Contacts of the helix formed by residues 885 - 906 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880B ILE* 3.7 13.7 - - + -
881B ARG 3.2 4.9 + - - +
882B VAL* 3.4 20.0 - - - +
883B ALA 3.3 1.0 - - - -
884B ASP* 1.3 76.9 - - - +
886B LEU* 1.3 58.1 + - - +
888B HIS* 3.6 7.0 - - + +
889B ILE* 2.8 56.8 + - + +
1121B VAL* 3.7 26.7 - - + -
1123B ILE* 4.9 9.9 - - + -
1148B HIS* 5.3 0.4 - - + +
1151B ILE* 4.1 19.5 - - + -
1152B LEU* 3.9 28.9 - - + +
1155B CYS* 4.3 12.8 - - + -
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Residues in contact with LEU 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882B VAL 5.0 0.6 + - - -
883B ALA 4.9 3.8 + - - +
884B ASP 3.3 0.6 - - - -
885B LEU* 1.3 74.7 - - - +
887B GLN* 1.3 62.4 + - - +
889B ILE* 4.0 2.9 - - + -
890B THR* 2.9 46.8 + - - +
1152B LEU* 4.0 34.1 - - + +
1156B LEU* 5.3 13.2 - - + -
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Residues in contact with GLN 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883B ALA 5.5 0.4 + - - -
884B ASP* 3.0 19.1 + - - +
886B LEU* 1.3 78.9 - - - +
888B HIS* 1.3 65.4 + - - +
890B THR* 3.3 5.6 + - - -
891B GLN* 2.9 60.6 + - - +
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Residues in contact with HIS 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B ILE* 3.4 45.4 - - + +
884B ASP* 2.8 17.7 + - + +
885B LEU* 3.6 11.2 - - + +
887B GLN* 1.3 80.0 - - - +
889B ILE* 1.3 66.7 + - - +
891B GLN* 3.9 9.1 + - - +
892B MET* 3.0 57.9 + - + +
903B GLU* 4.9 8.7 + - - -
1148B HIS* 5.0 13.5 + + - -
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Residues in contact with ILE 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885B LEU* 2.8 40.4 + - + +
886B LEU* 4.0 5.2 - - + +
888B HIS* 1.3 74.4 - - + +
890B THR* 1.3 64.8 + - - +
892B MET* 3.1 10.4 + - - +
893B LYS* 3.1 40.9 + - + +
900B PHE* 4.2 13.0 - - + -
1148B HIS* 3.2 48.0 - - + +
1149B ASP* 4.4 5.2 - - - +
1152B LEU* 3.6 27.4 - - + -
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Residues in contact with THR 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886B LEU* 2.9 37.8 + - - +
887B GLN* 3.7 6.3 - - - -
889B ILE* 1.3 78.8 - - - +
891B GLN* 1.3 64.8 + - + +
893B LYS* 3.0 19.7 + - + +
894B CYS* 3.4 15.2 + - - -
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Residues in contact with GLN 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B GLN* 2.9 58.4 + - - +
888B HIS* 3.9 7.5 + - - +
890B THR* 1.3 75.4 - - + +
892B MET* 1.3 63.8 + - + +
894B CYS* 3.0 32.4 + - - +
899B GLY* 5.0 2.4 + - - -
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Residues in contact with MET 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B HIS* 3.0 45.1 + - + +
889B ILE 3.1 8.5 + - - +
891B GLN* 1.3 79.0 - - + +
893B LYS* 1.3 56.6 + - - +
897B GLY* 3.2 11.4 - - - -
899B GLY* 3.2 44.2 + - - +
900B PHE* 3.1 52.5 + - + +
903B GLU* 3.5 31.9 - - - +
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Residues in contact with LYS 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889B ILE* 3.3 32.9 - - + +
890B THR* 3.0 12.4 + - + +
892B MET* 1.3 75.6 - - - +
894B CYS* 1.3 59.2 + - - +
896B GLU* 3.6 4.3 + - - -
897B GLY* 2.6 27.3 + - - -
900B PHE* 3.7 10.1 - - + -
1145B VAL* 3.9 19.0 - - + +
1149B ASP* 3.0 29.3 + - - -
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Residues in contact with CYS 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B THR* 3.4 15.1 + - - -
891B GLN* 3.0 28.5 + - - +
892B MET 4.2 0.5 - - - +
893B LYS* 1.3 76.5 - - - +
895B ALA* 1.3 61.6 + - + +
898B TYR* 2.8 32.4 + - - +
899B GLY 4.3 1.2 + - - -
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Residues in contact with ALA 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894B CYS* 1.3 77.9 - - + +
896B GLU* 1.3 73.5 + - - +
897B GLY 3.4 0.5 + - - -
898B TYR* 3.5 15.7 + - + +
901B LYS* 3.2 13.2 + - - -
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Residues in contact with GLU 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893B LYS 3.6 3.4 + - - -
