Contacts of the helix formed by residues 847 - 864 (chain A) in PDB entry 1PKG
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 847 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789A ILE* 3.5 17.0 - - - +
817A ILE* 4.0 6.3 - - - -
821A SER* 3.4 18.2 - - - +
822A ASN* 3.7 24.0 - - - +
839A GLU* 3.9 11.4 + - - +
845A VAL* 4.2 7.0 + - + +
846A TYR* 1.3 79.0 - - - +
848A PHE* 1.3 65.6 + - - +
849A GLU* 3.1 21.8 + - - +
850A SER* 3.1 24.6 + - - -
851A ASP* 3.8 1.9 + - - -
911A PRO* 5.2 1.9 - - - +
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Residues in contact with PHE 848 (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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784A ALA* 3.4 43.3 - - + -
787A ASN* 3.8 32.1 - - - -
788A CYS 3.9 4.3 - - - -
789A ILE* 3.9 12.1 - - + +
817A ILE* 3.7 26.6 - - + +
818A LYS* 6.0 0.2 - - - -
821A SER* 4.2 12.8 + - - -
847A THR* 1.3 76.4 - - - +
849A GLU* 1.3 64.6 + - + +
850A SER 3.2 3.6 + - - -
851A ASP* 3.6 13.3 + - - +
852A VAL* 3.7 11.5 + - - +
917A PHE* 4.3 4.5 - - - -
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Residues in contact with GLU 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A SER* 4.9 1.4 + - - -
847A THR* 3.1 28.7 - - - +
848A PHE* 1.3 83.6 + - + +
850A SER* 1.3 57.3 + - - +
851A ASP 3.6 0.4 - - - -
852A VAL* 3.5 18.1 - - + +
853A TRP 3.6 0.9 + - - -
911A PRO* 3.5 35.4 - - + +
912A LEU* 4.2 21.8 - - - +
914A ARG* 3.0 35.8 + - + +
915A PRO 5.3 2.0 - - - +
916A THR* 6.2 4.0 - - + -
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Residues in contact with SER 850 (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 ALA* 3.2 17.2 + - - +
839A GLU* 3.4 11.3 + - - -
840A SER* 3.0 23.5 + - - -
846A TYR* 4.2 7.0 - - - -
847A THR* 3.1 27.5 + - - -
849A GLU* 1.3 77.6 - - - +
851A ASP* 1.3 65.5 + - - +
852A VAL 3.1 1.1 - - - -
853A TRP* 3.4 8.8 + - - +
854A SER* 3.3 15.6 + - - -
914A ARG* 4.1 2.7 - - - +
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Residues in contact with ASP 851 (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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780A MET* 3.5 16.3 - - + +
788A CYS 4.4 0.9 - - - +
789A ILE* 3.0 21.4 - - - +
790A HIS* 2.6 27.4 + - - +
791A ARG* 2.9 28.7 + - - +
792A ASP 4.8 0.3 + - - -
793A LEU* 3.8 4.8 - - + +
847A THR 3.8 1.2 + - - -
848A PHE 3.6 5.6 + - - +
850A SER* 1.3 75.7 - - - +
852A VAL* 1.3 66.2 + - - +
854A SER* 3.0 10.8 + - - -
855A TYR* 2.9 23.4 + - - +
917A PHE* 3.5 20.0 - - + -
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Residues in contact with VAL 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 PHE 3.7 12.3 - - - +
849A GLU* 3.5 16.2 - - - +
850A SER 3.1 0.4 - - - -
851A ASP* 1.3 78.5 - - - +
853A TRP* 1.3 65.9 + - - +
855A TYR* 3.3 2.6 + - - +
856A GLY 3.1 14.7 + - - -
906A CYS* 3.6 33.0 - - + +
914A ARG* 4.2 6.5 - - + -
915A PRO* 3.2 29.4 - - + +
916A THR* 4.6 1.8 - - - -
917A PHE* 3.6 34.5 - - + +
920A ILE* 4.0 5.6 - - + -
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Residues in contact with TRP 853 (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 LYS 5.0 1.4 + - - -
835A TRP 3.5 10.4 + - - -
