Contacts of the helix formed by residues 843 - 859 (chain A) in PDB entry 3IAY
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 CYS 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A ARG* 4.1 0.2 - - - -
841A ASP 3.8 1.8 + - - -
842A SER* 1.3 77.4 - - - +
844A SER* 1.3 65.7 + - - +
845A LEU* 3.2 5.6 - - - -
846A VAL* 3.2 39.7 + - - +
847A SER* 3.3 8.8 + - - -
886A LYS 3.3 18.6 - - - +
887A LEU 3.8 8.7 - - - -
888A ILE 3.4 19.3 - - - +
889A ILE* 3.8 10.8 - - + +
957A TYR* 4.1 17.5 - - - -
961A GLN* 4.0 15.2 - - - +
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Residues in contact with SER 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ARG* 4.0 23.7 - - - +
842A SER 3.9 1.4 + - - -
843A CYS* 1.3 70.9 - - - +
845A LEU* 1.3 60.0 + - - +
847A SER* 4.3 4.0 - - - -
848A ILE* 2.8 50.1 + - - +
885A SER 3.9 4.5 + - - -
886A LYS* 3.2 30.6 + - - +
888A ILE 4.4 2.6 + - - -
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Residues in contact with LEU 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A CYS* 3.9 9.2 - - - -
844A SER* 1.3 79.4 + - - +
846A VAL* 1.3 66.9 + - + +
848A ILE* 4.2 2.1 - - - +
849A VAL* 3.1 32.7 + - + +
873A THR* 3.9 26.5 - - + -
877A ILE* 3.8 23.6 - - + -
882A VAL* 4.2 20.6 - - + -
886A LYS* 3.0 36.1 + - + +
887A LEU* 3.7 23.3 - - + -
957A TYR* 4.5 10.3 - - + +
962A LEU* 5.3 3.4 - - + -
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Residues in contact with VAL 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A ALA* 4.2 13.2 - - + -
842A SER* 4.8 5.8 - - - +
843A CYS* 3.2 25.9 + - - +
845A LEU* 1.3 77.7 - - + +
847A SER* 1.3 66.1 + - - +
849A VAL* 3.4 1.0 + - - +
850A MET* 2.9 47.2 + - + +
961A GLN* 3.7 39.5 - - + +
962A LEU* 3.9 17.9 - - + +
965A PRO* 4.3 5.6 - - + -
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Residues in contact with SER 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ARG* 3.5 16.6 + - - -
836A ALA 3.5 7.8 + - - -
837A SER* 3.7 23.8 + - - +
839A ARG 4.6 0.7 + - - -
842A SER* 3.5 22.5 - - - -
843A CYS 3.3 4.0 + - - -
844A SER* 3.3 7.4 + - - -
846A VAL* 1.3 78.1 - - - +
848A ILE* 1.3 60.3 + - - +
850A MET* 3.8 0.5 - - - +
851A ASN* 2.9 39.5 + - - -
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Residues in contact with ILE 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A SER* 2.8 40.0 + - - +
845A LEU* 4.2 2.2 - - - +
847A SER* 1.3 73.5 - - - +
849A VAL* 1.3 66.6 + - + +
851A ASN* 3.3 9.1 + - + +
852A LYS* 3.0 54.0 + - + +
869A PHE* 5.3 1.8 - - + -
886A LYS* 4.0 30.1 - - + +
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Residues in contact with VAL 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A LEU* 3.1 24.9 + - + +
846A VAL 4.0 1.6 - - - +
848A ILE* 1.3 79.6 - - + +
850A MET* 1.3 66.1 + - - +
852A LYS* 3.2 2.1 + - - +
853A VAL* 2.8 29.8 + - + +
869A PHE* 3.8 26.4 - - + -
870A VAL* 4.6 6.1 - - + -
873A THR* 3.8 34.1 - - + +
962A LEU* 4.1 12.3 - - + -
966A ILE* 4.0 18.4 - - + -
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Residues in contact with MET 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A GLN* 5.0 0.4 - - - +
835A LEU* 3.9 20.6 - - + -
836A ALA* 3.7 9.4 - - - +
837A SER* 3.6 38.4 - - - +
846A VAL* 2.9 39.7 + - + +
847A SER 3.8 3.1 - - - +
849A VAL* 1.3 77.8 - - - +
851A ASN* 1.3 57.3 + - - +
853A VAL* 3.3 1.7 + - - +
854A LEU* 2.9 36.7 + - + +
965A PRO* 3.7 15.5 - - + +
966A ILE* 3.7 24.2 - - + -
969A ILE* 4.3 22.6 - - + +
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Residues in contact with ASN 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A GLN* 2.8 28.5 + - - -
837A SER* 3.3 24.9 + - - +
838A VAL* 5.7 0.2 - - - +
847A SER* 2.9 25.2 + - - +
848A ILE* 3.5 8.2 - - - +
849A VAL 3.2 0.2 - - - -
850A MET* 1.3 76.1 - - - +
