Contacts of the helix formed by residues 823 - 844 (chain A) in PDB entry 1T65
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 823 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A LEU* 5.6 0.5 - - - +
729A HIS* 4.2 17.7 - - + +
732A ASP* 3.0 16.2 + - - +
821A LEU* 4.4 0.2 - - - -
822A LYS* 1.3 78.0 - - - +
824A GLN* 1.3 60.2 + - - +
825A LYS* 3.1 8.8 + - - +
826A PHE* 3.0 67.4 + - + +
827A PHE* 3.4 9.2 + - - +
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Residues in contact with GLN 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A ILE* 3.8 22.6 - - - +
820A GLY* 3.7 9.1 - - - -
821A LEU* 3.0 47.7 + - - +
822A LYS 3.7 0.4 + - - -
823A ASN* 1.3 74.2 - - - +
825A LYS* 1.3 57.8 + - + +
827A PHE* 3.3 23.2 + - - +
828A ASP* 3.0 62.3 + - - +
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Residues in contact with LYS 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A ASN* 3.1 9.5 - - - +
824A GLN* 1.3 79.9 - - + +
826A PHE* 1.3 69.8 + - + +
828A ASP* 3.3 15.4 + - + +
829A GLU* 3.1 22.6 + - - +
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Residues in contact with PHE 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ASN* 3.2 33.5 - - + +
728A LEU* 4.1 12.3 - - + +
729A HIS* 4.9 2.9 - - - +
823A ASN* 3.0 46.4 + - + +
825A LYS* 1.3 79.8 - - + +
827A PHE* 1.3 62.4 + - - +
829A GLU* 3.4 19.4 + - - +
830A LEU* 3.1 22.9 + - - +
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Residues in contact with PHE 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A LEU* 3.7 20.0 - - + +
732A ASP* 5.7 0.7 - - + +
736A VAL* 3.9 24.7 - - + -
813A PHE* 3.5 48.0 - + + -
815A ILE 5.2 0.4 - - - -
816A ILE* 3.5 26.5 - - + -
821A LEU* 3.5 26.5 - - + -
823A ASN 3.4 5.6 + - - +
824A GLN* 3.3 23.7 + - - +
825A LYS 3.2 0.4 - - - -
826A PHE* 1.3 77.5 - - - +
828A ASP* 1.3 72.9 + - - +
830A LEU* 3.1 3.1 + - - +
831A ARG* 3.0 38.4 + - - +
914A ILE* 4.3 6.3 - - + -
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Residues in contact with ASP 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A ILE* 5.6 0.3 - - - +
824A GLN* 3.0 53.7 + - - +
825A LYS* 3.3 17.2 + - + +
827A PHE* 1.3 82.9 - - - +
829A GLU* 1.3 57.5 + - - +
831A ARG* 3.6 5.7 + - - +
832A MET* 3.1 27.9 + - - +
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Residues in contact with GLU 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ASN* 6.6 0.2 - - - -
825A LYS 3.1 11.0 + - - +
826A PHE* 3.6 25.8 - - - +
828A ASP* 1.3 76.4 - - - +
830A LEU* 1.3 64.4 + - - +
832A MET* 3.4 14.6 + - + +
833A ASN* 2.8 40.3 + - - +
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Residues in contact with LEU 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A PRO 3.8 10.5 - - - +
724A GLY* 3.9 29.4 - - - +
725A PHE* 4.3 2.0 - - - -
727A ASN* 5.1 5.2 - - + +
728A LEU* 4.0 18.6 - - + -
813A PHE* 3.6 34.3 - - + -
826A PHE 3.1 17.0 + - - +
827A PHE* 3.7 4.7 - - - +
829A GLU* 1.3 76.7 - - - +
831A ARG* 1.3 64.9 + - - +
833A ASN* 3.1 22.7 + - + +
834A TYR* 3.1 47.6 + - + -
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Residues in contact with ARG 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A LEU* 4.2 9.2 + - + +
813A PHE* 2.9 47.1 + - + +
814A SER* 3.5 20.0 + - - +
827A PHE* 3.0 24.8 + - + +
828A ASP* 3.9 6.3 - - - +
830A LEU* 1.3 77.2 - - - +
832A MET* 1.3 63.5 + - - +
834A TYR* 3.1 8.2 + - - +
835A ILE* 3.1 31.4 + - + +
914A ILE* 3.5 40.1 + - - +
916A PHE* 3.6 37.4 - - - -
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Residues in contact with MET 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A ASP 3.1 18.7 + - - +
829A GLU* 3.6 15.0 - - + +
830A LEU 3.2 0.2 - - - -
831A ARG* 1.3 77.6 - - - +
833A ASN* 1.3 70.4 + - - +
835A ILE* 3.3 10.5 + - + +
836A LYS* 3.0 42.1 + - + +
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Residues in contact with ASN 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A GLU* 2.8 38.8 + - - +
830A LEU* 3.1 17.1 + - + +
832A MET* 1.3 89.7 - - - +
834A TYR* 1.3 61.7 + - + +
836A LYS* 3.3 17.9 + - - +
837A GLU* 3.1 32.8 + - + +
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Residues in contact with TYR 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A PHE* 3.6 29.6 - + - -
677A LEU* 4.9 0.2 - - + -
