Contacts of the helix formed by residues 923 - 945 (chain N) in PDB entry 4G7H
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 GLY 923 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918N ALA 3.5 0.2 + - - -
919N PHE* 3.1 22.9 + - - -
920N LEU 4.6 0.8 + - - -
921N ARG 3.6 1.4 - - - -
922N LEU* 1.3 78.5 - - - +
924N MET* 1.3 60.3 + - - -
925N GLU 3.6 1.3 - - - -
927N THR* 2.5 34.6 + - - -
1213N ARG* 6.1 2.0 - - - -
7O ASP* 3.8 12.3 - - - -
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Residues in contact with MET 924 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766N ALA 4.6 9.6 - - - +
767N HIS* 3.6 37.0 - - + +
769N LEU* 4.0 4.2 - - - +
919N PHE* 3.5 33.7 - - + -
923N GLY* 1.3 69.0 - - - +
925N GLU* 1.3 62.1 + - - +
927N THR* 3.0 3.8 + - - -
928N ALA* 2.8 30.3 + - - +
1211N MET* 4.0 23.6 - - + -
1213N ARG* 4.6 7.0 - - - +
2O ALA* 5.1 0.9 - - + -
6O ILE* 4.3 14.6 - - + -
7O ASP* 3.1 17.8 + - - +
10O PHE* 3.7 37.5 - - + -
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Residues in contact with GLU 925 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924N MET* 1.3 77.8 - - - +
926N LYS* 1.3 59.2 + - + +
928N ALA* 3.3 4.6 + - - +
929N ARG* 3.0 59.8 + - - +
2O ALA* 3.9 25.1 - - + +
3O GLU 3.7 9.7 - - - +
4O PRO* 3.7 13.7 - - - +
5O GLY* 3.1 28.0 + - - -
6O ILE* 4.2 3.0 + - + +
7O ASP* 3.5 12.3 + - - +
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Residues in contact with LYS 926 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889N ALA 4.7 0.3 - - - +
890N VAL* 3.0 38.7 + - + +
891N GLU* 4.4 18.8 + - - +
892N ASP* 4.8 4.2 + - - +
922N LEU* 3.8 47.4 + - + +
923N GLY 3.9 1.2 + - - -
924N MET 3.3 0.6 - - - -
925N GLU* 1.3 79.8 - - + +
927N THR* 1.3 60.6 + - - +
929N ARG* 3.2 27.9 + - - +
930N LEU* 2.9 28.1 + - - +
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Residues in contact with THR 927 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769N LEU* 4.0 17.3 - - + -
890N VAL* 5.9 0.2 - - - -
915N VAL* 3.7 38.4 - - + +
918N ALA* 3.2 26.4 + - + -
919N PHE* 3.2 8.4 - - + +
923N GLY 2.5 24.9 + - - -
924N MET 3.0 4.6 + - - -
926N LYS* 1.3 72.5 - - - +
928N ALA* 1.3 60.6 + - - +
930N LEU* 3.5 7.8 - - + +
931N LEU* 2.9 31.9 + - + +
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Residues in contact with ALA 928 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639N LEU* 4.3 11.8 - - + +
766N ALA* 4.3 26.7 - - + +
769N LEU* 4.3 1.9 - - + +
924N MET 2.8 12.3 + - - +
925N GLU* 3.4 12.1 - - - +
927N THR* 1.3 76.5 - - - +
929N ARG* 1.3 62.0 + - - +
931N LEU* 3.2 13.9 + - - +
932N ASP* 3.0 28.6 + - - +
2O ALA* 4.6 6.7 - - + +
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Residues in contact with ARG 929 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889N ALA* 4.0 19.7 + - - +
891N GLU* 4.6 17.6 + - - -
925N GLU* 3.0 51.7 + - - +
926N LYS* 3.2 31.6 + - - +
928N ALA* 1.3 76.6 - - + +
930N LEU* 1.3 56.2 + - - +
932N ASP* 3.3 8.0 + - - +
933N ALA* 3.0 29.4 + - - +
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Residues in contact with LEU 930 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886N VAL* 4.1 25.4 - - + -
889N ALA* 3.8 23.0 - - + +
890N VAL* 4.0 15.0 - - + -
899N LEU* 5.5 0.2 - - + -
914N LEU* 4.4 19.1 - - + +
915N VAL* 5.0 4.7 - - + -
918N ALA* 3.7 30.5 - - + -
926N LYS 2.9 19.3 + - - +
927N THR* 3.5 9.2 - - + +
929N ARG* 1.3 72.9 - - - +
931N LEU* 1.3 59.1 + - + +
