Contacts of the helix formed by residues 974 - 994 (chain A) in PDB entry 2RD0
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 974 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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964A ILE 4.6 5.1 + - - -
965A SER 5.2 4.0 - - - +
967A GLY* 4.9 11.2 - - - -
970A GLU 5.3 0.7 - - - +
971A CYS* 3.9 27.2 + - + +
972A THR 3.9 1.6 - - - -
973A LYS* 1.3 80.2 - - - +
975A ARG* 1.3 60.6 + - - +
976A GLU* 3.1 15.5 + - - +
977A PHE* 3.0 25.4 + - - +
978A GLU* 2.9 30.4 + - - +
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Residues in contact with ARG 975 (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 THR* 1.3 71.8 - - - +
976A GLU* 1.3 65.9 + - + +
978A GLU* 3.5 30.1 + - - +
979A ARG* 3.3 22.3 + - - +
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Residues in contact with GLU 976 (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 ILE* 4.8 4.9 - - - +
964A ILE* 3.6 22.2 - - + +
965A SER* 3.2 34.4 + - - +
974A THR* 3.8 13.2 - - - +
975A ARG* 1.3 82.5 - - + +
977A PHE* 1.3 57.0 + - - +
979A ARG* 3.5 29.7 + - - +
980A PHE* 3.2 22.2 + - - +
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Residues in contact with PHE 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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956A LEU* 5.4 2.9 - - + -
961A LEU* 3.6 30.1 - - + -
964A ILE* 4.5 17.5 - - + -
971A CYS 3.9 16.2 - - - +
972A THR* 3.3 31.2 - - + -
973A LYS* 5.1 0.4 - - - -
974A THR* 3.0 21.9 + - - +
976A GLU* 1.3 78.9 - - - +
978A GLU* 1.3 61.7 + - + +
980A PHE* 3.2 18.7 + + - +
981A GLN* 2.9 57.3 + - + +
1043A MET* 3.7 23.6 - - + -
1049A GLY 5.8 0.9 - - - -
1050A GLY 5.4 2.5 - - - -
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Residues in contact with GLU 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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973A LYS* 5.1 19.4 - - + +
974A THR 2.9 19.4 + - - +
975A ARG* 3.5 44.0 + - + +
977A PHE* 1.3 72.9 - - + +
979A ARG* 1.3 67.5 + - - +
980A PHE 2.9 2.2 + - - -
981A GLN* 3.0 23.4 + - - +
982A GLU* 3.2 12.6 + - - +
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Residues in contact with ARG 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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894A ILE* 4.2 5.2 + - - +
895A ASP* 3.5 33.1 + - - +
898A THR* 3.3 40.0 + - - +
899A ARG* 5.3 4.0 - - - +
964A ILE* 4.2 5.3 - - - +
975A ARG 3.3 16.0 + - - +
976A GLU* 3.5 37.7 + - - +
978A GLU* 1.3 77.4 - - - +
980A PHE* 1.3 65.4 + - - +
982A GLU* 3.3 19.0 - - - +
983A MET* 3.4 18.5 - - + +
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Residues in contact with PHE 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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898A THR* 3.7 27.6 - - + -
901A CYS* 4.5 6.7 - - + -
902A ALA* 3.5 32.1 - - + -
905A CYS* 5.0 3.6 - - + -
956A LEU* 4.1 29.4 - - + -
964A ILE* 4.1 15.9 - - + -
976A GLU 3.2 12.0 + - - +
977A PHE* 3.2 28.5 + + - +
978A GLU 2.9 1.8 + - - -
979A ARG* 1.3 79.7 - - - +
981A GLN* 1.3 80.0 + - + +
983A MET* 2.8 25.1 + - + +
984A CYS* 3.3 25.8 + - - -
1043A MET* 5.1 4.5 - - + -
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Residues in contact with GLN 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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972A THR 5.2 0.7 - - - +
