Contacts of the helix formed by residues 891 - 908 (chain A) in PDB entry 6PUO
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 891 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885A CYS* 2.3 52.2 + - - +
888A ILE* 3.0 23.6 + - + +
890A ALA* 1.3 84.8 - - + +
892A LEU* 1.3 62.2 + - - +
893A TYR 3.6 1.6 - - - -
894A PRO* 3.6 15.5 - - + -
895A GLY* 3.2 13.5 + - - -
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Residues in contact with LEU 892 (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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821A PHE* 3.6 35.0 - - + -
822A GLN* 5.3 0.2 - - - -
823A PRO* 3.7 43.5 - - + -
885A CYS 5.1 0.4 - - - -
886A ARG* 5.4 6.3 - - + +
888A ILE 4.9 1.8 - - - -
889A PRO* 4.1 13.4 + - + +
890A ALA 3.6 2.6 + - - -
891A THR* 1.3 76.6 - - - +
893A TYR* 1.3 69.4 + - + +
894A PRO* 4.0 0.2 - - - +
895A GLY* 3.1 4.2 + - - -
896A ARG* 2.9 26.1 + - - -
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Residues in contact with TYR 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A LEU* 1.3 84.0 - - + +
894A PRO* 1.4 70.7 - - + +
896A ARG* 3.2 20.3 + - - +
897A VAL* 3.0 41.3 + - + +
955D ILE* 2.6 30.6 + - + +
956D LEU* 4.5 6.9 - - - +
957D ILE 5.3 7.6 - - - -
958D HIS* 6.2 1.1 - - - -
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Residues in contact with PRO 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A CYS* 3.7 16.4 - - - -
890A ALA 5.3 0.4 - - - +
891A THR* 3.6 23.8 - - + +
892A LEU 4.0 0.2 - - - +
893A TYR* 1.4 93.0 - - + +
895A GLY* 1.3 56.0 + - - +
897A VAL* 3.3 11.1 - - + +
898A ILE* 3.0 37.0 + - + +
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Residues in contact with GLY 895 (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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821A PHE* 4.4 5.2 - - - -
882A GLY 4.3 8.5 - - - -
885A CYS* 3.3 19.0 - - - -
886A ARG* 4.6 6.5 - - - -
891A THR 3.2 6.9 + - - -
892A LEU 3.1 8.7 + - - -
894A PRO* 1.3 79.1 - - - +
896A ARG* 1.3 57.0 + - - +
898A ILE* 3.5 2.2 + - - -
899A LEU* 2.9 38.0 + - - +
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Residues in contact with ARG 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A LEU* 2.8 24.0 + - + +
818A MET* 2.6 31.1 + - - +
821A PHE* 3.6 42.7 - - + +
892A LEU* 2.9 10.4 + - - +
893A TYR* 3.2 26.0 + - + +
895A GLY* 1.3 76.9 - - - +
897A VAL* 1.3 59.3 + - + +
899A LEU* 3.8 4.4 - - - +
900A SER* 3.0 27.6 + - - -
954D ALA* 2.6 45.3 + - - +
955D ILE* 6.4 0.2 - - - -
957D ILE 3.8 11.4 + - - -
958D HIS* 4.9 2.3 - - - +
959D ASN* 4.5 15.7 - - - +
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Residues in contact with VAL 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A TYR* 3.0 37.0 + - + +
894A PRO* 3.3 20.9 - - + +
896A ARG* 1.3 78.7 - - + +
898A ILE* 1.3 63.4 + - + +
900A SER* 2.4 26.8 + - - +
901A LEU* 3.0 20.0 + - + +
955D ILE* 3.7 38.4 - - + +
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Residues in contact with ILE 898 (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 LEU* 3.7 34.0 - - + +
881A ALA* 4.7 4.0 - - + -
882A GLY* 3.7 29.2 - - - +
885A CYS* 5.6 3.6 - - + -
894A PRO* 3.0 24.4 + - + +
895A GLY* 4.0 2.9 - - - +
897A VAL* 1.3 82.3 - - + +
899A LEU* 1.3 56.6 + - - +
901A LEU* 3.3 10.3 + - + +
902A ASP* 2.9 25.8 + - - +
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Residues in contact with LEU 899 (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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813A PHE* 4.0 23.0 - - + -
817A LEU* 3.3 24.1 - - + +
821A PHE* 5.0 17.3 - - + -
832A ILE* 6.0 2.2 - - + -
878A LEU 5.5 1.1 - - - +
879A PHE* 5.1 17.7 - - + +
882A GLY* 3.7 35.2 - - - +
883A LEU* 4.3 2.5 - - - +
886A ARG* 5.5 4.3 - - + -
895A GLY 2.9 26.9 + - - +
896A ARG* 4.0 3.4 - - - +
898A ILE* 1.3 76.5 - - + +
900A SER* 1.3 56.9 + - - +
902A ASP* 3.5 7.8 - - + +
903A PHE* 2.9 22.7 + - - +
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Residues in contact with SER 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A LEU* 3.8 19.4 - - - +
896A ARG 3.0 14.2 + - - -
897A VAL* 2.4 32.6 + - - +