933N ALA* 3.3 1.4 + - + +
934N LEU* 2.9 48.3 + - + +
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Residues in contact with LEU 931 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639N LEU* 4.4 9.9 - - + -
731N LEU* 3.6 25.1 - - + +
769N LEU* 4.0 29.2 - - + -
779N ALA* 3.5 29.2 - - + +
780N LYS* 4.2 0.2 - - - -
781N PRO* 4.0 14.6 - - + -
915N VAL* 3.7 24.9 - - + -
927N THR* 2.9 30.5 + - + +
928N ALA 3.5 4.7 - - - +
930N LEU* 1.3 75.6 - - + +
932N ASP* 1.3 61.5 + - - +
934N LEU* 3.3 5.2 + - + +
935N LYS* 2.9 29.5 + - - +
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Residues in contact with ASP 932 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637N LEU 3.5 0.9 - - - +
638N LYS* 3.6 28.1 + - + +
639N LEU* 3.0 28.8 + - - +
640N HIS* 5.5 0.3 + - - -
729N HIS* 3.0 26.8 + - - -
731N LEU* 5.2 0.4 - - - -
928N ALA* 3.0 15.2 + - - +
929N ARG* 3.7 8.9 - - - +
931N LEU* 1.3 77.4 - - - +
933N ALA* 1.3 57.9 + - - +
935N LYS* 3.2 22.8 + - - +
936N TYR* 2.9 27.5 + - - +
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Residues in contact with ALA 933 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885N ILE* 4.5 11.4 - - + +
889N ALA* 3.7 22.0 - - + -
929N ARG 3.0 16.8 + - - +
930N LEU* 3.6 5.4 - - + +
932N ASP* 1.3 73.9 - - - +
934N LEU* 1.3 66.1 + - - +
936N TYR* 3.2 6.2 + - - +
937N TYR* 2.9 39.2 + - + -
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Residues in contact with LEU 934 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781N PRO* 4.0 28.0 - - + -
785N ILE* 3.3 10.5 - - - +
789N LEU* 3.7 26.6 - - + +
882N PHE* 3.8 22.7 - - + -
885N ILE* 4.6 12.1 - - + -
886N VAL* 4.9 1.1 - - + -
911N LEU* 4.3 8.5 - - + -
914N LEU* 4.3 9.0 - - + -
915N VAL* 4.7 10.5 - - + -
930N LEU* 2.9 44.1 + - + +
931N LEU* 3.6 6.7 - - - +
933N ALA* 1.3 75.1 - - - +
935N LYS* 1.3 57.1 + - - +
937N TYR* 4.8 1.3 - - - +
938N GLY* 2.9 25.3 + - - +
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Residues in contact with LYS 935 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635N PRO 2.7 29.8 + - - +
636N GLN* 4.2 2.6 + - - +
637N LEU 2.7 23.8 + - - -
638N LYS* 5.2 5.4 - - - +
729N HIS* 3.9 20.0 - - + +
730N PRO* 4.4 5.2 - - + -
731N LEU* 4.8 5.6 - - + -
785N ILE* 3.9 23.1 - - + +
931N LEU 2.9 14.1 + - - +
932N ASP* 3.2 28.7 + - - +
934N LEU* 1.3 76.7 - - - +
936N TYR* 1.3 74.5 + - - +
938N GLY* 3.7 0.2 - - - -
939N PHE* 2.9 50.1 + - + +
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Residues in contact with TYR 936 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179L PHE 4.5 8.3 + - - -
180L GLN* 4.0 35.6 - - + +
932N ASP 2.9 14.0 + - - +
933N ALA* 3.5 9.9 - - - +
935N LYS* 1.3 86.5 - - - +
937N TYR* 1.3 92.0 + + - +
939N PHE* 3.7 4.8 - - - +
940N THR* 2.5 50.4 + - + +
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Residues in contact with TYR 937 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176L ARG* 5.5 4.5 + - - -
198L ARG* 4.7 12.0 + - - -
789N LEU* 4.7 2.9 - - + -
881N LEU* 6.0 3.4 - - + -
885N ILE* 3.5 53.4 - - + -
888N GLU* 5.2 4.2 + - - -
933N ALA* 2.9 37.9 + - + +
934N LEU 4.5 0.9 - - - +
936N TYR* 1.3 100.9 - + - +
938N GLY* 1.3 64.0 + - - +
940N THR* 3.3 6.1 + - + -
941N PHE* 2.9 52.2 + + + -
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Residues in contact with GLY 938 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784N ASP 3.7 0.2 - - - +
785N ILE* 3.7 26.7 - - - -
788N GLY* 3.4 6.1 - - - -