977A PHE* 2.9 46.0 + - + +
978A GLU* 3.0 12.7 + - - +
980A PHE* 1.3 80.4 - - + +
982A GLU* 1.3 64.6 + - - +
984A CYS* 3.0 16.4 + - - +
985A TYR* 3.0 54.0 + - + -
1040A MET* 5.2 0.8 - - - +
1043A MET* 3.2 26.8 - - + +
1050A GLY 3.3 13.9 + - - +
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Residues in contact with GLU 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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829A LEU* 5.7 0.5 - - - +
978A GLU 3.2 8.6 + - - +
979A ARG* 3.3 15.0 - - - +
981A GLN* 1.3 77.6 - - - +
983A MET* 1.3 69.9 + - - +
985A TYR* 3.3 10.4 + - - +
986A LYS* 2.7 63.9 + - - +
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Residues in contact with MET 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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829A LEU* 4.0 10.3 - - + +
830A ASP 3.4 21.8 - - - +
831A LEU* 3.6 22.9 - - + -
898A THR* 4.8 11.7 - - - -
899A ARG* 3.3 49.4 - - - +
902A ALA* 4.3 6.3 - - + -
979A ARG* 3.4 23.8 - - + +
980A PHE* 2.8 15.0 + - - +
982A GLU* 1.3 79.7 - - - +
984A CYS* 1.3 50.9 + - - +
986A LYS* 3.1 5.6 + - - +
987A ALA* 2.7 36.5 + - - +
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Residues in contact with CYS 984 (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 ALA* 3.8 23.3 - - - -
905A CYS* 4.8 5.8 - - - -
906A VAL* 3.7 16.7 - - + +
980A PHE* 3.7 38.4 - - - -
981A GLN* 3.0 9.3 + - - +
983A MET* 1.3 77.5 - - - +
985A TYR* 1.3 58.3 + - + +
987A ALA* 2.9 4.0 + - - +
988A TYR* 2.7 38.0 + - - +
1039A PHE* 4.3 16.8 - - + -
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Residues in contact with TYR 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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981A GLN* 3.0 57.3 + - + -
982A GLU* 3.7 9.0 - - - +
984A CYS* 1.3 76.6 - - + +
986A LYS* 1.3 58.6 + - + +
988A TYR* 4.9 3.4 - - - -
989A LEU* 3.0 33.6 + - - +
1036A LEU* 3.8 26.3 - - + +
1039A PHE* 3.6 35.2 - + - -
1040A MET* 3.4 39.3 - - + +
1043A MET* 4.1 6.9 - - - -
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Residues in contact with LYS 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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829A LEU* 3.4 26.3 - - + +
982A GLU* 2.7 47.8 + - - +
983A MET 3.5 6.5 - - - +
985A TYR* 1.3 78.4 - - + +
987A ALA* 1.3 56.8 + - - +
989A LEU* 3.8 7.5 - - + +
990A ALA* 2.9 30.7 + - - +
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Residues in contact with ALA 987 (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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824A TRP* 3.3 24.9 + - + +
829A LEU* 4.2 1.5 - - - +
831A LEU* 3.5 26.0 - - + -
902A ALA 5.3 1.6 - - - +
906A VAL* 3.9 18.8 - - + -
983A MET 2.7 19.6 + - - +
984A CYS* 2.9 5.4 + - - +
986A LYS* 1.3 70.5 - - - +
988A TYR* 1.3 65.2 + - - +
990A ALA* 3.2 0.7 + - - -
991A ILE* 3.1 22.7 + - - +
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Residues in contact with TYR 988 (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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906A VAL* 3.8 18.0 - - + +
909A PHE* 4.1 5.8 - + - -
910A ILE* 4.2 20.4 - - + -
984A CYS 2.7 19.4 + - - +
985A TYR* 4.6 3.1 - - - +
987A ALA* 1.3 73.3 - - - +
