Contacts of the helix formed by residues 865 - 883 (chain A) in PDB entry 1T5Z
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 865 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786A ARG* 4.7 4.3 + - - +
790A LEU* 4.4 6.4 - - - +
793A GLU* 5.1 5.5 + - - +
861A LYS 3.2 8.5 + - - -
862A LEU* 2.5 35.3 + - - +
864A ASP* 1.3 77.1 - - - +
866A VAL* 1.3 60.1 + - - +
867A GLN 3.3 0.4 - - - -
868A PRO* 3.4 12.9 - - - +
869A ILE* 3.2 25.8 - - - +
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Residues in contact with VAL 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A GLY* 3.8 34.3 - - - +
746A VAL* 4.7 11.6 - - + +
747A PHE* 3.9 25.1 - - + -
790A LEU* 4.4 10.5 - - + -
811A LEU* 4.4 12.8 - - + -
862A LEU 3.4 17.3 - - - +
863A LEU* 3.6 15.5 - - - +
864A ASP 2.8 0.8 + - - -
865A SER* 1.3 80.8 - - - +
867A GLN* 1.3 60.2 + - - +
869A ILE* 3.4 9.9 + - - +
870A ALA* 3.0 24.1 + - + +
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Residues in contact with GLN 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A SER* 6.3 0.4 - - - -
743A GLY* 5.7 3.6 - - - -
811A LEU* 3.8 27.3 + - - +
814A SER* 4.0 18.2 + - - -
815A ILE* 4.8 9.3 - - - +
863A LEU 4.3 6.3 + - - +
864A ASP* 2.8 12.4 + - - +
866A VAL* 1.3 80.2 - - - +
868A PRO* 1.3 63.9 - - + +
870A ALA* 3.1 10.9 + - - +
871A ARG* 2.8 29.8 + - - +
913A PRO* 3.5 32.6 - - + +
914A ILE 5.5 3.8 - - - +
915A TYR* 3.4 26.0 - - + +
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Residues in contact with PRO 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A ARG* 3.3 28.3 - - - +
864A ASP 2.9 26.9 - - - +
865A SER* 3.4 13.7 - - - +
867A GLN* 1.3 80.7 - - + +
869A ILE* 1.3 61.2 + - - +
871A ARG* 3.3 8.8 - - + +
872A GLU* 3.0 27.4 + - - +
915A TYR* 4.3 13.4 - - + +
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Residues in contact with ILE 869 (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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746A VAL* 4.2 8.1 - - + -
783A GLN* 4.7 3.6 - - + +
786A ARG* 3.6 51.8 - - + +
787A MET* 3.9 23.8 - - + +
790A LEU* 4.5 22.0 - - + -
865A SER* 3.2 21.8 - - - +
866A VAL* 3.5 7.4 - - - +
867A GLN 3.2 0.2 - - - -
868A PRO* 1.3 74.0 - - - +
870A ALA* 1.3 66.5 + - - +
872A GLU* 3.2 11.1 + - - +
873A LEU* 2.9 34.9 + - + +
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Residues in contact with ALA 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A MET* 4.0 21.7 - - + +
743A GLY* 4.3 16.6 - - - +
746A VAL* 5.6 2.2 - - + +
866A VAL 3.0 14.1 + - - +
867A GLN* 3.1 18.4 + - - +
869A ILE* 1.3 77.0 - - - +
871A ARG* 1.3 52.1 - - - +
873A LEU* 3.3 4.3 + - - +
874A HIS* 2.7 50.1 + - + +
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Residues in contact with ARG 871 (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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867A GLN 2.8 13.0 + - - +
868A PRO* 3.3 14.1 - - + +
870A ALA* 1.3 75.8 - - - +
872A GLU* 1.3 67.2 + - + +
874A HIS* 2.9 11.7 + - - +
875A GLN* 2.9 30.7 + - + +
906A ILE* 3.3 32.8 + - - +
907A LEU* 3.4 39.5 + - - +
909A GLY* 5.0 2.0 - - - +
915A TYR* 6.1 0.4 - - - +
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Residues in contact with GLU 872 (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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782A SER* 4.6 7.1 + - - -
783A GLN* 3.8 33.7 + - + +
786A ARG* 2.6 45.5 + - - +
868A PRO 3.0 14.5 + - - +
869A ILE* 3.2 7.7 + - - +
871A ARG* 1.3 78.4 - - + +
873A LEU* 1.3 57.0 + - - +
875A GLN* 3.3 6.5 + - - +
876A PHE* 2.9 29.9 + - - +
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Residues in contact with LEU 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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742A MET* 3.8 22.0 - - + +
746A VAL* 3.4 33.2 - - + -
780A MET* 3.6 32.8 - - + -
783A GLN* 4.1 18.8 - - + -
787A MET* 4.0 13.7 - - + -
869A ILE* 2.9 26.6 + - + +
870A ALA 3.7 3.6 - - - +
872A GLU* 1.3 73.7 - - - +
874A HIS* 1.3 61.1 + - - +
876A PHE* 3.8 4.1 - - + +
877A THR* 2.9 32.9 + - - +
931A DHT 4.0 16.1 - - + +
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Residues in contact with HIS 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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739A TYR 4.1 9.5 + - - -
