3 57.3 + - - +
883B SER* 3.3 2.3 + - - -
884B LEU* 2.9 36.8 + - + +
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Residues in contact with ILE 881 (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 LYS* 5.8 3.6 - - + -
876B PRO* 3.6 37.7 - - + +
877B ASN 3.1 11.0 + - - +
878B LEU* 3.5 24.9 - - + +
880B ALA* 1.3 73.6 - - - +
882B ARG* 1.3 60.4 + - - +
884B LEU* 3.3 8.3 + - + +
885B GLU* 2.8 35.3 + - + +
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Residues in contact with ARG 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B LEU* 2.7 36.2 + - + +
879B ASN* 3.4 17.7 - - - +
881B ILE* 1.3 73.6 - - - +
883B SER* 1.3 61.4 + - - +
885B GLU* 3.5 7.4 + - + +
886B ALA* 3.2 21.8 + - - +
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Residues in contact with SER 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B VAL* 5.0 0.3 - - - +
759B VAL* 5.8 0.9 - - - -
760B ALA 3.7 17.4 + - - +
761B TRP* 3.7 16.3 - - - -
762B ALA* 3.1 31.3 + - - +
879B ASN 2.9 22.5 + - - -
880B ALA 3.5 4.9 - - - -
881B ILE 3.2 0.2 - - - -
882B ARG* 1.3 75.8 - - - +
884B LEU* 1.3 64.6 + - - +
886B ALA* 3.3 9.2 + - - +
887B VAL* 3.2 25.6 + - - +
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Residues in contact with LEU 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759B VAL* 3.9 26.5 - - + -
761B TRP* 4.4 6.5 - - + -
773B GLU 4.9 0.2 - - - +
776B ALA* 4.1 25.8 - - + +
777B ALA* 4.0 13.7 - - + +
780B ILE* 4.1 24.7 - - + -
781B VAL* 3.8 24.0 - - + -
876B PRO* 5.9 1.8 - - + -
880B ALA* 2.9 23.2 + - + +
881B ILE* 3.8 7.6 - - + +
883B SER* 1.3 73.8 - - - +
885B GLU* 1.3 60.8 + - - +
887B VAL* 3.2 5.2 + - + +
888B ILE* 2.9 42.1 + - + +
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Residues in contact with GLU 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881B ILE* 2.8 23.9 + - + +
882B ARG* 3.6 9.0 - - - +
884B LEU* 1.3 78.7 - - - +
886B ALA* 1.3 56.4 + - - +
888B ILE* 3.8 22.7 - - - +
889B ARG* 3.0 35.4 + - + +
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Residues in contact with ALA 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B VAL* 3.8 19.1 - - + -
882B ARG 3.2 12.7 + - - +
883B SER* 3.5 11.7 - - - +
884B LEU 3.3 0.2 - - - -
885B GLU* 1.3 76.0 - - - +
887B VAL* 1.3 62.7 + - - +
889B ARG* 3.5 21.3 + - - +
890B VAL* 3.0 29.5 + - - +
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Residues in contact with VAL 887 (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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744B VAL* 3.6 12.6 - - + -
757B VAL* 4.1 16.4 - - + -
758B ASN 3.6 22.4 - - - +
759B VAL* 3.9 16.6 - - + -
760B ALA 4.6 1.6 - - - +
781B VAL* 4.0 31.0 - - + -
785B ILE* 5.7 0.2 - - + -
883B SER 3.2 17.1 + - - +
884B LEU* 3.2 10.5 + - - +
886B ALA* 1.3 74.0 - - - +
888B ILE* 1.3 60.8 + - - +
890B VAL* 3.3 1.9 + - - +
891B HIS* 2.9 37.7 + - + +
898B MET* 5.4 1.6 - - - -
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Residues in contact with ILE 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B ILE* 3.9 26.9 - - + -
781B VAL* 4.7 3.6 - - + -
884B LEU* 2.9 29.5 + - + +
885B GLU* 3.8 24.9 - - - +
887B VAL* 1.3 73.5 - - - +
889B ARG* 1.3 56.0 + - - +
891B HIS 3.7 0.3 - - - -
892B SER* 2.8 35.0 + - - -
898B MET* 3.6 44.4 - - + +
900B ARG 5.6 4.5 - - - +
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Residues in contact with ARG 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B VAL* 4.8 5.3 - - - +
885B GLU* 3.0 22.0 + - + +
886B ALA* 3.6 23.0 + - - +
888B ILE* 1.3 78.0 - - - +
890B VAL* 1.3 89.4 + - - +
892B SER* 2.8 22.4 + - - -
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Residues in contact with VAL 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B VAL* 3.7 22.9 - - + +
745B ASP* 4.4 14.8 - - + -
747B VAL* 3.4 32.1 - - + -
886B ALA 3.0 14.1 + - - +
887B VAL 3.8 3.1 - - - +
889B ARG* 1.3 110.8 - - - +
891B HIS* 1.3 66.3 + - + +
892B SER 3.6 0.3 + - - -
893B LYS* 3.7 17.3 + - - +
894B TYR* 3.8 5.2 - - + -
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Residues in contact with HIS 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B VAL* 4.8 5.1 + - + -
747B VAL* 3.8 21.0 - - + +
754B GLY 3.6 11.7 - - - -
756B ASN 3.1 27.8 + - - -
757B VAL* 3.5 34.7 - - + +
758B ASN 4.7 1.6 + - - -
785B ILE* 4.7 2.2 - - + -
887B VAL* 2.9 25.3 + - + +
888B ILE 3.7 0.4 - - - -
890B VAL* 1.3 82.3 - - + +
892B SER* 1.3 60.7 + - - +
893B LYS 3.0 5.2 - - - -
894B TYR* 3.0 21.1 + + - -
895B TRP* 3.0 35.1 + + + -
898B MET* 3.7 16.9 - - + +
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Residues in contact with SER 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B ILE* 2.8 16.7 + - - -
889B ARG* 2.8 23.3 + - - -
891B HIS* 1.3 76.6 - - - +
893B LYS* 1.3 61.0 + - - +
894B TYR 3.4 0.2 + - - -
895B TRP 4.0 0.2 - - - +
898B MET* 3.4 26.0 - - - +
899B GLN* 3.0 33.6 - - - +
900B ARG 5.1 2.0 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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