Contacts of the helix formed by residues 976 - 988 (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 GLN 976 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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928B ARG* 6.1 0.4 - - - +
975B MET* 1.3 73.4 - - - +
977B GLU* 1.3 71.8 + - + +
978B THR 3.3 0.2 + - - -
979B ILE* 3.5 28.4 + - + +
980B TYR 5.2 0.2 + - - -
1006B VAL* 6.1 3.2 - - - +
1009B CYS* 3.6 22.6 - - + +
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Residues in contact with GLU 977 (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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925B MET* 3.1 42.1 - - + +
926B LYS* 6.1 0.2 - - + -
975B MET* 3.1 23.0 - - - +
976B GLN* 1.3 93.6 + - + +
978B THR* 1.3 63.1 + - + +
979B ILE 3.6 0.2 - - - -
980B TYR* 5.1 3.1 + - - +
981B ASP* 4.3 6.6 - - - +
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Residues in contact with THR 978 (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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925B MET 4.2 4.9 - - - +
926B LYS* 3.8 41.7 - - + +
954B ILE* 5.2 6.2 - - + +
972B GLN* 4.0 6.0 + - - -
974B PRO* 3.8 6.1 - - - +
975B MET* 2.8 30.8 + - + +
977B GLU* 1.3 85.5 - - + +
979B ILE* 1.3 62.6 + - - +
980B TYR 3.3 2.7 - - - +
981B ASP* 3.4 19.2 + - - +
982B PHE* 3.0 23.6 + - - +
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Residues in contact with ILE 979 (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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974B PRO* 4.6 2.7 - - - -
975B MET 3.1 13.6 + - - +
976B GLN* 3.5 21.9 + - + +
977B GLU 3.6 0.4 - - - -
978B THR* 1.3 75.7 - - - +
980B TYR* 1.3 62.6 + - - +
982B PHE* 3.3 6.5 + - - +
983B TRP* 3.1 34.5 + - + -
1009B CYS* 3.6 24.0 - - - -
1010B LYS 4.4 4.7 - - - +
1011B TYR* 3.8 21.1 - - + +
1019B TYR* 3.7 33.2 - - + -
1020B LYS* 6.1 1.6 - - - +
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Residues in contact with TYR 980 (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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945B ILE* 3.7 22.8 - - + +
977B GLU 5.1 2.6 + - - +
978B THR* 3.3 0.6 - - - +
979B ILE* 1.3 79.0 - - - +
981B ASP* 1.3 63.1 + - - +
983B TRP* 3.3 2.0 + - + +
984B ARG* 2.9 50.4 + - + +
1019B TYR* 3.3 34.8 - - + -
1020B LYS* 3.7 43.0 - - + +
1021B ASP* 2.7 32.0 + - - -
1022B ILE* 4.0 14.8 - - + -
1044B LYS* 4.1 6.6 + - - -
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Residues in contact with ASP 981 (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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926B LYS* 4.6 11.6 - - - +
942B LEU* 3.7 20.2 - - + +
945B ILE* 4.9 2.6 - - - +
953B TYR 4.3 7.7 - - - +
954B ILE* 3.5 12.6 - - + +
977B GLU 4.3 4.7 - - - +
978B THR* 3.4 29.6 + - - +
980B TYR* 1.3 80.4 - - - +
982B PHE* 1.3 62.2 + - - +
984B ARG* 3.2 28.5 + - - +
985B MET* 3.1 24.8 + - - +
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Residues in contact with PHE 982 (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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954B ILE* 3.8 13.6 - - + +
971B THR* 4.9 5.2 - - + -
972B GLN 5.2 2.9 - - - -
974B PRO* 3.4 28.7 - - + -
978B THR 3.0 13.1 + - - +
979B ILE 3.3 8.5 - - - +
981B ASP* 1.3 78.8 - - - +
983B TRP* 1.3 70.0 + + - +
985B MET* 3.3 13.0 + - + +
986B VAL* 3.0 49.1 + - + +
