Contacts of the helix formed by residues 923 - 946 (chain J) in PDB entry 4XLN
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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918J ALA 3.8 0.2 + - - -
919J PHE 4.0 5.6 - - - -
922J LEU* 1.3 79.4 - - - +
924J MET* 1.3 63.0 + - - -
925J GLU 3.4 1.8 - - - -
926J LYS* 3.0 13.4 + - - +
927J THR* 2.7 29.7 + - - -
7K ASP* 3.8 12.1 - - - -
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Residues in contact with MET 924 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766J ALA 3.8 13.7 - - - +
767J HIS* 3.5 51.8 - - + +
769J LEU* 3.8 3.6 - - + +
919J PHE* 3.8 37.9 - - + -
923J GLY* 1.3 70.5 - - - -
925J GLU* 1.3 58.4 + - - +
927J THR* 3.2 8.0 + - - -
928J ALA* 2.9 27.5 + - + +
1210J SER 5.6 0.2 - - - +
1211J MET* 4.5 9.0 - - + +
6K ILE* 4.4 7.4 - - + -
7K ASP* 2.9 25.1 + - - +
10K PHE* 4.1 24.7 - - + -
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Residues in contact with GLU 925 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638J LYS* 5.1 0.2 + - - -
924J MET* 1.3 74.8 - - - +
926J LYS* 1.3 66.2 + - + +
928J ALA* 3.0 9.5 + - - +
929J ARG* 3.0 42.8 + - - +
2K ALA* 4.8 11.7 - - + -
3K GLU 4.4 1.1 - - - +
4K PRO* 3.7 11.6 - - - +
5K GLY* 2.7 35.3 + - - -
6K ILE* 3.0 25.4 + - + +
7K ASP* 3.4 16.8 + - - +
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Residues in contact with LYS 926 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889J ALA 5.0 3.0 - - - +
890J VAL* 4.0 34.6 + - + +
922J LEU* 4.3 15.7 - - + -
923J GLY* 3.0 22.2 + - - +
925J GLU* 1.3 78.0 - - + +
927J THR* 1.3 57.4 + - - +
929J ARG* 3.5 32.0 + - - +
930J LEU* 2.9 30.0 + - - +
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Residues in contact with THR 927 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769J LEU* 4.2 6.3 - - + -
915J VAL* 3.7 23.8 - - + +
918J ALA* 4.0 11.0 + - + -
919J PHE* 3.4 44.7 + - + +
922J LEU* 4.9 0.6 - - - +
923J GLY 2.7 22.7 + - - -
924J MET* 3.5 6.2 - - - -
926J LYS* 1.3 74.4 - - - +
928J ALA* 1.3 60.6 + - - +
930J LEU* 3.5 8.7 - - + +
931J LEU* 2.9 36.6 + - + +
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Residues in contact with ALA 928 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638J LYS* 3.9 14.4 - - - +
639J LEU* 3.5 28.6 - - + +
766J ALA* 4.9 9.9 - - + +
769J LEU* 4.6 1.8 - - + +
924J MET 2.9 12.6 + - - +
925J GLU* 3.2 13.5 - - - +
927J THR* 1.3 75.1 - - - +
929J ARG* 1.3 65.7 + - - +
931J LEU* 3.0 10.6 + - - +
932J ASP* 3.0 24.4 + - - +
2K ALA* 5.0 2.5 - - + -
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Residues in contact with ARG 929 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638J LYS* 4.0 24.9 - - - +
889J ALA* 4.3 20.9 + - - +
890J VAL 4.8 3.0 + - - -
891J GLY* 5.9 1.0 - - - -
925J GLU* 3.0 30.6 + - - +
926J LYS* 4.0 40.8 - - - +
928J ALA* 1.3 76.2 - - - +
930J LEU* 1.3 57.1 + - - +
932J ASP* 3.4 3.3 + - - +
933J ALA* 2.9 30.2 + - - +
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Residues in contact with LEU 930 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885J ILE* 6.5 0.2 - - + -
886J VAL* 3.8 29.4 - - + +
889J ALA* 4.1 21.7 + - + +
890J VAL* 4.4 13.0 - - + -
914J LEU* 4.6 11.7 - - + +
915J VAL* 5.1 5.4 - - + -
918J ALA* 3.6 31.0 - - + -
926J LYS 2.9 19.0 + - - +
927J THR* 3.5 12.1 - - + +
929J ARG* 1.3 77.6 - - - +
931J LEU* 1.3 58.1 + - + +
933J ALA* 3.2 3.0 + - + +
934J LEU* 2.9 54.7 + - + +
