Contacts of the helix formed by residues 836 - 848 (chain A) in PDB entry 4C2M
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 THR 836 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A LEU* 1.3 77.1 - - - +
837A ALA* 1.3 60.0 + - - +
838A GLU* 3.3 13.5 + - - +
839A GLY 2.9 19.6 + - - -
840A ASN* 2.9 26.7 + - - -
914A ASP 5.4 0.2 + - - -
915A GLY* 2.9 12.1 + - - +
916A THR 3.4 24.9 - - - +
917A MET* 3.5 19.5 - - + +
919A LYS* 4.7 3.8 - - - +
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Residues in contact with ALA 837 (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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836A THR* 1.3 74.0 - - - +
838A GLU* 1.3 62.2 + - - +
840A ASN* 3.4 7.6 + - - +
841A LYS* 3.1 22.9 + - - +
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Residues in contact with GLU 838 (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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836A THR* 3.3 10.2 + - - +
837A ALA* 1.3 79.9 - - - +
839A GLY* 1.3 60.8 + - - +
841A LYS* 3.3 9.6 + - - +
842A TRP* 3.2 61.2 + - + +
914A ASP 4.9 4.2 - - - +
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Residues in contact with GLY 839 (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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835A LEU* 4.1 7.4 - - - -
836A THR* 2.9 16.6 + - - -
838A GLU* 1.3 73.7 - - - +
840A ASN* 1.3 58.5 + - - +
841A LYS 3.1 1.6 - - - -
842A TRP* 3.2 24.0 + - - +
843A ARG* 3.0 26.5 + - - +
911A CYS* 3.8 4.4 - - - -
915A GLY* 3.9 14.4 - - - -
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Residues in contact with ASN 840 (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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835A LEU* 3.3 39.8 + - - +
836A THR 2.9 13.7 + - - +
837A ALA* 4.0 6.7 - - - +
838A GLU 3.4 0.2 - - - -
839A GLY* 1.3 76.3 - - - +
841A LYS* 1.3 61.2 + - - +
843A ARG* 3.5 6.1 + - - +
844A THR* 3.1 32.8 + - + +
985A ARG* 2.8 39.3 + - - +
987A TYR* 5.9 2.6 - - - -
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Residues in contact with LYS 841 (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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837A ALA 3.1 13.2 + - - +
838A GLU* 3.4 12.1 - - - +
839A GLY 3.1 0.2 - - - -
840A ASN* 1.3 74.7 - - - +
842A TRP* 1.3 72.9 + - + +
844A THR* 3.1 6.3 + - - +
845A ASP* 2.9 54.0 + - - +
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Residues in contact with TRP 842 (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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838A GLU* 3.2 47.0 + - + +
839A GLY* 3.3 19.7 - - - +
841A LYS* 1.3 84.2 - - + +
843A ARG* 1.3 65.0 + - - +
845A ASP* 3.4 5.6 + - - +
846A ILE* 3.0 32.0 + - + +
910A LYS* 3.1 64.7 - - + +
911A CYS* 4.1 7.6 - - - -
914A ASP* 3.8 16.8 - - + -
915A GLY* 3.7 20.4 - - - -
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Residues in contact with ARG 843 (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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835A LEU* 4.3 3.1 - - + -
839A GLY 3.0 12.6 + - - +
840A ASN* 3.6 10.9 + - - +
841A LYS 3.1 0.2 - - - -
842A TRP* 1.3 77.7 - - - +
844A THR* 1.3 72.5 + - - +
846A ILE* 3.3 2.7 + - - +
847A LEU* 2.9 44.8 + - + +
907A VAL* 4.1 13.3 - - + +
911A CYS* 4.0 14.6 - - - -
944A MET 4.3 0.7 - - - -
945A CYS* 2.6 30.1 + - - +
983A LYS 2.9 28.7 + - - -
984A GLY* 4.2 2.6 - - - -
985A ARG* 3.7 51.3 - - - +
988A SER* 4.7 2.0 + - - -
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Residues in contact with THR 844 (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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840A ASN* 3.1 20.3 + - + +
841A LYS* 3.1 8.7 + - - +
843A ARG* 1.3 94.1 - - - +
845A ASP* 1.3 65.4 + - - +
847A LEU* 3.8 8.0 - - + +
848A LYS* 3.0 34.8 + - - +
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Residues in contact with ASP 845 (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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841A LYS* 2.9 54.2 + - - +
842A TRP* 3.7 7.1 + - - +
844A THR* 1.3 83.2 + - - +
846A ILE* 1.3 63.2 + - + +
848A LYS* 3.4 20.7 + - - +
849A THR* 3.8 11.3 - - - +
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Residues in contact with ILE 846 (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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842A TRP* 3.0 20.3 + - + +
843A ARG 3.9 2.9 - - - +
845A ASP* 1.3 74.4 - - + +
847A LEU* 1.3 65.5 + - - +
849A THR* 2.8 29.4 + - - +
903A ILE* 3.9 10.0 - - + +
906A GLN* 3.8 49.4 - - + +
907A VAL* 3.6 25.8 - - + -
910A LYS* 4.1 26.5 - - + -
911A CYS* 5.6 0.4 - - - -
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Residues in contact with LEU 847 (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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843A ARG* 2.9 59.3 + - + +
844A THR* 3.8 8.1 - - - +
846A ILE* 1.3 77.3 - - - +
848A LYS* 1.3 58.8 + - - +
849A THR 3.0 0.9 + - - -
850A SER* 2.7 27.0 + - - -
851A VAL* 4.2 1.6 + - - +
903A ILE* 4.4 9.2 - - + -
907A VAL* 4.0 15.5 - - + -
945A CYS 4.9 1.6 - - - +
946A LEU* 4.0 25.4 - - + -
981A TYR* 4.5 1.6 - - + +
983A LYS* 4.0 36.4 - - + +
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Residues in contact with LYS 848 (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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844A THR* 3.0 19.0 + - - +
845A ASP* 3.6 12.6 - - - +
846A ILE 3.2 0.6 - - - -
847A LEU* 1.3 76.1 - - - +
849A THR* 1.3 57.7 + - + +
850A SER 3.2 1.6 - - - -
851A VAL* 3.1 32.8 - - + +
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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