Contacts of the helix formed by residues 961 - 989 (chain D) in PDB entry 1C1G
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 ALA 961 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C ALA* 4.4 20.0 - - + +
678C LEU* 4.7 6.7 - - + -
681C LEU* 4.3 25.1 - - + +
957D ARG* 3.2 17.8 + - + +
958D LEU 4.0 1.1 - - - +
960D THR* 1.3 77.3 + - - +
962D LEU* 1.3 61.0 + - - +
964D LYS* 3.7 11.3 - - - +
965D LEU* 3.2 22.3 + - - +
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Residues in contact with LEU 962 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C ALA* 5.8 1.3 - - + -
958D LEU* 3.1 34.4 + - + +
959D ALA* 3.1 14.6 + - + +
961D ALA* 1.3 75.1 - - - +
963D GLN* 1.3 65.9 + - + +
965D LEU* 3.1 43.0 + - + +
966D GLU* 3.2 12.3 + - - +
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Residues in contact with GLN 963 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959D ALA 3.5 9.3 - - - +
960D THR* 3.2 28.0 + - - +
962D LEU* 1.3 77.4 - - + +
964D LYS* 1.3 70.5 + - + +
965D LEU 3.5 0.2 - - - -
966D GLU* 4.0 10.5 - - - +
967D GLU* 3.1 27.0 + - - +
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Residues in contact with LYS 964 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681C LEU* 4.1 22.5 - - + +
684C ALA* 5.3 0.2 - - - +
960D THR* 3.1 29.7 + - - +
961D ALA* 3.7 5.3 - - - -
962D LEU 3.2 0.8 - - - -
963D GLN* 1.3 88.4 + - - +
965D LEU* 1.3 68.0 + - - +
966D GLU 3.3 0.4 - - - -
967D GLU* 2.6 53.3 + - - +
968D ALA* 3.2 23.4 + - - +
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Residues in contact with LEU 965 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C ALA* 5.3 5.6 - - + -
680C LYS* 3.2 51.6 + - + +
681C LEU* 4.4 0.4 - - - +
684C ALA* 5.3 0.5 - - - +
961D ALA 3.2 11.4 + - - +
962D LEU* 3.1 37.7 + - + +
964D LYS* 1.3 81.9 - - - +
966D GLU* 1.3 69.0 + - + +
968D ALA* 3.9 2.0 - - - +
969D GLU* 3.1 51.7 + - - +
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Residues in contact with GLU 966 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962D LEU* 3.5 17.3 - - - +
963D GLN* 4.0 10.7 - - - +
965D LEU* 1.3 84.1 - - + +
967D GLU* 1.3 56.9 + - - +
969D GLU* 3.4 16.2 - - - +
970D LYS* 2.7 56.7 + - - +
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Residues in contact with GLU 967 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963D GLN 3.1 16.8 + - - +
964D LYS* 2.6 38.7 + - - +
965D LEU 3.4 0.6 + - - -
966D GLU* 1.3 74.2 - - - +
968D ALA* 1.3 67.9 + - - +
970D LYS* 3.0 25.3 + - + +
971D ALA* 3.2 12.4 + - - +
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Residues in contact with ALA 968 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681C LEU* 6.1 0.4 - - + -
684C ALA* 3.9 30.8 - - + +
685C GLU* 6.1 0.9 - - + -
688C ALA* 5.8 3.6 - - - +
964D LYS 3.2 18.4 + - - +
965D LEU 3.9 2.2 - - - +
967D GLU* 1.3 79.1 + - - +
969D GLU* 1.3 62.4 + - - +
971D ALA* 3.5 8.5 + - - +
972D ALA* 3.2 18.6 + - - +
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Residues in contact with GLU 969 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C LYS* 5.7 3.4 - - + +
684C ALA* 6.0 3.8 - - + -
965D LEU* 3.1 41.8 + - + +
966D GLU* 3.4 21.8 - - - +
967D GLU 3.1 0.2 - - - -
968D ALA* 1.3 74.9 - - - +
970D LYS* 1.3 54.9 + - + +
972D ALA* 2.7 31.3 + - - +
973D ASP* 3.0 17.6 - - - +
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Residues in contact with LYS 970 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966D GLU* 2.7 62.2 + - - +
967D GLU* 3.0 13.9 + - + +
