Contacts of the helix formed by residues 814 - 831 (chain A) in PDB entry 3DKO
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 814 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A VAL* 3.5 20.2 - - - +
812A LYS* 3.8 4.6 + - + +
813A PHE* 1.3 79.8 - - - +
815A SER* 1.3 63.8 + - - +
816A ALA* 3.1 20.3 + - - +
817A SER* 2.7 27.7 + - - -
818A ASP* 3.1 6.8 + - - -
877A ARG* 3.5 29.5 + - - +
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Residues in contact with SER 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A ALA* 3.5 37.5 + - - +
753A GLY* 5.8 0.9 - - - -
754A TYR 4.3 8.3 + - - -
755A VAL* 3.9 9.4 - - - +
814A THR* 1.3 73.5 - - - +
816A ALA* 1.3 56.4 + - - +
818A ASP* 3.3 13.8 + - - +
819A VAL* 3.0 31.0 + - - +
883A PHE* 3.7 4.9 - - - -
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Residues in contact with ALA 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A THR* 3.1 11.3 + - - +
815A SER* 1.3 76.5 - - - +
817A SER* 1.3 63.1 + - - +
819A VAL* 3.3 19.4 + - - +
820A TRP 3.4 6.2 + - - -
877A ARG* 4.0 35.4 - - + +
880A ARG* 3.1 18.1 + - + +
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Residues in contact with SER 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A THR* 6.0 0.2 - - - -
804A ALA* 3.7 15.4 + - - +
806A GLU* 3.6 15.7 + - - -
807A ALA* 4.2 7.0 - - - -
812A LYS 4.0 7.4 - - - -
813A PHE* 3.4 12.0 - - - +
814A THR* 2.7 38.2 + - - -
816A ALA* 1.3 75.7 - - - +
818A ASP* 1.3 64.0 + - - +
820A TRP* 3.2 6.4 + - - +
821A SER* 3.2 21.9 + - - -
880A ARG* 3.8 8.0 - - - +
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Residues in contact with ASP 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A MET* 3.6 13.3 - - + +
754A TYR 4.4 0.9 - - - +
755A VAL* 3.6 11.8 - - - +
756A HIS* 2.9 30.1 + - - +
757A ARG* 3.1 26.1 + - - -
759A LEU* 3.6 7.6 - - + +
813A PHE* 5.7 0.3 - - - -
814A THR 3.1 13.2 + - - +
815A SER* 3.3 14.0 + - - +
817A SER* 1.3 77.6 + - - +
819A VAL* 1.3 56.6 + - - +
821A SER* 3.2 11.4 + - - -
822A TYR* 2.8 27.7 + - - +
883A PHE* 3.8 14.8 - - + -
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Residues in contact with VAL 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A SER 3.0 20.0 + - - +
816A ALA* 3.5 12.1 - - - +
817A SER 3.2 0.6 - - - -
818A ASP* 1.3 74.5 - - - +
820A TRP* 1.3 66.2 + - - +
822A TYR* 3.2 3.5 + - - +
823A GLY 3.0 17.7 + - - -
872A CYS* 3.4 26.2 - - + +
880A ARG* 3.9 16.6 - - + -
881A PRO* 3.3 28.9 - - + +
882A LYS* 4.7 0.9 - - - -
883A PHE* 3.6 31.9 - - + +
886A ILE* 4.1 5.8 - - + -
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Residues in contact with TRP 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A ARG 4.8 2.2 + - - -
802A TRP 3.7 9.9 + - - -
803A THR 3.8 7.4 + - - -
804A ALA* 3.7 26.9 - - + -
805A PRO* 3.5 25.8 - - + -
816A ALA 3.4 3.4 + - - -
817A SER 3.2 10.6 + - - +
819A VAL* 1.3 78.3 - - - +
821A SER* 1.3 63.2 + - - +
823A GLY 3.1 10.6 + - - -
824A ILE* 3.2 22.3 + - + +
837A TYR* 4.7 3.5 + - - -
849A ILE* 3.7 40.6 - - + +
854A ARG* 3.9 10.1 - - - -
872A CYS 3.3 12.3 + - - +
873A TRP* 3.2 57.3 + + + -
874A GLN 3.7 8.5 - - - -
875A LYS* 4.5 1.1 - - - -
880A ARG* 3.7 22.0 - - - +
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Residues in contact with SER 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A ARG 5.3 4.2 + - - -
758A ASP* 5.7 0.2 - - - -
759A LEU* 3.5 32.4 + - - +
802A TRP* 2.7 27.4 + - - +
803A THR* 4.4 3.8 - - - -
817A SER 3.2 10.6 + - - -
818A ASP* 3.4 13.6 + - - -
820A TRP* 1.3 77.2 - - - +
822A TYR* 1.3 63.5 + - - +
824A ILE* 3.0 8.3 + - - +
825A VAL* 2.9 25.2 + - - +
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Residues in contact with TYR 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A LEU* 2.7 33.3 + - + +
742A ILE* 3.8 21.5 - - + -
743A ALA* 3.6 27.3 - - + +
759A LEU* 3.7 10.9 - - + +
818A ASP 2.8 17.2 + - - +
819A VAL* 3.4 8.1 - - - +
821A SER* 1.3 74.6 - - - +
823A GLY* 1.3 58.6 + - - +
825A VAL* 3.0 8.3 + - + +
826A MET* 2.8 54.9 + - + +
872A CYS* 4.2 2.0 - - - -
883A PHE* 3.7 22.4 - + + -
886A ILE* 3.5 29.8 - - + -
890A LEU* 3.3 18.2 - - + +
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Residues in contact with GLY 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A VAL 3.0 10.9 + - - -
820A TRP 3.1 5.3 + - - -
822A TYR* 1.3 76.1 - - - +
