Contacts of the helix formed by residues 976 - 988 (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 GLN 976 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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928A ARG* 6.1 0.4 - - - +
975A MET* 1.3 74.2 - - - +
977A GLU* 1.3 71.7 + - + +
978A THR 3.3 0.3 + - - -
979A ILE* 3.5 28.0 + - + +
980A TYR 5.2 0.2 + - - -
1006A VAL* 6.1 3.2 - - - +
1009A CYS* 3.6 21.5 - - + +
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Residues in contact with GLU 977 (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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925A MET* 3.1 41.1 - - + +
926A LYS* 6.0 0.2 - - - +
975A MET* 3.1 22.4 - - - +
976A GLN* 1.3 94.4 + - + +
978A THR* 1.3 63.0 + - + +
979A ILE 3.6 0.2 - - - -
980A TYR* 5.1 3.2 + - - +
981A ASP* 4.3 6.9 - - - +
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Residues in contact with THR 978 (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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925A MET 4.2 4.9 - - - +
926A LYS* 3.7 42.2 - - + +
954A ILE* 5.2 6.2 - - + +
972A GLN* 4.0 6.0 + - - -
974A PRO* 3.7 6.1 - - - +
975A MET* 2.8 30.4 + - + +
977A GLU* 1.3 84.6 - - + +
979A ILE* 1.3 62.8 + - - +
980A TYR 3.3 2.5 - - - -
981A ASP* 3.4 19.9 + - - +
982A PHE* 3.0 23.8 + - - +
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Residues in contact with ILE 979 (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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974A PRO* 4.6 3.4 - - + -
975A MET 3.1 13.7 + - - +
976A GLN* 3.5 22.3 + - + +
977A GLU 3.6 0.2 - - - -
978A THR* 1.3 76.0 - - - +
980A TYR* 1.3 63.5 + - - +
982A PHE* 3.3 6.9 + - - +
983A TRP* 3.1 33.6 + - + +
1009A CYS* 3.6 23.8 - - - -
1010A LYS 4.4 4.9 - - - +
1011A TYR* 3.8 20.2 - - + +
1019A TYR* 3.7 35.0 - - + -
1020A LYS* 6.1 1.1 - - - +
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Residues in contact with TYR 980 (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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945A ILE* 3.7 22.4 - - + +
976A GLN 5.2 0.4 + - - -
977A GLU 5.1 2.8 + - - +
978A THR* 4.4 0.2 - - - +
979A ILE* 1.3 77.3 - - - +
981A ASP* 1.3 62.0 + - - +
983A TRP* 3.3 2.2 + - + +
984A ARG* 2.9 51.5 + - + +
1019A TYR* 3.3 35.2 - - + -
1020A LYS* 3.7 42.2 - - + +
1021A ASP* 2.7 33.1 + - - -
1022A ILE* 4.0 14.8 - - + -
1044A LYS* 4.1 7.1 + - - -
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Residues in contact with ASP 981 (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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926A LYS* 4.6 11.6 - - - +
942A LEU* 3.7 20.1 - - + +
945A ILE* 4.9 2.8 - - - +
953A TYR 4.3 7.6 - - - +
954A ILE* 3.5 13.7 - - + +
977A GLU 4.3 5.0 - - - +
978A THR* 3.4 29.0 + - - +
980A TYR* 1.3 80.5 - - - +
982A PHE* 1.3 62.4 + - - +
984A ARG* 3.2 28.6 + - - +
985A MET* 3.1 24.4 + - - +
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Residues in contact with PHE 982 (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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954A ILE* 3.8 12.3 - - + +
971A THR* 4.9 5.4 - - + -
972A GLN 5.2 2.9 - - - -
974A PRO* 3.4 30.1 - - + -
978A THR 3.0 13.3 + - - +
979A ILE* 3.4 8.5 - - - +
981A ASP* 1.3 79.0 - - - +
983A TRP* 1.3 70.6 + + - +
985A MET* 3.3 13.0 + - + +
986A VAL* 3.0 50.2 + - + +