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Residues in contact with LEU 931 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639J LEU* 5.0 5.4 - - + -
731J LEU* 3.9 24.9 - - + +
769J LEU* 4.1 28.7 - - + -
779J ALA* 3.5 28.7 - - + +
780J LYS* 4.2 6.1 - - - -
781J PRO* 4.3 5.4 - - + -
915J VAL* 4.0 35.4 - - + -
927J THR* 2.9 26.1 + - + +
928J ALA* 3.0 9.8 + - - +
930J LEU* 1.3 76.1 - - + +
932J ASP* 1.3 58.4 + - - +
934J LEU* 3.3 11.0 + - + +
935J LYS* 2.9 26.5 + - - +
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Residues in contact with ASP 932 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637J LEU 3.1 5.4 - - - +
638J LYS* 3.2 27.5 - - + +
639J LEU* 2.9 32.2 + - - +
729J HIS* 3.0 16.5 + - - -
731J LEU* 5.1 0.8 - - - +
928J ALA 3.0 11.4 + - - +
929J ARG* 4.0 4.7 - - - +
930J LEU 3.3 0.2 - - - -
931J LEU* 1.3 73.3 - - - +
933J ALA* 1.3 60.6 + - - +
935J LYS* 3.0 37.3 + - - +
936J TYR* 2.9 29.8 + - - +
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Residues in contact with ALA 933 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885J ILE* 4.9 9.6 - - + -
889J ALA* 3.7 23.8 - - + -
929J ARG 2.9 18.6 + - - +
930J LEU* 3.4 4.7 - - + +
932J ASP* 1.3 74.9 - - - +
934J LEU* 1.3 65.6 + - + +
936J TYR* 3.3 4.9 + - - +
937J TYR* 2.9 35.3 + - + +
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Residues in contact with LEU 934 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781J PRO* 4.6 19.7 - - + -
785J ILE* 3.4 8.1 - - - +
789J LEU* 4.0 27.2 - - + +
882J PHE* 4.5 16.2 - - + -
885J ILE* 5.2 8.5 - - + +
886J VAL* 4.5 11.0 - - + -
911J LEU* 5.2 4.7 - - + -
914J LEU* 5.8 4.5 - - + -
915J VAL* 4.7 8.5 - - + -
930J LEU* 2.9 47.9 + - + +
931J LEU* 3.5 18.6 - - + +
933J ALA* 1.3 76.0 - - + +
935J LYS* 1.3 58.0 + - - +
937J TYR* 5.1 1.6 - - - -
938J GLY* 2.9 29.3 + - - +
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Residues in contact with LYS 935 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635J PRO 2.6 27.2 + - - +
636J GLN 4.3 2.0 + - - -
637J LEU 2.9 22.2 + - - -
729J HIS* 3.4 22.4 - - + +
730J PRO* 3.9 14.6 - - + -
731J LEU* 4.7 5.8 - - + -
785J ILE* 3.7 22.6 - - + +
931J LEU 2.9 13.2 + - - +
932J ASP* 3.0 20.7 + - - +
934J LEU* 1.3 76.9 - - - +
936J TYR* 1.3 76.5 + - - +
939J PHE* 2.9 55.9 + - + +
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Residues in contact with TYR 936 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H PHE 4.9 3.6 + - - -
180H GLN* 3.6 40.5 + - + +
680I ASP* 5.5 7.0 - - - -
635J PRO 5.4 6.3 - - - -
932J ASP 2.9 17.0 + - - +
933J ALA* 3.8 4.3 - - - +
935J LYS* 1.3 88.8 - - - +
937J TYR* 1.3 98.7 + + - +
939J PHE* 3.3 4.9 - - + +
940J THR* 2.9 41.7 + - + +
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Residues in contact with TYR 937 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176H ARG* 3.7 24.7 + - - -
178H ALA* 5.2 3.5 - - - +
198H ARG* 4.1 17.8 + - - -
789J LEU* 5.2 1.1 - - + -
881J LEU* 5.1 7.2 - - + -
885J ILE* 3.5 51.8 - - + -
933J ALA* 2.9 23.7 + - + +
934J LEU* 4.6 1.1 - - - +
936J TYR* 1.3 100.5 - + - +
938J GLY* 1.3 58.3 + - - +
940J THR* 3.2 7.6 + - - -
941J LEU* 2.9 42.0 + - + +
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Residues in contact with GLY 938 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785J ILE* 4.3 7.9 - - - -
788J GLY* 3.8 1.6 - - - -
789J LEU* 3.7 27.4 - - - +
934J LEU 2.9 19.6 + - - -
937J TYR* 1.3 76.9 - - - +
939J PHE* 1.3 51.8 + - - +
941J LEU* 3.3 4.4 + - - +
942J SER* 2.7 38.9 + - - -
