Contacts of the helix formed by residues 885 - 906 (chain A) in PDB entry 1RPM
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 LEU 885 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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880A ILE* 3.7 14.1 - - + -
881A ARG 3.2 4.7 + - - +
882A VAL* 3.4 20.2 - - - +
883A ALA 3.3 1.4 - - - -
884A ASP* 1.3 76.6 - - - +
886A LEU* 1.3 57.2 + - - +
888A HIS* 3.4 6.8 + - + +
889A ILE* 2.8 57.5 + - + +
1121A VAL* 3.7 26.9 - - + -
1123A ILE* 4.9 8.7 - - + -
1148A HIS* 5.3 0.4 - - + +
1151A ILE* 4.1 19.5 - - + -
1152A LEU* 3.9 28.0 - - + +
1155A CYS* 4.2 13.7 - - + -
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Residues in contact with LEU 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A VAL 5.0 0.8 + - - -
883A ALA 4.9 3.7 + - - +
884A ASP 3.3 0.6 - - - -
885A LEU* 1.3 74.3 - - - +
887A GLN* 1.3 61.2 + - - +
889A ILE* 4.0 3.1 - - + -
890A THR* 2.8 47.4 + - - +
1152A LEU* 4.0 34.5 - - + +
1156A LEU* 5.3 13.5 - - + -
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Residues in contact with GLN 887 (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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883A ALA 5.5 0.2 + - - -
884A ASP* 3.0 18.8 + - - +
886A LEU* 1.3 78.6 - - - +
888A HIS* 1.3 65.7 + - - +
890A THR* 3.3 5.6 + - - -
891A GLN* 2.9 60.3 + - - +
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Residues in contact with HIS 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ILE* 3.4 46.9 - - + +
884A ASP* 2.8 15.7 + - + +
885A LEU* 3.5 11.4 - - + +
887A GLN* 1.3 79.8 - - - +
889A ILE* 1.3 67.4 + - - +
891A GLN* 3.3 9.5 + - - +
892A MET* 3.0 58.2 + - + +
903A GLU* 4.9 7.8 + - - -
1148A HIS* 5.0 13.5 + + - -
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Residues in contact with ILE 889 (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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885A LEU* 2.8 40.4 + - + +
886A LEU* 4.0 4.7 - - + +
888A HIS* 1.3 75.6 - - + +
890A THR* 1.3 65.3 + - - +
892A MET* 3.1 9.9 + - - +
893A LYS* 3.1 41.5 + - + +
900A PHE* 4.2 13.5 - - + -
1148A HIS* 3.2 47.6 - - + +
1149A ASP* 4.4 5.8 - - - +
1152A LEU* 3.6 27.6 - - + -
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Residues in contact with THR 890 (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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886A LEU* 2.8 38.3 + - - +
887A GLN* 3.7 5.8 - - - -
889A ILE* 1.3 78.5 - - - +
891A GLN* 1.3 64.7 + - + +
893A LYS* 3.0 20.2 + - - +
894A CYS* 3.4 15.7 + - - -
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Residues in contact with GLN 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A GLN* 2.9 61.9 + - - +
888A HIS* 3.9 7.5 + - - +
890A THR* 1.3 73.3 - - + +
892A MET* 1.3 64.5 + - + +
894A CYS* 3.0 31.5 + - - +
899A GLY* 5.0 2.4 + - - -
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Residues in contact with MET 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A HIS* 3.0 42.2 + - + +
889A ILE 3.3 8.5 - - - +
891A GLN* 1.3 77.8 - - - +
893A LYS* 1.3 56.8 + - - +
894A CYS 3.4 0.2 - - - -
897A GLY* 3.2 11.1 - - - -
899A GLY* 3.2 43.9 + - - +
900A PHE* 3.1 52.7 + - + +
903A GLU* 3.5 32.8 - - - +
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Residues in contact with LYS 893 (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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889A ILE* 3.3 32.9 - - + +
890A THR* 3.0 11.8 + - + +
892A MET* 1.3 75.4 - - - +
894A CYS* 1.3 59.0 + - - +
895A ALA 3.6 0.2 + - - -
896A GLU* 3.6 4.2 + - - -
897A GLY* 2.6 27.2 + - - -
900A PHE* 3.7 10.3 - - + -
1145A VAL* 3.9 18.6 - - + +
1149A ASP* 3.0 29.4 + - - -
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Residues in contact with CYS 894 (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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890A THR* 3.4 15.4 + - - -
891A GLN* 3.0 29.0 + - - +
892A MET 4.2 0.5 - - - +
893A LYS* 1.3 77.2 - - - +
895A ALA* 1.3 59.9 + - + +
898A TYR* 2.8 32.6 + - - +
899A GLY 4.3 1.2 + - - -
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Residues in contact with ALA 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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894A CYS* 1.3 77.9 - - + +
896A GLU* 1.3 73.2 + - - +
897A GLY 3.4 0.2 + - - -
898A TYR* 3.5 16.3 + - + +
901A LYS* 3.2 13.2 + - - -