824A ILE* 1.3 61.2 + - - +
826A MET* 3.3 12.4 - - - +
827A TRP* 3.1 16.6 + - - +
869A MET* 3.9 3.0 - - - +
872A CYS* 3.7 20.2 - - - -
873A TRP* 3.3 24.0 - - - -
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Residues in contact with ILE 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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801A ARG 3.6 17.3 - - - +
802A TRP* 3.3 31.0 - - + +
820A TRP* 3.2 20.3 + - + +
821A SER 3.0 8.3 + - - +
823A GLY* 1.3 75.3 - - - +
825A VAL* 1.3 55.6 + - - +
827A TRP* 3.0 6.7 + - + +
828A GLU* 2.9 27.2 + - - +
836A PRO* 3.6 24.7 - - + -
837A TYR* 3.7 27.8 - - + +
855A LEU* 4.3 4.9 - - + -
873A TRP* 3.3 29.4 - - + +
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Residues in contact with VAL 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A LEU* 4.4 3.4 - - + -
742A ILE* 3.8 33.9 - - + -
759A LEU* 3.8 14.4 - - + -
760A ALA* 3.7 37.5 - - - +
761A ALA* 4.5 11.7 - - + +
764A ILE* 4.7 1.1 - - + -
821A SER 2.9 18.2 + - - +
822A TYR* 3.0 11.2 + - + +
824A ILE* 1.3 71.1 - - - +
826A MET* 1.3 65.4 + - - +
828A GLU* 3.2 10.1 + - - +
829A VAL* 2.9 29.4 + - + +
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Residues in contact with MET 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A LEU* 3.7 21.5 - - + +
822A TYR* 2.8 54.7 + - + +
823A GLY* 3.3 12.1 - - - +
825A VAL* 1.3 72.4 - - - +
827A TRP* 1.3 58.4 + - - +
829A VAL* 3.3 1.7 + - - +
830A MET* 3.0 33.1 + - - +
865A LEU* 3.5 48.9 - - + +
868A LEU* 3.9 24.7 - - + -
869A MET* 3.7 22.4 - - + -
872A CYS* 4.4 1.6 - - - -
890A LEU* 4.9 2.0 - - + -
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Residues in contact with TRP 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 GLY 3.1 8.1 + - - +
824A ILE* 3.0 9.2 + - - +
826A MET* 1.3 76.8 - - - +
828A GLU* 1.3 72.9 + - + +
830A MET 3.3 1.3 + - - +
831A SER* 3.0 34.8 + - - -
834A GLU* 3.6 38.8 - - + -
835A ARG 3.6 12.8 - - - -
836A PRO* 3.5 28.3 - - + -
837A TYR 4.4 0.4 - - - -
838A TRP* 3.7 28.3 - + - -
855A LEU* 3.6 28.1 - - + +
856A PRO* 3.0 29.0 + - + +
858A PRO* 3.7 19.1 - - + +
869A MET* 3.9 18.5 - - - +
873A TRP* 4.2 9.0 - + + -
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Residues in contact with GLU 828 (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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720A ASP* 4.7 6.8 - - - +
723A LEU* 4.7 1.1 - - - -
761A ALA* 3.0 40.5 + - + +
762A ARG* 4.7 1.4 + - - +
802A TRP* 2.9 44.2 + - - -
824A ILE 2.9 15.9 + - - +
825A VAL* 3.5 15.5 - - - +
827A TRP* 1.3 73.8 - - + +
829A VAL* 1.3 60.7 + - - +
831A SER* 3.3 6.6 + - - -
832A TYR 3.1 3.6 + - - -
833A GLY* 2.7 34.1 + - - -
834A GLU 4.1 10.1 - - - +
836A PRO* 3.8 20.6 - - + +
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Residues in contact with VAL 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A LEU* 3.8 28.9 - - + -
723A LEU* 3.5 15.1 - - + +
735A LEU* 3.8 49.5 - - + +
738A MET* 4.9 6.5 - - + -
739A LEU* 3.6 23.3 - - + -
742A ILE* 4.7 0.4 - - + -
761A ALA* 5.2 1.3 - - + -
825A VAL* 2.9 23.9 + - + +
826A MET 3.7 3.6 - - - +
827A TRP 3.2 0.2 - - - -
828A GLU* 1.3 76.8 - - + +
830A MET* 1.3 62.1 + - - +
831A SER 3.1 0.2 - - - -
832A TYR* 3.0 19.9 + - - -
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Residues in contact with MET 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A VAL* 4.7 11.4 - - + -
735A LEU* 3.7 42.9 - - + +
739A LEU* 4.2 8.7 - - + -
826A MET 3.0 20.8 + - - +
827A TRP 3.3 0.2 + - - -
829A VAL* 1.3 82.3 - - - +
831A SER* 1.3 57.7 + - - +
832A TYR* 3.4 12.0 - - - -
858A PRO* 3.5 26.7 - - + +
859A MET 4.1 9.5 - - - +
860A ASP 5.0 1.1 - - - +
861A CYS* 3.9 14.1 - - + -
862A PRO* 4.3 14.6 - - + -
865A LEU* 3.6 28.3 - - + -
869A MET* 3.8 14.6 - - + -
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Residues in contact with SER 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ASP* 4.9 1.4 - - - +
827A TRP* 3.0 25.6 + - - -
828A GLU* 3.3 8.5 + - - -
829A VAL 3.1 0.2 - - - -
830A MET* 1.3 79.1 - - - +
832A TYR* 1.3 69.1 + - - +
834A GLU* 3.2 44.8 + - - +
858A PRO* 4.0 16.4 - - - -
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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) + - + + + + + -
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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