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Residues in contact with PHE 939 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678I PRO* 5.6 0.2 - - - +
680I ASP* 4.2 7.5 - - - +
681I GLY* 3.5 42.3 + - - +
684I PHE* 4.2 10.1 - + - -
635J PRO* 4.6 8.7 - - + -
730J PRO* 3.9 28.3 - - + -
784J ASP* 3.4 30.7 - - + -
785J ILE* 3.5 22.6 - - + +
935J LYS* 2.9 45.6 + - + +
936J TYR* 3.3 5.6 - - + +
938J GLY* 1.3 73.7 - - - +
940J THR* 1.3 58.8 + - - +
942J SER* 3.1 8.1 + - - -
943J THR* 2.8 30.2 + - - -
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Residues in contact with THR 940 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680I ASP* 4.1 18.2 + - - +
978I ARG* 4.7 10.5 - - - +
936J TYR* 2.9 36.4 + - + +
937J TYR* 3.7 8.2 - - - -
939J PHE* 1.3 77.0 - - - +
941J LEU* 1.3 58.7 + - - +
943J THR* 3.2 6.8 + - - -
944J THR* 2.9 42.4 + - + +
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Residues in contact with LEU 941 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788J GLY* 4.1 7.6 - - - +
789J LEU* 3.8 19.1 - - + -
791J TYR* 4.4 2.9 - - - -
792J ILE* 3.6 53.4 - - + -
860J LEU* 5.4 4.0 - - + -
881J LEU* 4.5 13.9 - - + -
885J ILE* 4.7 9.0 - - + -
937J TYR* 2.9 32.7 + - + +
938J GLY 3.5 4.0 - - - +
940J THR* 1.3 75.2 - - - +
942J SER* 1.3 60.0 + - - +
944J THR* 2.9 11.6 + - + +
945J SER* 2.9 30.5 + - - -
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Residues in contact with SER 942 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678I PRO* 3.9 31.6 - - - +
784J ASP* 2.7 33.7 + - - -
787J LEU* 4.9 4.3 - - - -
788J GLY* 3.0 12.4 + - - -
938J GLY 2.7 20.5 + - - -
939J PHE* 3.3 9.1 - - - -
941J LEU* 1.3 75.6 - - - +
943J THR* 1.3 60.6 + - - +
945J SER* 2.4 23.4 + - - -
946J GLY 3.6 2.8 + - - -
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Residues in contact with THR 943 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677I MET* 4.7 0.3 - - - +
678I PRO 3.3 13.8 + - - +
679I PHE* 3.5 31.4 - - + -
680I ASP* 2.7 25.3 + - - +
978I ARG* 3.6 19.7 - - - +
983I PHE* 3.4 22.2 - - + -
939J PHE 2.8 17.5 + - - -
940J THR* 3.3 11.5 - - - -
942J SER* 1.3 75.5 - - - +
944J THR* 1.3 66.0 + - + +
946J GLY* 3.2 11.6 + - - -
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Residues in contact with THR 944 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978I ARG* 5.7 3.1 - - - +
983I PHE* 4.0 10.0 - - - +
984I GLU* 3.2 42.4 + - - +
791J TYR* 5.2 1.0 - - - -
792J ILE* 5.8 0.3 - - - +
940J THR* 2.9 26.8 + - + +
941J LEU* 2.9 26.1 + - + +
943J THR* 1.3 75.4 - - + +
945J SER* 1.3 64.5 + - - +
946J GLY 3.3 0.3 + - - -
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Residues in contact with SER 945 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984I GLU* 4.1 1.6 - - - +
985I GLY* 3.5 19.2 + - - -
787J LEU* 5.7 0.2 - - - +
791J TYR* 3.5 45.1 + - - -
941J LEU 2.9 13.3 + - - -
942J SER* 2.4 30.4 + - - -
944J THR* 1.3 79.2 + - - +
946J GLY* 1.3 62.6 + - - +
947J ILE* 3.3 22.7 + - - +
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Residues in contact with GLY 946 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677I MET* 4.6 7.0 - - - -
983I PHE* 4.4 5.6 - - - -
985I GLY* 4.0 3.0 - - - +
986I PRO 3.2 22.7 - - - +
987I ILE* 3.7 24.9 - - - +
942J SER 3.6 1.5 + - - -
943J THR 3.2 11.6 + - - -
944J THR 3.2 4.1 - - - -
945J SER* 1.3 80.7 + - - +
947J ILE* 1.3 65.8 + - - +
948J THR 3.3 0.7 + - - -
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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