969D GLU* 1.3 75.3 - - + +
971D ALA* 1.3 62.3 + - - +
972D ALA 3.3 0.2 + - - -
973D ASP* 3.4 11.6 + - - +
974D GLU* 3.2 30.4 + - - +
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Residues in contact with ALA 971 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688C ALA* 6.3 3.4 - - + -
967D GLU 3.2 8.1 + - - +
968D ALA* 3.7 11.2 - - - +
970D LYS* 1.3 79.5 - - - +
972D ALA* 1.3 54.5 + - - +
974D GLU* 3.4 18.7 - - - +
975D SER* 2.8 32.0 + - - +
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Residues in contact with ALA 972 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C ALA 6.0 0.4 - - - +
687C ALA* 5.4 14.1 - - + -
688C ALA* 5.8 8.3 - - + +
691C SER* 5.5 4.9 - - - +
968D ALA 3.2 12.1 + - - +
969D GLU* 2.7 21.2 + - - +
971D ALA* 1.3 67.3 - - - +
973D ASP* 1.3 56.8 + - - +
975D SER* 2.8 29.0 + - - -
976D GLU* 3.2 11.2 + - - +
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Residues in contact with ASP 973 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969D GLU* 3.0 20.3 + - - +
970D LYS* 3.6 10.7 - - - +
972D ALA* 1.3 74.2 - - - +
974D GLU* 1.3 63.3 + - + +
976D GLU* 3.0 19.5 + - - +
977D ARG* 3.2 24.1 + - + +
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Residues in contact with GLU 974 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C MET* 5.3 0.5 - - - +
970D LYS* 3.2 13.1 + - + +
971D ALA* 3.4 27.7 + - - +
973D ASP* 1.3 78.3 - - + +
975D SER* 1.3 56.4 + - - +
977D ARG* 3.7 13.9 + - - +
978D GLY* 3.2 23.2 + - - -
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Residues in contact with SER 975 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688C ALA* 5.9 2.7 - - - -
691C SER* 4.2 27.4 - - - +
692C GLU* 5.4 1.3 - - - -
695C MET* 4.1 23.5 - - - +
971D ALA* 2.8 15.0 + - - +
972D ALA* 2.8 19.1 + - - -
974D GLU* 1.3 72.4 - - - +
976D GLU* 1.3 54.6 + - - -
979D MET* 3.2 24.7 + - - +
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Residues in contact with GLU 976 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C SER* 6.1 1.3 - - - -
972D ALA 3.2 6.9 + - - +
973D ASP* 3.0 12.4 + - - +
975D SER* 1.3 73.2 - - - +
977D ARG* 1.3 60.0 + - + +
978D GLY 3.4 0.2 - - - -
979D MET* 3.7 21.0 - - + +
980D LYS* 2.5 61.5 + - - +
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Residues in contact with ARG 977 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973D ASP* 3.2 22.8 + - + +
974D GLU* 3.9 11.4 - - - +
976D GLU* 1.3 76.4 - - + +
978D GLY* 1.3 59.1 + - - +
980D LYS* 2.9 31.8 + - - +
981D VAL* 3.2 13.4 + - - +
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Residues in contact with GLY 978 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C MET* 4.8 11.7 - - - -
974D GLU 3.2 13.7 + - - -
975D SER 4.3 1.6 - - - -
977D ARG* 1.3 78.7 - - - +
979D MET* 1.3 61.1 + - - +
981D VAL* 3.3 13.7 + - - +
982D ILE* 3.2 25.7 + - - +
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Residues in contact with MET 979 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C SER* 4.9 17.3 - - - +
694C GLY* 5.0 11.0 - - - -
695C MET* 4.8 13.0 - - + +
698C ILE* 5.6 1.3 - - + -
975D SER 3.2 21.5 + - - +
976D GLU* 3.8 22.7 - - + +
977D ARG 3.2 0.8 - - - -
978D GLY* 1.3 75.5 - - - +
980D LYS* 1.3 64.4 + - + +
982D ILE* 3.3 11.4 - - + +
983D GLU* 3.2 37.9 + - + +
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Residues in contact with LYS 980 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976D GLU* 2.5 61.3 + - - +
977D ARG* 2.9 18.8 + - - +
979D MET* 1.3 82.4 - - + +