836A MET 3.2 15.9 + - - -
837A ALA* 3.4 34.5 - - + -
838A PRO* 3.1 31.6 - - + -
849A GLU 3.6 3.6 + - - -
850A SER 3.4 5.3 + - - +
851A ASP 3.2 0.2 - - - -
852A VAL* 1.3 77.2 - - - +
854A SER* 1.3 60.2 + - - +
856A GLY* 2.8 23.0 + - - -
857A ILE* 3.2 21.6 + - + +
870A TYR* 4.7 5.3 + - - -
883A ILE* 4.4 18.8 - - + -
888A ARG* 3.5 34.3 - - - -
906A CYS 3.5 12.5 + - - +
907A TRP* 3.1 43.3 + + + -
908A ASP 3.9 2.9 - - - -
914A ARG* 3.5 16.8 - - - +
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Residues in contact with SER 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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791A ARG* 5.6 4.2 + - - -
792A ASP* 6.0 0.2 - - - -
793A LEU* 3.6 32.7 - - - +
835A TRP* 2.7 29.2 + - - +
836A MET* 4.8 1.0 - - - +
850A SER 3.3 12.3 + - - -
851A ASP* 3.0 10.9 + - - -
853A TRP* 1.3 75.6 - - - +
855A TYR* 1.3 57.4 + - - +
857A ILE* 3.0 9.4 + - - +
858A PHE* 2.9 26.1 + - - +
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Residues in contact with TYR 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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773A SER 2.9 20.7 + - - -
776A VAL* 3.9 21.3 - - + -
777A ALA* 3.4 28.4 - - + +
793A LEU* 3.6 11.4 - - + +
851A ASP 2.9 6.9 + - - +
852A VAL 3.3 8.5 - - - +
854A SER* 1.3 74.3 - - - +
856A GLY* 1.3 59.2 + - - +
858A PHE* 3.3 14.5 + + - +
859A LEU* 2.9 57.8 + - + +
906A CYS* 4.1 6.5 - - - -
917A PHE* 3.4 26.9 - + + -
920A ILE* 3.5 28.9 - - + +
924A ILE* 3.2 18.7 - - - +
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Residues in contact with GLY 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 VAL 3.1 6.1 + - - -
853A TRP 2.8 11.9 + - - -
855A TYR* 1.3 75.9 - - - +
857A ILE* 1.3 61.6 + - - -
858A PHE 2.8 5.4 + - - -
859A LEU* 3.0 5.9 + - - +
860A TRP* 2.9 21.0 + - - +
903A MET* 3.8 10.6 - - - +
906A CYS* 4.0 13.9 - - - -
907A TRP* 3.4 16.3 - - - -
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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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834A LYS 3.6 17.5 - - - +
835A TRP* 3.3 30.7 - - + +
853A TRP* 3.2 26.4 + - + +
854A SER 3.0 11.2 + - - +
856A GLY* 1.3 70.3 - - - +
858A PHE* 1.3 55.3 + - - +
860A TRP* 3.4 8.3 - - - +
861A GLU* 3.0 25.2 + - - +
869A PRO* 3.7 21.5 - - + -
870A TYR* 3.4 18.4 - - - +
889A MET* 3.4 23.3 - - + -
907A TRP* 3.3 18.3 - - + +
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Residues in contact with PHE 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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678A LEU* 4.1 14.8 - - + -
772A PHE 4.4 3.1 - - - -
773A SER* 4.8 0.2 - - - -
776A VAL* 3.8 34.8 - - + -
793A LEU* 4.8 2.5 - - + -
794A ALA* 4.0 7.6 - - - -
795A ALA* 3.8 26.5 - - + -
798A ILE* 3.4 23.8 - - + -
854A SER 2.9 11.3 + - - +
855A TYR* 3.4 31.2 - + - +
856A GLY 2.9 0.6 - - - -
857A ILE* 1.3 76.8 - - - +
859A LEU* 1.3 66.0 + - + +
860A TRP 3.1 1.1 - - - -
861A GLU* 3.2 9.3 + - - +
862A LEU* 2.9 61.4 + - + +
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Residues in contact with LEU 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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773A SER* 3.6 24.5 - - - +
