Contacts of the helix formed by residues 923 - 946 (chain D) in PDB entry 2O5J
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918D ALA 3.5 0.4 + - - -
919D PHE 3.2 15.5 + - - -
920D LEU 4.5 1.4 + - - -
921D ARG 3.7 0.6 - - - -
922D LEU* 1.3 81.2 - - - +
924D MET* 1.3 60.3 + - - +
925D GLU* 3.8 3.4 - - - -
926D LYS* 3.5 6.2 + - - +
927D THR* 2.7 32.4 + - - -
7E ASP* 4.7 4.7 - - - -
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Residues in contact with MET 924 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766D ALA 4.1 1.3 - - - +
767D HIS* 2.8 65.3 - - + +
769D LEU* 3.6 19.9 - - + +
919D PHE* 4.3 19.3 + - + -
923D GLY* 1.3 67.0 - - - +
925D GLU* 1.3 60.8 + - - +
927D THR* 2.8 30.7 + - - -
928D ALA 3.1 3.6 + - - -
1211D MET* 4.2 23.8 - - + -
6E ILE* 4.1 7.9 - - - -
7E ASP* 3.3 24.9 + - - +
10E PHE* 4.1 20.2 - - + -
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Residues in contact with GLU 925 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766D ALA 6.0 0.4 - - - -
923D GLY* 5.0 1.7 - - - -
924D MET* 1.3 81.5 + - - +
926D LYS* 1.3 67.9 + - - +
928D ALA* 3.1 25.9 + - - +
929D ARG* 3.1 33.8 + - - +
2E ALA* 4.0 24.8 + - + +
3E GLU 4.3 5.6 - - - +
5E GLY* 5.1 6.5 - - - +
6E ILE* 3.2 24.9 + - + +
7E ASP* 2.5 36.7 - - - +
8E LYS* 5.8 2.9 - - - +
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Residues in contact with LYS 926 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889D ALA 5.3 0.9 - - - -
890D VAL* 3.6 41.9 - - - +
891D GLU* 4.3 9.3 - - - +
892D ASP* 4.9 12.7 + - - +
922D LEU* 3.8 34.9 - - + +
923D GLY 3.7 7.8 - - - +
924D MET 3.1 0.8 + - - -
925D GLU* 1.3 84.1 - - + +
927D THR* 1.3 60.8 + - - +
929D ARG* 3.2 46.8 - - - +
930D LEU 3.4 4.5 + - - -
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Residues in contact with THR 927 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769D LEU* 4.7 2.2 - - + -
915D VAL* 3.5 40.6 - - + +
918D ALA* 3.2 9.4 + - + -
919D PHE* 3.2 32.2 - - + +
922D LEU* 4.7 4.7 - - - +
923D GLY 2.7 19.3 + - - -
924D MET 2.8 12.0 + - - -
926D LYS* 1.3 76.5 - - - +
928D ALA* 1.3 58.1 + - - +
930D LEU* 3.0 10.0 + - + +
931D LEU* 2.8 30.9 + - + +
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Residues in contact with ALA 928 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D LEU* 3.6 38.7 - - + +
766D ALA* 4.7 9.2 - - + +
769D LEU* 4.8 6.4 - - + +
924D MET 3.1 2.7 + - - +
925D GLU* 3.1 23.1 + - + +
927D THR* 1.3 79.2 - - - +
929D ARG* 1.3 61.1 + - - +
931D LEU* 3.1 19.1 + - + +
932D ASP* 3.2 13.2 + - - +
2E ALA* 5.1 5.4 - - + +
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Residues in contact with ARG 929 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889D ALA* 4.0 19.1 - - + +
925D GLU* 3.1 40.0 + - - +
926D LYS* 3.2 46.0 - - - +
928D ALA* 1.3 77.6 - - + +
930D LEU* 1.3 57.0 + - - +
932D ASP* 3.3 5.5 + - - +
933D ALA* 2.9 28.0 + - - +
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Residues in contact with LEU 930 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886D VAL* 4.0 27.6 - - + +
889D ALA* 3.6 26.9 - - + +
890D VAL* 4.7 6.3 - - + -
899D LEU* 6.2 0.2 - - + -
914D LEU* 4.0 23.8 - - + +
915D VAL* 5.0 9.0 - - + +
918D ALA* 4.1 23.8 - - + -
922D LEU* 5.4 2.5 - - + -
926D LYS 3.4 7.2 + - - +
927D THR* 3.0 12.1 + - + +
929D ARG* 1.3 78.5 - - - +
931D LEU* 1.3 64.3 + - + +
933D ALA* 3.2 3.0 + - + +
934D LEU* 2.9 42.9 + - + +