899A LEU* 1.3 77.0 - - - +
901A LEU* 1.3 71.3 + - - +
903A PHE* 3.1 7.0 + - - +
904A ILE* 3.1 29.8 + - - +
951D ALA* 5.1 9.5 - - - +
954D ALA* 4.8 10.8 - - - -
955D ILE* 4.7 10.5 - - - +
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Residues in contact with LEU 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A LEU* 4.0 13.5 - - + +
897A VAL* 3.0 21.8 + - + +
898A ILE* 3.8 13.0 - - + +
900A SER* 1.3 87.2 + - - +
902A ASP* 1.3 58.1 + - - +
904A ILE* 3.2 25.8 + - + +
905A LEU* 2.9 27.2 + - - +
955D ILE* 4.9 12.3 - - + -
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Residues in contact with ASP 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A PHE* 4.9 3.8 - - + -
875A ALA* 3.2 27.3 - - - +
878A LEU* 3.6 15.2 - - + +
879A PHE* 3.2 42.4 - - - +
898A ILE 2.9 18.0 + - - +
899A LEU* 3.5 11.4 - - + +
900A SER 3.2 0.2 - - - -
901A LEU* 1.3 74.1 - - - +
903A PHE* 1.3 59.6 + - - +
905A LEU* 3.2 2.9 + - - +
906A PHE* 2.9 45.6 + - - -
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Residues in contact with PHE 903 (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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810A LEU* 3.8 37.7 - - + -
813A PHE* 3.4 32.2 - + + -
814A ALA* 3.8 21.5 - - + -
817A LEU* 4.2 9.9 - - + -
899A LEU 2.9 13.7 + - - +
900A SER* 3.1 11.4 + - - +
902A ASP* 1.3 74.5 - - - +
904A ILE* 1.3 68.0 + - + +
906A PHE* 3.4 3.2 + - - +
907A CYS* 2.9 37.7 + - + +
947D SER* 4.5 11.0 - - - -
950D VAL* 3.6 29.4 - - + -
951D ALA* 5.5 3.8 - - + -
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Residues in contact with ILE 904 (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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900A SER* 3.1 18.5 + - - +
901A LEU* 3.5 31.6 - - + +
903A PHE* 1.3 80.1 - - + +
905A LEU* 1.3 58.3 + - - +
907A CYS* 3.1 14.7 - - - -
908A LEU* 3.0 40.5 + - + +
947D SER 5.1 2.0 - - - +
948D PHE* 3.7 31.6 - - + -
951D ALA* 3.7 30.1 - - + -
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Residues in contact with LEU 905 (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 LEU* 3.8 33.9 - - + +
874A GLY* 3.9 7.4 - - - +
875A ALA* 3.6 37.6 - - + +
878A LEU* 5.0 9.0 - - + -
901A LEU 2.9 15.6 + - - +
902A ASP* 3.2 9.6 + - - +
904A ILE* 1.3 79.0 - - - +
906A PHE* 1.3 60.9 + - - +
908A LEU* 3.6 16.8 + - + +
909A ARG* 3.7 8.7 + - - +
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Residues in contact with PHE 906 (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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806A TYR* 2.7 42.5 + + - +
809A PHE* 4.9 12.8 - + - -
810A LEU* 4.1 15.4 - - + +
813A PHE* 5.5 7.6 - + + -
836A LEU* 3.9 39.5 - - + -
839A LEU* 5.3 9.4 - - + -
872A ASP* 5.6 2.0 - - - -
875A ALA* 3.6 27.1 - - + -
876A ILE* 4.8 2.9 - - + -
879A PHE* 5.0 0.9 - + - -
902A ASP* 2.9 55.0 + - - +
903A PHE* 4.0 6.3 - - - +
905A LEU* 1.3 76.6 - - - +
907A CYS* 1.3 63.4 + - - +
909A ARG* 3.2 12.3 - - + +
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Residues in contact with CYS 907 (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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810A LEU* 4.0 19.7 - - + +
903A PHE* 2.9 23.0 + - + +
904A ILE* 3.1 29.8 + - - -
906A PHE* 1.3 75.1 - - - +
908A LEU* 1.3 71.0 + - - +
909A ARG 3.1 1.4 + - - -
910A LEU* 3.4 18.2 + - + +
911A MET 4.8 0.5 + - - -
943D VAL* 5.9 6.9 - - + +
947D SER* 3.5 33.9 - - - -
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Residues in contact with LEU 908 (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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868A TRP* 4.3 6.6 - - - -
871A LEU* 5.9 4.3 - - + -
904A ILE* 3.0 38.3 + - + +
905A LEU* 3.8 15.3 - - + +
906A PHE 3.3 0.6 - - - -
907A CYS* 1.3 86.3 - - - +
909A ARG* 1.3 61.4 + - - +
910A LEU 3.2 0.9 + - - -
911A MET* 3.4 23.8 + - + +
944D TRP* 4.5 23.3 - - + -
1035D PHE* 5.8 11.0 - - + -
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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
------------------------------------------------------------
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