Contacts of the helix formed by residues 872 - 886 (chain A) in PDB entry 3ZFM
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 LYS 872 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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809A VAL* 4.6 2.7 - - - -
868A ASN 5.7 5.1 + - - -
870A ARG 5.1 4.3 - - - +
871A PRO* 1.3 77.2 - - - +
873A PHE* 1.3 67.0 + - - +
874A GLY* 3.2 5.6 - - - +
875A GLN* 2.8 34.6 + - + +
876A ILE* 3.0 20.9 + - - +
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Residues in contact with PHE 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A ALA* 4.0 11.4 - - + +
734A MET* 3.5 49.6 - - + -
735A LYS* 3.7 23.6 - - + +
738A ALA* 4.2 12.3 - - + -
805A SER* 3.6 24.0 - - - -
808A ASP* 3.6 33.2 - - + -
809A VAL* 3.7 10.1 - - + -
812A TYR* 3.6 27.1 - + + -
872A LYS* 1.3 72.5 - - - +
874A GLY* 1.3 61.4 + - - +
876A ILE* 3.2 14.5 + - + +
877A VAL* 3.1 27.4 + - - +
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Residues in contact with GLY 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735A LYS* 3.7 32.0 - - - +
872A LYS* 3.2 4.1 - - - +
873A PHE* 1.3 76.8 - - - +
875A GLN* 1.4 59.8 + - - +
877A VAL* 3.5 4.0 + - - +
878A ASN* 3.2 30.1 + - - -
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Residues in contact with GLN 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870A ARG 4.6 1.0 - - - +
871A PRO* 3.5 16.3 - - + +
872A LYS* 2.8 53.3 + - + +
874A GLY* 1.4 73.7 - - - +
876A ILE* 1.4 58.9 + - - +
878A ASN* 3.4 9.9 + - - +
879A THR* 2.9 33.5 + - - +
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Residues in contact with ILE 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A ALA* 3.7 13.7 - - + -
809A VAL* 3.9 18.8 - - + -
812A TYR* 3.6 36.8 - - + -
858A LEU* 4.1 15.9 - - + -
862A CYS* 4.1 9.9 - - - -
871A PRO* 3.9 16.6 - - + -
872A LYS 3.0 18.7 + - - +
873A PHE* 3.2 27.6 + - + +
875A GLN* 1.4 74.3 - - - +
877A VAL* 1.4 57.5 + - - +
879A THR* 3.1 9.9 + - - -
880A LEU* 3.0 36.9 + - + +
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Residues in contact with VAL 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A ARG* 3.5 41.3 - - + +
731A ALA* 3.7 33.7 - - + +
732A ALA* 3.7 10.1 - - + +
735A LYS* 4.8 8.5 - - + -
873A PHE 3.1 16.6 + - - +
874A GLY* 3.8 6.7 - - - +
876A ILE* 1.4 73.7 - - - +
878A ASN* 1.3 56.8 + - - +
880A LEU* 3.4 7.7 + - - +
881A ASP* 2.9 37.5 + - - +
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Residues in contact with ASN 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A GLY 3.2 20.5 + - - +
875A GLN* 3.5 13.4 - - - +
876A ILE 3.3 0.2 - - - -
877A VAL* 1.3 75.2 - - - +
879A THR* 1.3 56.6 + - - +
881A ASP* 3.5 7.4 + - - +
882A LYS* 3.0 34.6 + - + +
885A ARG* 4.4 8.1 + - - -
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Residues in contact with THR 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854A ALA 5.4 0.2 - - - +
858A LEU* 3.9 25.0 - - + +
875A GLN* 2.9 16.0 + - - +
876A ILE* 3.4 12.5 - - - -
878A ASN* 1.3 73.2 - - - +
880A LEU* 1.3 62.9 + - - +
882A LYS* 3.4 8.4 + - - +
883A MET* 3.3 43.6 + - + +
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Residues in contact with LEU 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A VAL* 3.9 17.0 - - + +
727A LEU* 3.7 9.0 - - + +
728A ARG* 3.7 32.8 - - + +
731A ALA* 4.4 2.0 - - + -
812A TYR* 3.3 24.5 - - - +
816A MET* 4.8 1.3 - - + -
855A LEU* 4.0 23.6 - - + -
858A LEU* 3.8 20.9 - - + -
876A ILE* 3.0 28.0 + - + +
877A VAL* 4.0 3.1 - - - +
879A THR* 1.3 71.8 - - - +
881A ASP* 1.4 59.3 + - - +
883A MET* 3.3 10.0 + - - +
884A ILE* 3.1 33.6 + - - +
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Residues in contact with ASP 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A ARG* 2.7 49.4 + - - +
877A VAL* 2.9 24.2 + - - +
878A ASN* 3.7 7.7 + - - +
879A THR 3.4 0.2 - - - -
880A LEU* 1.4 73.3 - - - +
882A LYS* 1.4 58.0 + - - +
884A ILE* 3.3 10.1 + - - +
885A ARG* 2.9 57.5 + - + +
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Residues in contact with LYS 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878A ASN* 3.0 21.7 + - - +
879A THR* 3.6 8.5 - - - +
880A LEU 3.4 0.4 - - - -
881A ASP* 1.4 75.6 - - - +
883A MET* 1.4 56.5 + - + +
885A ARG* 3.8 21.7 - - - +
886A ASN* 3.2 27.7 + - - +
889A SER* 4.5 1.0 + - - -
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Residues in contact with MET 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A VAL* 4.5 4.3 - - + -
854A ALA* 3.4 40.8 - - + +
855A LEU* 3.8 26.0 - - + +
858A LEU* 4.8 1.8 - - + -
879A THR* 3.3 33.9 + - + +
880A LEU* 3.4 17.0 - - + +
881A ASP 3.2 0.2 - - - -
882A LYS* 1.4 75.6 - - + +
884A ILE* 1.4 59.2 + - - +
885A ARG 3.3 0.2 - - - -
886A ASN 3.0 23.7 - - - +
887A PRO* 3.4 1.0 - - - +
889A SER* 3.8 17.7 - - - +
890A LEU* 3.3 34.8 - - + +
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Residues in contact with ILE 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721A ILE* 4.1 30.6 - - + +
724A VAL* 3.8 24.2 - - + +
725A GLY* 4.6 7.6 - - - +
728A ARG* 4.3 16.6 - - + -
880A LEU 3.1 19.9 + - - +
881A ASP* 3.3 20.4 + - - +
883A MET* 1.4 74.4 - - - +
885A ARG* 1.3 64.9 + - + +
886A ASN 3.5 0.3 + - - -
887A PRO* 3.6 10.9 - - - +
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Residues in contact with ARG 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878A ASN* 4.4 8.9 + - - -
881A ASP* 2.9 37.7 + - - +
882A LYS* 3.8 34.3 - - - +
884A ILE* 1.3 78.0 - - + +
886A ASN* 1.4 58.0 + - + +
887A PRO* 3.4 7.8 - - - +
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Residues in contact with ASN 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882A LYS 3.2 17.3 + - - +
883A MET 3.0 5.5 - - - +
885A ARG* 1.4 76.8 - - + +
887A PRO* 1.4 57.7 - - - +
888A ASN* 3.0 32.5 + - - +
889A SER* 2.7 38.3 + - - +
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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