Contacts of the helix formed by residues 822 - 841 (chain A) in PDB entry 6CIM
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 822 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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821A ALA* 1.3 79.3 - - - +
823A LYS* 1.3 66.6 + - - +
824A GLU* 3.8 15.1 + - - +
825A GLU* 3.5 24.2 + - - +
826A ARG* 3.2 21.5 + - - +
828A ARG* 5.7 0.5 + - - -
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Residues in contact with LYS 823 (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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822A SER* 1.3 74.8 - - - +
824A GLU* 1.3 66.1 + - - +
826A ARG* 3.4 9.9 + - - +
827A LYS* 2.9 62.1 + - + +
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Residues in contact with GLU 824 (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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822A SER* 3.3 16.9 - - - +
823A LYS* 1.3 86.2 + - - +
825A GLU* 1.3 57.5 + - - +
827A LYS* 3.3 13.4 + - + +
828A ARG* 2.9 54.3 + - - +
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Residues in contact with GLU 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A ASN 4.4 2.3 - - - +
821A ALA* 3.5 22.3 - - + +
822A SER* 3.5 21.1 + - - +
823A LYS 3.3 0.6 - - - -
824A GLU* 1.3 78.9 - - - +
826A ARG* 1.3 58.4 + - - +
828A ARG* 3.3 19.8 + - - +
829A TRP* 2.9 58.8 + - + +
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Residues in contact with ARG 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A LYS* 5.2 6.9 - - - +
809A GLN* 4.6 5.3 - - - +
810A LEU* 4.0 23.2 - - - +
815A VAL* 5.1 7.9 - - - +
819A PRO 5.0 5.1 + - - -
820A ASN* 4.8 1.8 + - - -
821A ALA* 3.2 37.6 + - + +
822A SER 3.2 17.0 - - - +
823A LYS* 3.4 7.8 + - - +
824A GLU 3.3 0.2 - - - -
825A GLU* 1.3 72.8 - - - +
827A LYS* 1.3 61.3 + - + +
829A TRP* 3.2 31.0 + - + +
830A GLN* 2.9 29.1 + - - +
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Residues in contact with LYS 827 (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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823A LYS* 2.9 56.6 + - + +
824A GLU* 3.7 11.9 - - + +
826A ARG* 1.3 78.4 - - + +
828A ARG* 1.3 58.8 + - + +
830A GLN* 3.4 9.5 + - - +
831A ALA* 2.9 28.5 + - - +
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Residues in contact with ARG 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A SER* 5.7 0.2 + - - -
824A GLU* 2.9 36.1 + - - +
825A GLU* 3.7 27.0 - - - +
827A LYS* 1.3 73.8 - - + +
829A TRP* 1.3 59.5 + - + +
831A ALA* 3.7 7.3 - - + +
832A THR* 2.8 39.7 + - - +
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Residues in contact with TRP 829 (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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809A GLN* 3.6 27.8 - - + +
810A LEU* 4.0 11.7 - - + -
812A ILE* 4.0 18.5 - - + +
813A GLY* 3.2 33.5 - - - -
815A VAL* 3.6 31.0 - - + -
818A HIS* 5.8 1.8 - - + -
820A ASN 5.3 0.2 - - - -
821A ALA* 3.3 31.6 - - + -
825A GLU* 2.9 47.3 + - + +
826A ARG* 3.3 31.0 - - + +
828A ARG* 1.3 79.7 - - + +
830A GLN* 1.3 56.6 + - - +
832A THR* 3.3 4.7 + - - -
833A LEU* 3.0 28.3 + - - +
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Residues in contact with GLN 830 (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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805A TYR* 3.6 21.3 + - - +
809A GLN* 3.5 40.1 + - + +
826A ARG 2.9 12.9 + - - +
827A LYS* 3.8 8.7 + - - +
829A TRP* 1.3 72.9 - - - +
831A ALA* 1.3 61.7 + - - +
833A LEU* 3.3 1.6 + - - +
834A ASP* 2.9 50.4 + - - +
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Residues in contact with ALA 831 (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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827A LYS 2.9 17.6 + - - +
828A ARG* 3.7 9.9 - - + +
829A TRP 3.3 0.2 - - - -
830A GLN* 1.3 77.8 - - - +
832A THR* 1.3 56.7 + - - +
834A ASP* 3.4 6.0 + - - +
835A LYS* 2.9 40.5 + - + +
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Residues in contact with THR 832 (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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812A ILE* 4.5 12.0 - - + +
828A ARG* 2.8 23.7 + - - +