852A LYS* 1.3 59.6 + - + +
854A LEU* 3.4 3.1 + - - +
855A LYS* 3.0 28.2 + - - +
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Residues in contact with LYS 852 (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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848A ILE* 3.0 40.2 + - + +
849A VAL 3.8 2.9 - - - +
851A ASN* 1.3 75.5 - - + +
853A VAL* 1.3 60.0 + - - +
855A LYS* 3.3 10.0 + - + +
856A LYS* 2.9 44.6 + - - +
869A PHE* 3.7 36.2 - - + -
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Residues in contact with VAL 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A VAL* 2.8 27.1 + - + +
850A MET* 3.7 6.3 - - - +
852A LYS* 1.3 75.2 - - - +
854A LEU* 1.3 65.3 + - + +
856A LYS* 3.3 2.7 + - - +
857A ILE* 3.0 44.5 + - + +
866A ALA* 4.1 17.7 - - + +
869A PHE* 4.3 6.1 - - + -
870A VAL* 3.6 28.9 - - + -
966A ILE* 4.6 3.6 - - + -
969A ILE* 4.1 13.7 - - + -
970A VAL* 4.1 16.6 - - + -
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Residues in contact with LEU 854 (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 LEU* 3.8 29.2 - - + -
817A ALA* 4.2 10.8 - - + -
830A LEU* 4.4 13.2 - - + -
832A GLN* 3.5 38.8 - - + +
835A LEU* 4.0 13.5 - - + -
837A SER* 4.5 0.9 - - - +
850A MET* 2.9 21.9 + - + +
851A ASN* 3.8 4.3 - - - +
853A VAL* 1.3 77.9 - - + +
855A LYS* 1.3 57.0 + - - +
857A ILE* 4.9 2.2 - - + -
858A LEU* 2.8 49.0 + - + +
969A ILE* 4.1 20.9 - - + -
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Residues in contact with LYS 855 (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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830A LEU* 5.2 4.4 - - + +
851A ASN 3.0 17.4 + - - +
852A LYS* 3.6 10.1 - - + +
854A LEU* 1.3 76.6 - - - +
856A LYS* 1.3 64.7 + - + +
859A ILE* 3.0 50.4 + - + +
860A GLU* 3.1 31.7 + - - +
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Residues in contact with LYS 856 (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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852A LYS* 2.9 33.5 + - - +
853A VAL* 3.8 4.3 - - - +
855A LYS* 1.3 78.4 - - + +
857A ILE* 1.3 53.0 + - - +
860A GLU* 3.3 27.9 + - - +
861A ARG 2.9 7.6 + - - -
862A ASN* 2.7 43.6 + - + +
865A GLY* 4.0 6.1 + - - +
866A ALA* 3.8 27.6 - - + +
869A PHE* 4.1 27.5 - - + +
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Residues in contact with ILE 857 (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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599A TYR* 3.8 14.0 + - + +
853A VAL* 3.0 39.6 + - + +
854A LEU* 5.4 2.0 - - + -
856A LYS* 1.3 76.4 - - - +
858A LEU* 1.3 77.3 + - + +
861A ARG* 2.9 29.0 + - - +
862A ASN 4.2 3.4 - - - +
863A VAL* 4.3 25.4 - - + +
866A ALA* 3.9 17.0 - - + -
867A LEU* 6.4 0.2 - - + -
969A ILE* 5.2 1.6 - - + +
970A VAL* 4.3 10.8 - - + -
973A ILE* 3.7 35.7 - - + -
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Residues in contact with LEU 858 (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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599A TYR* 3.8 24.7 - - + +
807A PRO* 4.0 19.5 - - + +
809A LEU* 4.6 9.6 - - + -
817A ALA* 4.3 9.6 - - + +
818A GLY* 3.8 24.0 - - - +
819A LEU* 3.4 17.9 - - + +
830A LEU* 3.7 31.0 - - + -
854A LEU* 2.8 42.5 + - + +
857A ILE* 1.3 92.8 - - + +
859A ILE* 1.3 59.0 + - - +
861A ARG* 4.5 6.4 - - - +
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Residues in contact with ILE 859 (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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819A LEU* 3.5 33.0 - - + -
827A PHE* 4.1 25.6 - - + -
830A LEU* 4.4 14.8 - - + -
855A LYS* 3.0 36.4 + - + +
858A LEU* 1.3 79.4 - - - +
860A GLU* 1.3 73.4 - - + +
861A ARG* 3.3 7.9 + - - +
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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