789N LEU* 3.9 13.1 - - - +
934N LEU 2.9 19.7 + - - -
935N LYS 3.7 0.4 - - - -
937N TYR* 1.3 77.6 - - - +
939N PHE* 1.3 56.3 + - - +
942N SER* 2.9 30.0 + - - -
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Residues in contact with PHE 939 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680M ASP* 3.9 7.3 - - - +
681M GLY* 3.5 34.8 - - - +
684M PHE* 3.9 13.5 - + - -
635N PRO* 3.9 18.4 - - + -
730N PRO* 3.8 29.2 - - + -
784N ASP* 3.5 30.1 - - + -
785N ILE* 3.6 20.2 - - + +
935N LYS* 2.9 40.9 + - + +
936N TYR* 3.7 5.2 - - - +
938N GLY* 1.3 73.3 - - - +
940N THR* 1.3 64.4 + - - +
942N SER* 2.5 22.4 + - - -
943N THR* 3.0 12.5 + - - +
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Residues in contact with THR 940 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680M ASP* 4.2 10.7 + - - +
936N TYR* 2.5 47.7 + - + +
937N TYR* 3.5 10.5 - - + -
939N PHE* 1.3 77.1 - - - +
941N PHE* 1.3 72.5 + - + +
943N THR* 3.1 20.4 + - - +
944N THR* 3.7 14.4 + - + +
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Residues in contact with PHE 941 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788N GLY* 4.0 11.2 - - - +
789N LEU* 4.9 3.1 - - + -
791N TYR* 4.7 2.2 - - + -
792N ILE* 3.5 49.8 - - + -
860N LEU* 4.9 7.2 - - + -
881N LEU* 3.5 28.3 - - + -
885N ILE* 4.2 4.3 - - + -
937N TYR* 2.9 52.2 + + + +
938N GLY 4.1 1.3 - - - +
940N THR* 1.3 83.9 - - + +
942N SER* 1.3 68.3 + - - +
944N THR* 3.4 10.6 + - - -
945N SER* 2.9 26.0 + - - -
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Residues in contact with SER 942 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678M PRO* 3.5 32.1 - - - +
680M ASP 5.1 1.2 + - - -
681M GLY 5.1 0.7 + - - -
784N ASP* 3.5 25.5 + - - +
787N LEU* 4.8 5.4 - - - -
788N GLY* 3.7 11.4 - - - +
938N GLY 2.9 16.6 + - - -
939N PHE* 2.5 23.8 + - - -
941N PHE* 1.3 77.6 - - - +
943N THR* 1.3 58.7 + - - +
945N SER* 2.5 24.7 + - - -
947N ILE* 4.7 0.2 - - - +
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Residues in contact with THR 943 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677M MET* 3.4 26.0 - - - +
678M PRO* 3.3 25.2 + - - +
679M PHE* 3.7 8.8 - - - -
680M ASP* 3.2 38.1 - - - +
976M ASP* 6.0 0.3 - - - -
978M ARG* 4.5 8.2 + - - +
983M ILE* 3.7 8.3 - - - +
939N PHE 3.1 16.2 - - - +
940N THR 3.1 13.5 - - - +
942N SER* 1.3 80.0 + - - +
944N THR* 1.3 63.5 + - + +
945N SER 3.5 0.2 + - - -
946N GLY* 4.0 2.3 + - - -
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Residues in contact with THR 944 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976M ASP* 5.1 10.8 - - + +
978M ARG* 5.8 1.8 - - - +
982M PRO 5.6 2.2 - - - +
983M ILE* 3.4 14.3 - - + +
984M GLU* 3.0 45.7 + - - +
791N TYR* 5.6 0.7 - - - -
940N THR* 3.7 14.9 + - + +
941N PHE* 3.4 16.9 + - - -
943N THR* 1.3 78.0 - - + +
945N SER* 1.3 66.7 + - - +
946N GLY 3.1 3.9 + - - -
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Residues in contact with SER 945 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984M GLU* 4.2 4.0 - - - +
985M GLY* 4.4 2.1 + - - -
791N TYR* 3.1 62.7 + - - -
941N PHE 2.9 16.1 + - - -
942N SER* 2.5 26.2 + - - -
944N THR* 1.3 77.3 + - - +
946N GLY* 1.3 61.8 + - - +
947N ILE* 3.1 19.8 + - - +
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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
------------------------------------------------------------
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