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Residues in contact with LEU 931 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639D LEU* 3.9 14.6 - - + -
731D LEU* 3.3 19.6 - - + +
769D LEU* 4.0 12.3 - - + -
779D ALA* 3.2 46.0 - - + +
781D PRO* 5.6 3.4 - - + +
915D VAL* 3.4 31.9 - - + -
927D THR* 2.8 20.3 + - + +
928D ALA* 3.1 22.9 + - - +
930D LEU* 1.3 77.6 - - + +
932D ASP* 1.3 62.4 + - - +
934D LEU* 3.4 4.7 + - - +
935D LYS* 2.9 21.8 + - - +
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Residues in contact with ASP 932 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D LEU 3.5 0.2 - - - +
638D LYS* 2.9 35.8 - - + +
639D LEU* 3.2 37.4 + - - +
729D HIS* 3.2 15.7 + - - -
731D LEU* 4.0 0.6 - - - +
928D ALA 3.2 5.4 + - - +
929D ARG* 3.8 7.6 - - - +
931D LEU* 1.3 75.2 - - - +
933D ALA* 1.3 57.9 + - - +
935D LYS* 2.7 38.5 + - - +
936D TYR* 2.7 34.0 + - - +
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Residues in contact with ALA 933 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638D LYS* 4.8 1.8 - - - +
885D ILE* 4.5 11.0 - - + +
889D ALA* 3.7 24.7 - - + -
929D ARG 2.9 13.9 + - - +
930D LEU* 3.3 12.6 - - + +
932D ASP* 1.3 78.6 - - - +
934D LEU* 1.3 61.0 + - - +
936D TYR* 3.3 1.9 + - - +
937D TYR* 2.8 39.2 + - + -
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Residues in contact with LEU 934 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781D PRO* 4.4 11.7 - - + -
785D ILE* 2.8 10.8 - - - +
789D LEU* 3.5 23.0 - - + +
882D PHE* 4.3 22.7 - - + -
885D ILE* 4.3 18.8 - - + -
886D VAL* 4.7 4.0 - - + -
911D LEU* 3.8 31.6 - - + -
914D LEU* 4.9 12.1 - - + -
915D VAL* 5.7 6.3 - - + -
930D LEU* 2.9 33.4 + - + +
931D LEU* 3.9 4.3 - - - +
933D ALA* 1.3 70.6 - - - +
935D LYS* 1.3 57.6 + - - +
937D TYR* 4.7 0.9 - - - +
938D GLY* 2.7 28.6 + - - -
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Residues in contact with LYS 935 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635D PRO 2.9 28.3 + - - +
636D GLN* 4.2 4.0 + - - +
637D LEU 3.9 3.4 + - - -
638D LYS* 3.7 12.9 - - - +
729D HIS* 3.6 14.8 - - + +
730D PRO* 3.8 7.6 - - + -
731D LEU* 4.3 11.0 - - + +
781D PRO* 5.8 0.2 - - - +
785D ILE* 3.5 12.9 - - + +
931D LEU 2.9 15.3 + - - +
932D ASP* 2.7 39.2 + - - +
934D LEU* 1.3 76.8 - - - +
936D TYR* 1.3 84.7 + - - +
939D PHE* 3.0 61.3 + - + -
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Residues in contact with TYR 936 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B PHE 5.0 6.9 + - - -
180B GLN* 5.0 13.0 - - + +
680C ASP* 5.5 7.4 - - - -
636D GLN* 6.2 4.0 - - + -
638D LYS* 5.2 3.8 - - - +
932D ASP 2.7 18.5 + - - +
933D ALA* 3.5 4.3 - - - +
935D LYS* 1.3 90.0 - - - +
937D TYR* 1.3 91.4 + + - +
939D PHE* 3.2 9.4 + - + +
940D THR* 2.8 49.0 + - + +
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Residues in contact with TYR 937 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ARG* 5.5 5.2 + - - -
789D LEU* 4.5 2.7 - - + -
881D LEU* 5.7 2.2 - - + -
884D ARG* 5.5 10.8 + - - -
885D ILE* 3.6 43.1 - - + -
888D GLU* 5.7 5.2 - - + +
933D ALA* 2.8 31.8 + - + +
934D LEU 4.4 1.1 - - - +
936D TYR* 1.3 104.9 - + - +
938D GLY* 1.3 65.7 + - - +
940D THR* 3.9 7.6 - - - -
941D PHE* 2.9 59.2 + + + -
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Residues in contact with GLY 938 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784D ASP 4.1 0.5 - - - +
785D ILE* 3.6 11.0 - - - -
788D GLY* 3.3 8.3 + - - -
