Contacts of the helix formed by residues 877 - 892 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767C PRO* 3.5 33.4 + - + +
768C PRO 2.8 30.5 + - - +
769C MET* 3.7 14.9 - - - +
773C GLU* 3.0 20.9 + - - +
875C LYS 3.8 1.2 + - - -
876C PRO* 1.3 78.0 - - - +
878C LEU* 1.3 63.0 + - - +
879C ASN* 3.0 10.7 + - - +
880C ALA* 2.8 32.1 + - - +
881C ILE* 3.1 16.6 + - - +
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Residues in contact with LEU 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767C PRO* 5.1 1.4 - - - +
877C ASN* 1.3 74.7 - - - +
879C ASN* 1.3 61.8 + - - +
880C ALA 3.4 0.2 - - - -
881C ILE* 3.8 19.1 - - + -
882C ARG* 3.0 51.3 + - + +
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Residues in contact with ASN 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762C ALA 3.3 16.6 + - - +
763C GLY* 3.8 24.3 + - - +
764C GLY 4.6 3.6 - - - +
766C ASP 3.7 7.1 - - - +
767C PRO* 3.4 29.0 - - - +
769C MET* 5.3 4.3 - - - -
877C ASN* 3.0 8.4 + - - +
878C LEU* 1.3 77.9 - - - +
880C ALA* 1.3 55.6 + - - +
882C ARG* 3.4 12.4 + - - +
883C SER* 2.7 37.6 + - - -
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Residues in contact with ALA 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761C TRP* 3.5 25.8 - - + -
769C MET* 4.4 2.6 - - - -
773C GLU* 3.3 35.9 - - + -
876C PRO* 4.3 6.3 - - + -
877C ASN* 2.8 14.1 + - - +
879C ASN* 1.3 73.7 - - - +
881C ILE* 1.3 65.9 + - - +
883C SER* 3.3 1.6 + - - -
884C LEU* 3.0 33.2 + - + +
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Residues in contact with ILE 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776C ALA* 6.1 0.2 - - + -
780C ILE* 6.0 4.9 - - + -
876C PRO* 3.9 31.0 - - + +
877C ASN 3.1 16.5 + - - +
878C LEU* 3.7 21.3 - - + +
880C ALA* 1.3 77.4 - - - +
882C ARG* 1.3 57.8 + - - +
884C LEU* 3.2 10.7 + - + +
885C GLU* 2.8 51.1 + - + +
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Residues in contact with ARG 882 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878C LEU* 3.0 43.4 + - + +
879C ASN* 3.8 12.7 - - - +
881C ILE* 1.3 75.9 - - + +
883C SER* 1.3 61.9 + - - +
885C GLU* 3.4 17.3 + - - +
886C ALA* 3.1 21.0 + - - +
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Residues in contact with SER 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759C VAL* 5.8 1.6 - - - -
760C ALA 3.6 20.3 - - - +
761C TRP* 3.9 14.9 - - - -
762C ALA* 3.2 28.0 + - - +
879C ASN 2.7 22.5 + - - -
880C ALA 3.6 4.7 - - - -
881C ILE 3.2 0.2 - - - -
882C ARG* 1.3 74.4 - - - +
884C LEU* 1.3 64.9 + - - +
886C ALA* 3.1 17.9 + - - +
887C VAL* 3.1 18.2 + - - +
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Residues in contact with LEU 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759C VAL* 4.1 15.7 - - + -
761C TRP* 4.1 11.2 - - + -
773C GLU 4.7 0.2 - - - +
776C ALA* 4.2 26.2 - - + +
777C ALA* 3.9 23.3 - - + +
780C ILE* 4.5 12.8 - - + -
781C VAL* 3.6 28.4 - - + +
876C PRO* 5.8 0.2 - - + -
880C ALA* 3.0 26.2 + - + +
881C ILE* 3.7 11.4 - - + +
883C SER* 1.3 72.1 - - - +
885C GLU* 1.3 61.3 + - + +
887C VAL* 3.0 6.9 + - + +
888C ILE* 2.8 40.2 + - + +