741A TRP* 4.5 7.9 + + - -
742A MET* 3.5 34.3 - - + +
815A ILE* 5.3 2.9 - - + -
870A ALA* 2.7 33.5 + - + +
871A ARG* 2.9 12.3 + - - +
873A LEU* 1.3 74.0 - - - +
875A GLN* 1.3 57.7 + - - +
877A THR* 2.9 21.4 - - + +
878A PHE* 2.9 15.4 + - - +
903A VAL* 3.9 29.2 - - + +
906A ILE* 3.7 37.5 - - + +
907A LEU* 3.9 15.3 - - + +
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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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871A ARG* 2.9 18.9 + - + +
872A GLU* 3.7 9.9 - - - +
874A HIS* 1.3 78.6 - - - +
876A PHE* 1.3 62.2 + - - +
878A PHE* 3.3 13.7 + - - +
879A ASP* 3.1 59.0 + - - +
907A LEU* 3.8 26.4 - - + +
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Residues in contact with PHE 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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697A PHE* 4.3 11.4 - + - -
701A LEU* 4.1 22.4 - - + -
778A SER 3.6 19.7 - - - -
779A ARG* 3.1 26.9 - - + -
780A MET* 3.8 13.7 - - + -
783A GLN* 3.6 21.5 - - - +
872A GLU 2.9 17.9 + - - +
873A LEU* 3.8 7.0 - - + +
875A GLN* 1.3 78.8 - - - +
877A THR* 1.3 64.4 + - - +
879A ASP* 3.4 6.9 + - - +
880A LEU* 3.1 29.1 + - + +
931A DHT 3.9 12.8 - - + -
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Residues in contact with THR 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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741A TRP* 5.2 0.2 - - + -
742A MET* 4.2 10.1 - - + -
873A LEU 2.9 19.8 + - - +
874A HIS* 2.9 31.0 - - + +
876A PHE* 1.3 81.0 - - - +
878A PHE* 1.3 63.8 + - - +
880A LEU* 3.2 5.1 + - - +
881A LEU* 2.9 22.9 + - - +
891A PHE* 3.8 2.6 - - - -
899A ILE* 3.3 34.4 - - + +
903A VAL* 4.9 2.7 - - + -
931A DHT 3.1 35.5 + - + +
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Residues in contact with PHE 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 HIS 2.9 19.2 + - - +
875A GLN* 3.4 16.4 - - - +
876A PHE 3.2 0.2 - - - -
877A THR* 1.3 77.7 - - - +
879A ASP* 1.3 79.4 + - - +
881A LEU* 3.3 14.2 + - + +
882A ILE* 3.4 39.1 + - + +
899A ILE* 4.0 24.2 - - + -
900A SER* 5.7 2.2 - - - -
903A VAL* 4.5 3.6 - - + -
904A PRO* 4.4 21.1 - - + -
907A LEU* 3.7 18.8 - - + -
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Residues in contact with ASP 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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875A GLN* 3.1 41.3 + - - +
876A PHE* 4.0 5.6 - - - +
878A PHE* 1.3 85.4 - - - +
880A LEU* 1.3 67.7 + - - +
882A ILE* 3.0 18.0 + - - +
883A LYS* 3.2 27.9 + - + +
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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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697A PHE* 3.6 26.7 - - + -
701A LEU* 3.5 34.3 - - + -
876A PHE* 3.1 22.0 + - + +
877A THR 3.4 9.2 - - - +
879A ASP* 1.3 77.6 - - - +
881A LEU* 1.3 56.0 + - - +
883A LYS* 3.5 14.4 - - - +
884A SER* 2.8 32.9 + - - -
887A VAL* 4.1 7.9 - - + -
889A VAL* 3.9 21.3 - - + -
891A PHE* 3.7 22.7 - - + -
931A DHT 3.8 7.6 - - - +
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Residues in contact with LEU 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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877A THR 2.9 11.5 + - - +
878A PHE* 3.5 11.9 - - + +
879A ASP 3.2 0.2 - - - -
880A LEU* 1.3 77.5 - - - +
882A ILE* 1.3 69.1 + - + +
884A SER* 2.7 25.9 + - - +
885A HIS* 4.8 0.3 + - - -
891A PHE* 3.7 35.1 - - + -
896A ALA* 3.9 31.4 - - + +
899A ILE* 3.9 24.0 - - + -
900A SER* 3.9 16.6 - - - -
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Residues in contact with ILE 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 PHE* 3.4 41.5 - - + +
879A ASP* 3.0 9.5 + - - +
881A LEU* 1.3 86.3 - - + +
883A LYS* 1.3 58.5 + - + +
885A HIS* 2.9 21.8 + - - -
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Residues in contact with LYS 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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697A PHE* 6.0 0.9 - - - -
779A ARG* 5.5 7.1 - - - +
879A ASP* 3.2 25.8 + - + +
880A LEU* 3.8 21.3 - - - +
882A ILE* 1.3 77.4 - - + +
884A SER* 1.3 65.8 + - - +
885A HIS* 3.2 9.2 - - - -
886A MET* 2.9 23.0 + - + +
887A VAL* 3.2 27.2 + - + +
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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