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Residues in contact with GLU 896 (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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893A LYS 3.6 3.4 + - - -
894A CYS 3.3 0.6 - - - -
895A ALA* 1.3 76.4 - - - +
897A GLY* 1.3 56.5 + - - +
901A LYS* 3.2 29.5 + - - +
1141A GLU* 5.4 0.2 - - - +
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Residues in contact with GLY 897 (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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892A MET 3.2 11.7 - - - -
893A LYS* 2.6 28.0 + - - -
896A GLU* 1.3 75.8 - - - +
898A TYR* 1.3 59.4 + - - +
899A GLY 3.3 2.7 - - - -
900A PHE* 3.2 8.1 + - - +
901A LYS* 2.8 33.6 + - - +
1141A GLU* 5.2 1.3 - - - -
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Residues in contact with TYR 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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894A CYS 2.8 16.9 + - - +
895A ALA* 3.5 17.6 + - + +
897A GLY* 1.3 73.1 - - - +
899A GLY* 1.3 61.6 + - - +
901A LYS* 3.3 21.6 - - + +
902A GLU* 2.8 73.3 + - + +
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Residues in contact with GLY 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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891A GLN 5.0 1.5 + - - -
892A MET* 3.2 32.3 + - - +
894A CYS 4.3 1.0 + - - -
897A GLY 3.3 0.8 - - - -
898A TYR* 1.3 84.5 - - - +
900A PHE* 1.3 55.9 + - - +
902A GLU* 4.1 2.7 - - - +
903A GLU* 2.9 30.0 + - - +
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Residues in contact with PHE 900 (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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888A HIS* 5.7 0.2 - - - -
889A ILE* 3.8 11.7 - - + -
892A MET* 3.1 55.3 + - + +
893A LYS* 3.7 23.3 - - + -
897A GLY* 3.2 6.5 + - - +
899A GLY* 1.3 73.8 - - - +
901A LYS* 1.3 57.0 + - - +
903A GLU* 3.7 0.8 - - - +
904A TYR* 2.8 37.8 + - - +
1141A GLU* 3.5 16.6 - - + +
1144A TYR* 3.8 17.5 - + + -
1145A VAL* 3.7 26.9 - - + -
1148A HIS* 3.5 50.5 - + + -
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Residues in contact with LYS 901 (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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895A ALA 3.2 19.4 + - - -
896A GLU* 3.2 34.7 + - - +
897A GLY 2.8 25.3 + - - +
898A TYR* 3.3 24.2 - - + +
900A PHE* 1.3 72.1 - - - +
902A GLU* 1.3 57.2 + - - +
904A TYR* 3.5 2.4 + - - +
905A GLU* 3.0 31.2 + - - +
1141A GLU* 3.6 22.0 - - + +
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Residues in contact with GLU 902 (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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898A TYR* 2.8 58.1 + - + +
899A GLY* 4.1 3.5 - - - +
901A LYS* 1.3 74.1 - - - +
903A GLU* 1.3 67.0 + - - +
905A GLU* 2.6 46.4 - - - +
906A SER* 3.3 3.3 + - - -
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Residues in contact with GLU 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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888A HIS* 4.9 8.0 + - - -
892A MET* 3.5 22.7 - - + +
899A GLY 2.9 19.9 + - - +
900A PHE* 3.7 4.0 - - - +
902A GLU* 1.3 76.1 - - - +
904A TYR* 1.3 62.2 + - - +
906A SER* 2.4 30.3 + - - -
907A PHE* 3.8 1.2 + - - -
1124A TYR* 3.4 31.3 - - + +
1144A TYR* 2.7 34.3 + - + +
1148A HIS* 4.5 6.4 + - - -
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Residues in contact with TYR 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 PHE 2.8 21.2 + - - +
901A LYS 3.9 2.0 - - - +
903A GLU* 1.3 73.9 - - - +
905A GLU* 1.3 63.8 + - - +
907A PHE* 3.1 43.2 + + - +
909A GLU* 5.0 8.9 + - - -
1131A ARG* 2.8 19.0 + - - -
1138A VAL* 2.5 32.3 + - + -
1139A GLN 3.1 15.9 + - - -
1140A THR* 3.5 16.2 - - - -
1141A GLU* 3.6 34.1 - - + -
1144A TYR* 3.5 25.8 - - + -
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Residues in contact with GLU 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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901A LYS 3.0 20.6 + - - +
902A GLU* 2.6 47.1 - - - +
904A TYR* 1.3 79.3 - - - +
906A SER* 1.3 74.1 + - - +
907A PHE 3.2 8.9 + - - +
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Residues in contact with SER 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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902A GLU 3.3 10.1 + - - -
903A GLU* 2.4 26.7 + - - -
905A GLU* 1.3 82.3 - - - +
907A PHE* 1.3 61.6 + - - +
908A PHE* 3.8 0.9 + - - +
1124A TYR* 2.7 33.7 + - - -
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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