829A TRP* 3.4 7.5 - - - -
831A ALA* 1.3 76.2 - - - +
833A LEU* 1.3 55.9 + - - +
835A LYS* 3.8 6.9 - - - +
836A HIS* 2.9 31.8 + - + +
869A LEU* 3.7 30.5 - - + -
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Residues in contact with LEU 833 (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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805A TYR* 3.9 28.5 - - + -
808A PHE* 3.6 24.7 - - + -
809A GLN* 4.0 17.5 - - + +
812A ILE* 3.6 22.4 - - + +
829A TRP 3.0 13.7 + - - +
830A GLN* 3.8 4.5 - - - +
832A THR* 1.3 76.2 - - - +
834A ASP* 1.3 60.2 + - - +
836A HIS* 3.3 1.6 + - + +
837A LEU* 2.9 47.7 + - + +
866A VAL* 3.7 29.8 - - + -
869A LEU* 4.5 4.5 - - + -
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Residues in contact with ASP 834 (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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805A TYR* 3.0 30.9 + - - -
830A GLN* 2.9 40.0 + - - +
831A ALA* 3.9 5.2 + - - +
833A LEU* 1.3 75.3 - - - +
835A LYS* 1.3 66.5 + - - +
837A LEU* 3.4 6.9 + - - +
838A ARG* 2.9 27.8 + - - +
843A LEU 4.4 2.4 - - - +
845A PRO* 4.1 31.2 - - + +
853A PHE* 6.1 0.2 - - - -
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Residues in contact with LYS 835 (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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831A ALA* 2.9 23.6 + - + +
832A THR* 3.8 5.2 - - - +
834A ASP* 1.3 76.6 - - - +
836A HIS* 1.3 57.2 + - - +
838A ARG* 3.3 22.8 + - - +
839A LYS* 2.9 29.6 + - - +
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Residues in contact with HIS 836 (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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832A THR* 2.9 18.5 + - + +
833A LEU* 3.9 3.8 - - + +
835A LYS* 1.3 76.5 - - - +
837A LEU* 1.3 58.7 + - + +
839A LYS* 4.3 10.5 - - + -
840A ARG* 2.9 46.1 + - + +
865A ALA* 2.8 40.5 + - + +
866A VAL* 4.5 2.0 + - - +
868A GLU* 2.9 30.1 + - + +
869A LEU* 3.5 33.0 - - + +
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Residues in contact with LEU 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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805A TYR* 5.0 3.1 - - + -
833A LEU* 2.9 49.2 + - + +
834A ASP* 3.9 7.2 - - - +
836A HIS* 1.3 74.9 - - - +
838A ARG* 1.3 60.5 + - - +
841A MET* 2.9 30.0 + - + -
842A ASN 2.9 23.4 + - - -
843A LEU* 3.1 25.8 + - + +
853A PHE* 5.0 13.7 - - + -
857A LEU* 4.1 29.4 - - + -
862A THR* 4.7 4.3 - - - -
865A ALA* 4.8 4.3 - - + -
866A VAL* 4.5 11.7 - - + -
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Residues in contact with ARG 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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834A ASP* 2.9 20.5 + - - +
835A LYS* 3.6 23.4 - - - +
837A LEU* 1.3 76.2 - - - +
839A LYS* 1.3 61.9 + - - +
842A ASN* 3.5 18.8 - - - +
843A LEU 3.4 21.4 + - - +
844A LYS* 5.3 0.9 - - - -
845A PRO* 3.2 37.7 - - + +
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Residues in contact with LYS 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 LYS 2.9 17.6 + - - +
836A HIS* 3.8 12.3 - - + +
837A LEU 3.2 0.2 - - - -
838A ARG* 1.3 80.5 - - - +
840A ARG* 1.3 73.8 + - + +
842A ASN* 4.4 1.9 + - - +
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Residues in contact with ARG 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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836A HIS* 2.9 32.5 + - + +
839A LYS* 1.3 83.3 - - + +
841A MET* 1.3 71.9 + - + +
842A ASN* 3.6 0.4 - - - +
861A GLU* 5.0 2.6 - - - +
865A ALA* 4.8 8.3 - - + +
868A GLU* 3.0 40.5 + - - -
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Residues in contact with MET 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 LEU* 2.9 19.2 + - + +
840A ARG* 1.3 82.5 - - - +
842A ASN* 1.3 70.2 + - - +
843A LEU* 3.2 26.0 + - + +
856A LYS 4.9 4.5 - - - +
859A THR* 5.5 1.6 - - - -
861A GLU* 3.5 55.4 - - + +
862A THR* 3.6 27.8 - - + -
865A ALA* 4.0 21.3 - - + -
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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
------------------------------------------------------------
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