989A LEU* 1.3 63.5 + - + +
991A ILE* 3.4 2.0 + - - +
992A ARG* 2.9 33.0 + - + +
1025A THR 2.9 29.8 + - - -
1026A LEU* 3.2 27.7 + - + +
1027A ALA* 3.6 4.7 + - - +
1035A ALA* 4.2 17.8 - - + +
1036A LEU* 4.9 7.2 - - + -
1038A TYR* 4.1 9.4 - - - -
1039A PHE* 3.7 48.2 - + + -
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Residues in contact with LEU 989 (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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985A TYR 3.0 20.2 + - - +
986A LYS* 4.0 8.1 - - + +
988A TYR* 1.3 85.2 - - + +
990A ALA* 1.3 62.1 + - - +
992A ARG* 3.3 13.5 - - + +
993A GLN* 3.2 21.2 + - + +
1032A GLU* 4.4 28.5 - - + +
1033A GLN* 5.3 0.4 - - - +
1036A LEU* 4.0 29.8 - - + -
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Residues in contact with ALA 990 (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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823A ILE* 4.3 1.1 - - + -
824A TRP* 4.0 11.4 - - + +
827A GLN* 3.3 30.3 - - - +
829A LEU* 3.9 9.2 - - + -
986A LYS 2.9 20.2 + - - +
987A ALA 3.5 4.7 - - - +
988A TYR 3.2 0.2 - - - -
989A LEU* 1.3 76.1 - - - +
991A ILE* 1.3 66.7 - - - +
992A ARG 3.1 1.1 - - - -
993A GLN* 3.0 12.7 + - - +
994A HIS* 3.0 21.2 - - - -
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Residues in contact with ILE 991 (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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820A MET* 3.8 35.2 - - + -
823A ILE* 3.7 24.2 - - + -
824A TRP* 3.5 29.8 - - + +
910A ILE* 3.6 31.2 - - + -
987A ALA 3.1 15.2 + - - +
988A TYR 4.1 0.4 - - - +
990A ALA* 1.3 72.3 - - - +
992A ARG* 1.3 67.0 + - - +
994A HIS* 3.1 12.5 + - - +
995A ALA* 3.3 10.9 + - - +
998A PHE* 3.6 22.2 - - + -
1026A LEU* 4.3 5.3 - - + +
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Residues in contact with ARG 992 (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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988A TYR* 2.9 24.3 + - + +
989A LEU* 3.3 17.5 - - - +
990A ALA 3.1 0.2 - - - -
991A ILE* 1.3 75.8 - - - +
993A GLN* 1.3 64.3 + - - +
995A ALA* 3.0 21.3 + - + +
1026A LEU* 2.5 50.3 + - + +
1027A ALA* 2.6 27.1 + - - +
1028A LEU 4.6 2.8 + - - -
1029A ASP 4.9 0.2 + - - -
1030A LYS 3.1 27.1 + - - -
1031A THR 4.2 4.3 + - - -
1032A GLU* 4.3 26.2 - - - +
1035A ALA* 3.1 14.2 - - - +
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Residues in contact with GLN 993 (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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827A GLN* 2.9 27.1 + - - +
989A LEU* 3.2 11.3 + - + +
990A ALA* 3.0 10.8 + - - +
992A ARG* 1.3 82.7 - - - +
994A HIS* 1.3 68.7 + - + +
995A ALA 3.7 1.6 + - - -
996A ASN* 4.7 4.2 - - - +
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Residues in contact with HIS 994 (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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594A LYS* 5.5 4.9 + - - -
596A GLU* 5.0 9.1 + - - +
823A ILE* 3.7 36.6 - - + +
827A GLN* 3.0 26.7 + - + -
990A ALA 3.0 24.7 - - - +
991A ILE 3.1 9.9 + - - +
993A GLN* 1.3 91.7 + - + +
995A ALA* 1.3 61.3 + - - -
996A ASN* 3.5 7.4 - - - -
997A LEU* 3.4 15.6 - - + +
998A PHE* 3.2 20.2 - - + -
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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