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Residues in contact with GLU 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C ILE* 2.8 38.4 + - + +
882C ARG* 3.6 18.4 + - - +
884C LEU* 1.3 75.8 - - + +
886C ALA* 1.3 56.6 + - - +
888C ILE* 3.9 12.9 - - + +
889C ARG* 3.0 31.7 + - - +
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Residues in contact with ALA 886 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744C VAL* 3.7 21.3 - - + -
882C ARG 3.1 10.9 + - - +
883C SER* 3.1 17.5 + - - +
885C GLU* 1.3 74.4 - - - +
887C VAL* 1.3 57.3 + - - +
889C ARG* 3.5 18.1 + - - +
890C VAL* 3.0 33.8 + - - +
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Residues in contact with VAL 887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744C VAL* 3.5 12.6 - - + -
757C VAL* 4.0 15.5 - - + -
758C ASN 3.6 20.9 - - - +
759C VAL* 4.0 16.8 - - + -
760C ALA 4.7 2.0 - - - +
781C VAL* 3.9 20.4 - - + -
883C SER 3.1 14.0 + - - +
884C LEU* 3.0 12.7 + - + +
886C ALA* 1.3 72.7 - - - +
888C ILE* 1.3 59.5 + - - +
890C VAL 3.3 0.7 + - - -
891C HIS* 2.9 37.3 + - + +
898C MET* 3.6 16.8 - - + -
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Residues in contact with ILE 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780C ILE* 3.8 27.8 - - + -
781C VAL* 4.9 1.3 - - + -
884C LEU* 2.8 30.2 + - + +
885C GLU* 3.9 12.3 - - + +
887C VAL* 1.3 72.2 - - - +
889C ARG* 1.3 58.6 - - - +
892C SER* 2.9 31.9 + - - -
898C MET* 3.4 45.2 - - + +
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Residues in contact with ARG 889 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744C VAL* 5.6 2.6 - - - +
745C ASP* 5.2 5.1 + - - -
885C GLU 3.0 18.4 + - - +
886C ALA* 3.7 18.9 + - - +
887C VAL 3.3 0.2 - - - -
888C ILE* 1.3 79.7 - - - +
890C VAL* 1.3 74.0 + - - +
892C SER* 2.8 21.7 + - - -
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Residues in contact with VAL 890 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744C VAL* 3.7 30.1 - - + +
745C ASP* 4.5 14.4 - - - +
747C VAL* 3.4 33.7 - - + -
886C ALA 3.0 21.6 + - - +
887C VAL 3.8 3.1 - - - +
889C ARG* 1.3 92.3 - - - +
891C HIS* 1.3 66.0 + - + +
892C SER 3.3 1.5 + - - -
893C LYS* 3.6 17.3 + - - +
894C TYR* 4.0 5.1 - - + -
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Residues in contact with HIS 891 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744C VAL* 4.4 6.9 + - + -
747C VAL* 3.9 21.1 - - + +
754C GLY* 3.8 10.0 + - - -
756C ASN 3.0 29.0 + - - -
757C VAL* 3.4 24.0 - - + -
758C ASN 4.6 1.4 + - - -
887C VAL* 2.9 38.3 + - + +
890C VAL* 1.3 80.5 - - + +
892C SER* 1.3 60.0 + - - +
893C LYS 3.0 5.2 - - - -
894C TYR* 3.1 10.3 + - - -
895C TRP* 3.1 44.5 + - + -
898C MET* 3.5 21.3 - - + +
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Residues in contact with SER 892 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888C ILE* 2.9 15.7 + - - -
889C ARG* 2.8 25.2 + - - -
891C HIS* 1.3 77.0 - - - +
893C LYS* 1.3 60.9 + - - +
894C TYR 3.3 0.4 + - - -
895C TRP 4.1 0.6 - - - +
898C MET* 3.4 24.4 - - - +
899C GLN* 2.9 34.1 - - - +
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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