722A LEU* 3.6 12.0 - - + +
723A PRO* 2.8 39.4 + - + +
806A CYS* 3.9 8.0 - - - -
809A ALA* 3.6 34.8 - - + -
810A LEU* 3.3 23.3 - - + +
813A PHE* 3.9 24.0 - + + -
830A LEU* 3.1 44.8 + - + +
831A ARG* 3.1 6.7 + - - +
833A ASN* 1.3 76.8 - - + +
835A ILE* 1.3 65.3 + - - +
837A GLU* 3.3 7.1 + - - +
838A LEU* 3.1 21.5 + - - +
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Residues in contact with ILE 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A LEU* 3.7 24.9 - - + -
831A ARG* 3.1 29.6 + - + +
832A MET* 3.6 11.7 - - + +
833A ASN 3.2 0.2 - - - -
834A TYR* 1.3 77.6 - - - +
836A LYS* 1.3 64.0 + - - +
838A LEU* 3.1 6.9 + - + +
839A ASP* 3.0 30.4 + - - +
856A PHE* 4.6 21.3 - - + -
916A PHE* 3.7 33.9 - - + -
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Residues in contact with LYS 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A MET* 3.0 27.8 + - + +
833A ASN* 3.5 22.4 + - - +
835A ILE* 1.3 79.0 - - - +
837A GLU* 1.3 63.6 + - - +
839A ASP* 3.2 14.1 + - + +
840A ARG* 3.0 55.2 + - + +
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Residues in contact with GLU 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A PHE* 3.5 62.8 - - + +
806A CYS* 4.2 3.0 - - - -
833A ASN* 3.1 20.2 + - + +
834A TYR 3.7 7.0 - - - +
835A ILE 3.2 0.4 - - - -
836A LYS* 1.3 76.7 - - - +
838A LEU* 1.3 66.5 + - - +
840A ARG* 3.3 43.4 + - - +
841A ILE* 3.1 23.0 + - - +
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Residues in contact with LEU 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A GLU* 4.9 3.6 - - - +
806A CYS* 3.8 21.9 - - + -
807A MET* 4.4 13.0 - - + +
810A LEU* 3.8 21.5 - - + -
834A TYR 3.1 14.4 + - - +
835A ILE* 3.1 10.7 + - + +
837A GLU* 1.3 72.0 - - - +
839A ASP* 1.3 65.1 + - - +
841A ILE* 2.6 38.6 - - + +
842A ILE* 3.1 19.0 + - + +
856A PHE* 4.3 22.0 - - + -
859A LEU* 4.1 31.0 - - + -
860A THR* 5.6 2.0 - - + -
863A LEU* 5.0 5.4 - - + -
916A PHE* 6.3 0.2 - - + -
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Residues in contact with ASP 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A ILE* 3.0 24.6 + - - +
836A LYS* 3.2 17.1 + - + +
838A LEU* 1.3 77.8 - - - +
840A ARG* 1.3 57.9 + - + +
842A ILE* 3.2 9.6 + - - +
843A ALA* 3.0 29.0 + - - +
856A PHE* 3.7 26.9 - - - +
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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 LYS* 3.0 40.8 + - + +
837A GLU* 3.3 40.8 + - - +
838A LEU 3.2 0.2 - - - -
839A ASP* 1.3 74.5 - - + +
841A ILE* 1.3 66.1 + - - +
843A ALA* 3.2 7.0 + - - +
844A CYS* 3.1 20.4 + - - +
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Residues in contact with ILE 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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674A LEU* 4.7 16.8 - - + -
800A THR* 4.5 0.4 - - - +
802A GLN* 3.3 49.6 - - + +
803A GLU* 3.3 21.1 - - + +
806A CYS* 4.9 4.7 - - + -
837A GLU 3.1 8.6 + - - +
838A LEU* 2.6 50.7 - - + +
840A ARG* 1.3 74.4 - - - +
842A ILE* 1.3 64.0 + - + +
844A CYS* 3.4 19.9 - - + +
845A LYS 4.9 0.2 + - - -
846A ARG* 4.7 2.8 + - - -
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Residues in contact with ILE 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A GLU* 4.8 3.4 - - - +
838A LEU* 3.1 23.3 + - + +
839A ASP* 3.5 9.4 - - - +
841A ILE* 1.3 81.0 - - + +
843A ALA* 1.3 57.8 + - - +
844A CYS 3.5 0.5 + - - -
845A LYS 4.6 0.5 + - - -
846A ARG* 3.0 38.1 + - - +
852A CYS* 3.8 34.8 - - + +
855A ARG* 3.9 19.3 - - + -
856A PHE* 4.0 40.2 - - + +
859A LEU* 4.0 21.5 - - + -
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Residues in contact with ALA 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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839A ASP 3.0 16.2 + - - +
840A ARG* 3.2 7.4 + - - +
842A ILE* 1.3 76.7 - - - +
844A CYS* 1.3 68.5 + - - +
845A LYS 3.5 0.4 - - - -
846A ARG 2.8 20.3 - - - +
852A CYS* 4.0 19.5 - - - -
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Residues in contact with CYS 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 ARG 3.1 11.3 + - - +
841A ILE* 3.4 18.4 - - + +
842A ILE 3.3 1.4 - - - -
843A ALA* 1.3 79.1 - - - +
845A LYS* 1.3 84.4 + - + +
846A ARG 4.6 0.5 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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