981D VAL* 1.3 56.6 + - - +
983D GLU* 3.8 4.6 - - - +
984D SER* 2.9 34.4 + - - +
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Residues in contact with VAL 981 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977D ARG 3.2 8.3 + - - +
978D GLY* 3.3 21.3 - - - +
980D LYS* 1.3 76.3 - - - +
982D ILE* 1.3 60.8 + - + +
984D SER* 4.2 3.9 - - - +
985D ARG* 3.1 28.4 + - + +
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Residues in contact with ILE 982 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C MET* 4.1 12.3 - - + +
698C ILE* 3.2 53.8 - - + +
699C GLU* 4.0 30.3 - - + +
702C ALA* 5.3 3.6 - - + -
978D GLY 3.2 18.9 + - - +
979D MET* 3.3 17.3 - - - +
981D VAL* 1.3 76.7 - - + +
983D GLU* 1.3 65.5 + - - +
985D ARG* 3.7 18.1 - - - +
986D ALA* 3.2 15.2 + - - +
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Residues in contact with GLU 983 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698C ILE* 4.1 22.4 - - + +
979D MET* 3.2 33.8 + - + +
980D LYS* 3.8 6.5 - - - +
982D ILE* 1.3 79.1 - - + +
984D SER* 1.3 64.6 + - - +
985D ARG 3.1 1.7 + - - -
986D ALA* 3.2 9.9 + - - +
987D GLN* 3.2 20.0 + - - +
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Residues in contact with SER 984 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980D LYS* 2.9 19.6 + - - +
981D VAL* 4.5 3.4 - - - -
983D GLU* 1.3 74.5 - - - +
985D ARG* 1.3 66.8 + - - +
987D GLN* 3.9 16.6 + - - +
988D LYS* 3.2 38.3 + - - +
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Residues in contact with ARG 985 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C ALA* 4.8 8.9 - - - +
706C GLU* 2.7 41.2 + - - +
981D VAL* 3.1 22.1 + - + +
982D ILE* 3.7 19.4 - - - +
983D GLU 3.2 0.2 - - - -
984D SER* 1.3 72.9 - - - +
986D ALA* 1.3 52.7 + - - +
987D GLN 2.6 16.1 + - - -
988D LYS* 2.6 21.3 + - - -
989D ASP* 2.8 22.4 - - - +
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Residues in contact with ALA 986 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698C ILE* 3.6 24.7 - - + +
701C ARG* 4.5 5.4 - - + -
702C ALA* 5.0 3.1 - - + +
705C ASP* 5.1 1.2 - - - +
708C LYS* 3.8 19.0 + - - +
982D ILE 3.2 14.0 + - - +
983D GLU 3.2 3.4 + - - +
985D ARG* 1.3 75.1 - - + +
987D GLN* 1.3 53.9 + - - +
989D ASP* 3.0 15.4 + - - +
990D GLU* 3.2 21.2 + - - +
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Residues in contact with GLN 987 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983D GLU* 3.2 19.9 + - - +
984D SER* 3.9 14.9 + - - +
985D ARG 2.6 5.3 + - - -
986D ALA* 1.3 70.7 - - - +
988D LYS* 1.3 60.9 + - - +
989D ASP 3.0 0.7 - - - -
990D GLU* 2.8 47.6 + - - +
991D GLU* 3.2 6.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 988 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984D SER* 3.2 25.6 + - - +
985D ARG* 2.6 16.7 + - - +
987D GLN* 1.3 75.3 + - + +
989D ASP* 1.3 58.4 + - - +
991D GLU* 3.3 10.8 - - - +
992D LYS* 3.0 34.8 + - + +
----------------------------------------------------------
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Residues in contact with ASP 989 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C ALA* 5.0 0.2 - - - -
705C ASP* 3.4 14.6 - - - +
706C GLU* 3.3 27.8 - - + +
708C LYS* 3.2 23.8 - - - +
709C MET* 5.8 0.7 - - - -
985D ARG* 2.8 30.8 - - - +
986D ALA* 3.0 22.0 + - - +
988D LYS* 1.3 79.3 - - - +
990D GLU* 1.3 64.7 + - - +
992D LYS* 3.4 16.4 - - + +
993D MET 3.2 10.2 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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