994B ILE* 3.9 30.3 - - + -
1011B TYR* 3.6 35.4 - + - -
1092B VAL* 3.7 23.3 - - + -
1094B HIS* 4.5 5.4 - + - -
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Residues in contact with TRP 983 (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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979B ILE* 3.1 33.9 + - + +
980B TYR* 3.3 5.1 + - + +
982B PHE* 1.3 81.5 - + - +
984B ARG* 1.3 59.9 + - - +
986B VAL* 3.2 22.7 + - + +
987B TRP* 2.9 24.9 + - - +
994B ILE* 3.9 25.4 - - + -
1011B TYR* 2.9 47.1 + + - -
1012B TRP* 4.3 7.9 - - + -
1019B TYR* 3.8 15.8 - + + -
1022B ILE* 3.5 24.1 - - + +
1024B VAL* 4.0 37.9 - - + -
1040B PHE* 4.8 11.9 - + - -
1042B VAL* 4.3 20.4 - - + -
1053B ILE* 4.6 3.1 - - + -
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Residues in contact with ARG 984 (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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942B LEU* 3.2 23.3 - - + +
943B GLN* 2.6 40.3 + - - +
945B ILE* 3.6 22.8 - - - +
951B SER* 2.5 33.1 + - - -
980B TYR* 2.9 45.4 + - + +
981B ASP* 3.2 28.3 + - - +
983B TRP* 1.3 76.9 - - - +
985B MET* 1.3 60.0 + - - +
987B TRP* 3.8 2.2 - - - +
988B HIS* 2.9 30.8 + - - +
1022B ILE* 3.4 17.6 - - + +
1044B LYS* 4.5 7.6 + - - +
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Residues in contact with MET 985 (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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940B VAL* 3.8 24.5 - - + -
942B LEU* 3.7 14.6 - - + -
954B ILE* 4.0 20.9 - - + -
969B ILE* 4.1 18.4 - - + -
971B THR* 4.4 4.7 - - + +
981B ASP 3.1 19.9 + - - +
982B PHE* 3.4 22.2 - - + +
984B ARG* 1.3 75.2 - - - +
986B VAL* 1.3 58.2 + - - +
988B HIS* 3.2 3.1 + - - -
989B GLU* 2.8 55.6 + - + +
1092B VAL* 3.9 38.1 - - + -
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Residues in contact with VAL 986 (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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982B PHE* 3.0 46.3 + - + +
983B TRP* 3.4 21.1 - - + +
985B MET* 1.3 76.8 - - + +
987B TRP* 1.3 60.9 + - + +
990B ASN* 3.3 2.1 + - - -
991B THR* 3.0 46.6 + - + +
994B ILE* 4.4 5.6 - - + -
1042B VAL* 6.1 0.2 - - + -
1051B ARG* 4.7 0.2 + - - -
1053B ILE* 3.6 33.6 - - + +
1092B VAL* 4.3 16.4 - - + -
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Residues in contact with TRP 987 (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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943B GLN* 6.1 0.4 - - - -
983B TRP 2.9 15.6 + - - +
984B ARG* 3.8 4.3 - - - +
986B VAL* 1.3 76.2 - - - +
988B HIS* 1.3 65.9 + - - +
990B ASN* 3.0 16.8 + - - +
1022B ILE* 4.3 12.6 - - + -
1042B VAL* 3.4 48.0 - - + -
1043B GLU* 4.0 4.3 - - - -
1044B LYS* 3.6 53.2 - - + +
1047B VAL* 4.2 21.0 - - + +
1049B GLU* 4.3 9.6 - - - -
1051B ARG* 3.0 71.7 + - + +
1053B ILE* 5.2 2.9 - - + -
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Residues in contact with HIS 988 (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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941B ARG 5.1 6.7 - - - -
942B LEU* 6.2 0.4 - - - -
943B GLN* 3.1 48.1 + - + +
984B ARG 2.9 18.4 + - - +
985B MET* 3.9 4.0 - - - +
987B TRP* 1.3 80.6 - - + +
989B GLU* 1.3 80.5 - - - +
990B ASN* 3.2 2.8 + - - +
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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