894B CYS 3.3 0.2 - - - -
895B ALA* 1.3 78.4 - - - +
897B GLY* 1.3 57.3 + - - +
901B LYS* 3.2 29.5 + - - +
1141B GLU* 5.4 0.2 - - - +
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Residues in contact with GLY 897 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892B MET 3.2 12.8 - - - -
893B LYS* 2.6 27.4 + - - -
894B CYS 3.2 0.2 + - - -
896B GLU* 1.3 76.2 - - - +
898B TYR* 1.3 58.9 + - - +
899B GLY 3.3 2.5 - - - -
900B PHE* 3.2 7.7 + - - +
901B LYS* 2.8 33.4 + - - +
1141B GLU* 5.2 1.3 - - - -
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Residues in contact with TYR 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894B CYS 2.8 17.0 + - - +
895B ALA* 3.5 16.1 + - + +
897B GLY* 1.3 72.3 - - - +
899B GLY* 1.3 61.4 + - - +
901B LYS* 3.3 22.8 - - + +
902B GLU* 2.8 72.7 + - + +
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Residues in contact with GLY 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B GLN 5.0 1.4 + - - -
892B MET* 3.2 31.4 + - - +
894B CYS 4.3 1.2 + - - -
897B GLY 3.3 0.4 - - - -
898B TYR* 1.3 83.9 - - - +
900B PHE* 1.3 55.9 + - - +
902B GLU* 4.1 3.5 - - - +
903B GLU* 2.9 30.0 + - - +
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Residues in contact with PHE 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889B ILE* 3.8 11.2 - - + -
892B MET* 3.1 56.8 + - + +
893B LYS* 3.7 23.6 - - + -
897B GLY* 3.7 6.3 - - - +
899B GLY* 1.3 74.8 - - - +
901B LYS* 1.3 57.0 + - - +
903B GLU* 3.7 0.8 - - - +
904B TYR* 2.8 37.2 + - - +
1141B GLU* 3.5 16.4 - - + +
1144B TYR* 3.8 17.3 - + + -
1145B VAL* 3.7 25.4 - - + -
1148B HIS* 3.5 50.9 - + + -
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Residues in contact with LYS 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895B ALA 3.2 18.4 + - - -
896B GLU* 3.2 32.7 + - - +
897B GLY 2.8 25.1 + - - +
898B TYR* 3.3 23.9 - - + +
900B PHE* 1.3 72.0 - - - +
902B GLU* 1.3 57.7 + - - +
904B TYR* 3.9 2.3 - - - +
905B GLU* 3.0 30.2 + - - +
1141B GLU* 3.5 23.3 + - + +
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Residues in contact with GLU 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898B TYR* 2.8 56.9 + - + +
899B GLY* 4.1 3.6 - - - +
901B LYS* 1.3 74.4 - - - +
903B GLU* 1.3 64.1 + - - +
905B GLU* 2.6 48.1 - - - +
906B SER* 3.3 5.2 + - - -
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Residues in contact with GLU 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888B HIS* 4.9 8.2 + - - -
892B MET* 3.5 22.6 - - + +
899B GLY 2.9 20.5 + - - +
900B PHE* 3.7 3.8 - - - +
902B GLU* 1.3 77.2 - - - +
904B TYR* 1.3 63.8 + - - +
906B SER* 2.4 29.8 + - - -
907B PHE* 3.8 1.6 + - - -
1124B TYR* 3.4 30.9 - - + +
1144B TYR* 2.6 33.2 + - + +
1148B HIS* 4.5 5.9 + - - -
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Residues in contact with TYR 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900B PHE 2.8 21.2 + - - +
901B LYS 3.9 2.2 - - - +
903B GLU* 1.3 73.2 - - - +
905B GLU* 1.3 64.6 + - - +
907B PHE* 3.1 43.7 + + - +
909B GLU* 5.0 9.7 + - - -
1131B ARG* 2.8 19.2 + - - -
1138B VAL* 2.5 32.2 + - + -
1139B GLN 3.1 15.9 + - - -
1140B THR* 3.5 15.3 - - - -
1141B GLU* 3.6 33.2 - - + -
1144B TYR* 3.5 25.5 - - + -
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Residues in contact with GLU 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901B LYS 3.0 20.1 + - - +
902B GLU* 2.6 45.4 - - - +
904B TYR* 1.3 78.5 - - - +
906B SER* 1.3 73.8 + - - +
907B PHE 3.2 9.2 - - - +
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Residues in contact with SER 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902B GLU 3.3 9.3 + - - -
903B GLU* 2.4 26.8 + - - -
905B GLU* 1.3 82.6 - - - +
907B PHE* 1.3 61.4 + - - +
908B PHE 3.8 0.5 + - - -
1124B TYR* 2.7 33.3 + - - -
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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