994A ILE* 3.9 31.0 - - + -
1011A TYR* 3.6 34.3 - + - -
1092A VAL* 3.7 22.4 - - + -
1094A HIS* 4.5 5.2 - + - -
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Residues in contact with TRP 983 (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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979A ILE* 3.1 34.4 + - + +
980A TYR* 3.3 5.1 + - + +
982A PHE* 1.3 80.8 - + - +
984A ARG* 1.3 60.6 + - - +
986A VAL* 3.2 21.7 + - + +
987A TRP* 2.9 25.3 + - - +
994A ILE* 3.9 25.1 - - + -
1011A TYR* 2.9 47.1 + + - -
1012A TRP* 4.3 7.6 - - + -
1019A TYR* 3.8 16.7 - + + -
1022A ILE* 3.5 24.2 - - + +
1024A VAL* 3.9 38.4 - - + -
1040A PHE* 4.8 11.9 - + - -
1042A VAL* 4.3 20.4 - - + -
1053A ILE* 4.6 3.4 - - + -
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Residues in contact with ARG 984 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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942A LEU* 3.2 23.1 - - + +
943A GLN* 2.6 40.7 + - - +
945A ILE* 3.6 23.9 - - - +
951A SER* 2.5 33.1 + - - -
980A TYR* 2.9 44.5 + - + +
981A ASP* 3.2 29.1 + - - +
983A TRP* 1.3 77.1 - - - +
985A MET* 1.3 59.0 + - - +
987A TRP* 3.8 2.0 - - - +
988A HIS* 2.9 31.7 + - - +
1022A ILE* 3.4 17.4 - - + +
1044A LYS* 4.5 7.7 + - - +
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Residues in contact with MET 985 (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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940A VAL* 3.8 24.2 - - + -
942A LEU* 3.7 13.7 - - + -
954A ILE* 4.0 21.1 - - + -
969A ILE* 4.1 17.3 - - + -
971A THR* 4.4 5.6 - - + +
981A ASP 3.1 20.1 + - - +
982A PHE* 3.4 21.1 - - + +
983A TRP 3.1 0.2 - - - -
984A ARG* 1.3 75.6 - - - +
986A VAL* 1.3 58.1 + - - +
988A HIS* 3.3 3.5 + - - -
989A GLU* 2.8 56.7 + - + +
1092A VAL* 3.9 38.1 - - + -
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Residues in contact with VAL 986 (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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982A PHE* 3.0 46.1 + - + +
983A TRP* 3.4 21.8 - - + +
985A MET* 1.3 77.3 - - + +
987A TRP* 1.3 61.1 + - - +
990A ASN* 3.3 1.7 + - - -
991A THR* 3.0 47.5 + - + +
994A ILE* 4.4 5.8 - - + -
1042A VAL* 6.1 0.2 - - + -
1051A ARG* 4.7 0.3 + - - -
1053A ILE* 3.6 33.8 - - + +
1092A VAL* 4.2 15.9 - - + -
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Residues in contact with TRP 987 (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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943A GLN* 6.1 0.7 - - - -
983A TRP 2.9 15.4 + - - +
984A ARG* 3.8 4.3 - - - +
986A VAL* 1.3 77.3 - - + +
988A HIS* 1.3 64.8 - - - +
990A ASN* 3.0 15.9 + - - +
1022A ILE* 4.3 12.1 - - + -
1042A VAL* 3.4 45.1 - - + -
1043A GLU* 4.0 4.0 - - - -
1044A LYS* 3.6 52.2 - - + +
1047A VAL* 4.2 20.4 - - + +
1049A GLU* 4.3 9.0 - - - -
1051A ARG* 3.0 72.1 + - + +
1053A ILE* 5.2 2.7 - - + -
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Residues in contact with HIS 988 (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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941A ARG 5.1 6.5 - - - -
942A LEU* 6.2 0.2 - - - -
943A GLN* 3.1 47.1 + - + +
984A ARG 2.9 19.2 + - - +
985A MET* 3.9 3.8 - - - +
987A TRP* 1.3 82.5 - - - +
989A GLU* 1.3 82.0 + - - +
990A ASN* 3.2 2.6 + - - +
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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