855A TYR* 2.9 59.1 + - + +
856A GLY* 3.0 1.5 + - - +
858A PHE* 1.3 82.1 - - + +
860A TRP* 1.3 62.2 + - - +
862A LEU* 3.3 3.8 + - + -
863A PHE* 3.1 37.7 + - + +
899A MET* 4.0 15.3 - - - +
902A ILE* 4.1 9.6 - - + -
903A MET* 3.4 43.6 - - + +
924A ILE* 6.2 0.2 - - + -
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Residues in contact with TRP 860 (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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856A GLY 2.9 11.6 + - - +
857A ILE 3.4 11.0 - - - +
859A LEU* 1.3 74.6 - - - +
861A GLU* 1.3 69.4 + - + +
864A SER* 2.7 39.4 + - - -
867A SER* 3.3 28.3 - - - -
868A SER 3.2 28.3 - - - -
869A PRO* 3.7 5.4 - - + -
871A PRO* 4.6 9.4 - - + -
889A MET* 3.2 49.6 - - + +
890A LEU* 3.0 33.9 + - + +
892A PRO* 3.7 20.8 - - + +
903A MET* 3.8 7.2 - - - -
907A TRP* 4.0 13.5 - + + -
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Residues in contact with GLU 861 (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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679A LEU* 4.2 10.9 - - - +
682A LEU* 3.9 2.0 - - - +
794A ALA* 3.8 0.7 - - - -
795A ALA* 3.1 40.9 + - + +
796A ARG 4.8 1.0 + - - -
835A TRP* 2.5 45.7 + - - +
857A ILE 3.0 14.5 + - - +
858A PHE* 3.2 8.9 + - - +
860A TRP* 1.3 78.5 - - + +
862A LEU* 1.3 60.2 + - - +
864A SER* 3.3 6.9 + - - -
866A GLY* 2.8 34.0 + - - -
867A SER 4.0 18.1 - - - +
868A SER* 5.5 0.2 - - - -
869A PRO* 4.3 7.7 - - + +
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Residues in contact with LEU 862 (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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678A LEU* 3.6 30.5 - - + -
682A LEU* 3.9 15.3 - - + +
769A LEU* 3.5 35.7 - - + +
772A PHE* 4.2 10.3 - - + -
773A SER* 3.2 36.1 - - - +
858A PHE* 2.9 36.3 + - + +
859A LEU* 3.4 7.6 - - + +
861A GLU* 1.3 78.3 - - - +
863A PHE* 1.3 66.3 + - + +
865A LEU* 3.4 15.6 + - - -
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Residues in contact with PHE 863 (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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766A LEU* 3.9 7.4 - - + -
769A LEU* 3.5 39.0 - - + -
770A LEU* 4.3 4.0 - - + -
773A SER* 3.4 26.5 - - - -
859A LEU* 3.1 31.8 + - + +
862A LEU* 1.3 83.2 - - + +
864A SER* 1.3 56.8 + - - +
865A LEU* 3.1 8.1 + - - +
892A PRO* 3.4 10.8 - - + +
894A HIS* 3.2 31.1 + - - +
895A ALA* 3.6 32.5 - - + -
896A PRO* 3.7 13.2 - - + -
899A MET* 3.7 34.1 - - + -
903A MET* 4.4 3.4 - - + -
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Residues in contact with SER 864 (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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686A ARG* 4.0 8.0 + - - -
860A TRP* 2.7 35.7 + - - -
861A GLU* 3.3 3.1 + - - -
863A PHE* 1.3 75.9 - - - +
865A LEU* 1.3 68.1 + - - +
866A GLY 3.2 0.5 + - - -
867A SER* 3.3 36.2 + - - -
892A PRO* 3.5 16.8 - - - +
893A GLU 5.6 0.7 - - - +
894A HIS* 5.4 2.0 - - - -
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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
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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