789D LEU* 3.2 30.8 - - - +
934D LEU 2.7 19.4 + - - -
937D TYR* 1.3 72.4 - - - +
939D PHE* 1.3 64.8 + - - +
942D SER* 3.2 23.9 + - - -
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Residues in contact with PHE 939 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C ASP* 3.2 29.3 - - + +
681C GLY* 4.3 4.0 - - - -
684C PHE* 3.9 6.3 - + - -
635D PRO* 4.3 22.7 - - + -
730D PRO* 3.5 35.7 - - + -
784D ASP* 3.9 12.6 - - + -
785D ILE* 3.1 39.5 - - + -
935D LYS* 3.0 43.4 + - + -
936D TYR* 3.4 8.1 - + + +
938D GLY* 1.3 76.3 - - - +
940D THR* 1.3 64.9 + - - +
942D SER* 2.5 25.3 + - - -
943D THR* 3.1 9.4 - - - +
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Residues in contact with THR 940 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C ASP* 5.0 9.9 + - - +
978C ARG* 5.8 4.7 - - - +
936D TYR* 2.8 39.0 + - + +
937D TYR* 3.7 8.3 - - - -
939D PHE* 1.3 75.6 - - - +
941D PHE* 1.3 71.7 + - + +
943D THR* 2.7 33.1 + - - +
944D THR* 3.2 11.4 + - + +
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Residues in contact with PHE 941 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788D GLY* 3.7 22.9 - - - +
789D LEU* 4.8 4.0 - - + -
791D TYR* 3.7 10.6 - + + -
792D ILE* 3.7 26.7 - - + -
860D LEU* 5.7 5.8 - - + -
881D LEU* 3.8 30.1 - - + -
885D ILE* 4.0 8.7 - - + -
937D TYR* 2.9 53.8 + + + +
938D GLY 4.5 0.2 - - - -
940D THR* 1.3 84.0 - - + +
942D SER* 1.3 52.8 + - - +
944D THR* 2.8 10.6 + - - -
945D SER* 2.8 37.2 + - - -
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Residues in contact with SER 942 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C PRO* 3.1 26.4 - - - +
679C PHE 3.7 8.3 + - - -
680C ASP 4.2 0.7 + - - -
784D ASP* 4.3 12.4 - - - +
787D LEU* 5.2 2.5 - - - -
788D GLY* 3.9 12.3 - - - -
938D GLY 3.2 16.5 + - - -
939D PHE* 2.5 24.0 + - - -
940D THR 3.0 0.6 + - - -
941D PHE* 1.3 74.3 - - - +
943D THR* 1.3 67.6 + - - +
945D SER* 2.6 22.5 + - - -
946D GLY 3.8 0.2 + - - -
947D ILE* 3.5 4.6 - - - +
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Residues in contact with THR 943 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C MET* 5.7 0.5 - - - +
678C PRO* 3.0 20.4 - - - +
679C PHE* 3.0 40.8 - - + -
680C ASP* 3.2 14.1 + - - +
976C ASP* 5.5 0.7 + - - -
978C ARG* 4.4 12.4 + - - -
983C ILE* 4.2 11.7 - - - +
987C ILE* 5.3 0.9 - - - +
939D PHE 3.1 16.2 - - - +
940D THR* 2.7 11.0 + - - +
942D SER* 1.3 80.6 + - - +
944D THR* 1.3 77.9 + - - +
946D GLY* 3.3 13.7 + - - -
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Residues in contact with THR 944 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976C ASP* 5.2 9.4 - - - +
978C ARG* 5.8 2.0 - - - +
983C ILE* 4.1 11.3 - - - +
984C GLU* 4.0 28.3 + - - +
791D TYR* 4.5 5.7 + - - -
940D THR* 3.9 8.7 - - + +
941D PHE* 2.8 33.1 + - - -
943D THR* 1.3 83.3 + - - +
945D SER* 1.3 61.2 + - - +
946D GLY* 2.9 8.0 + - - -
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Residues in contact with SER 945 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946C ARG* 5.8 0.7 + - - -
984C GLU 3.4 12.2 - - - +
985C GLY* 5.3 0.2 - - - -
787D LEU 5.4 0.7 + - - -
791D TYR* 3.4 49.2 - - - -
941D PHE 2.8 18.8 + - - -
942D SER* 2.6 25.2 + - - -
944D THR* 1.3 72.5 - - - +
946D GLY* 1.3 61.1 + - - +
947D ILE* 3.0 25.2 + - - +
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Residues in contact with GLY 946 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C PRO* 5.0 2.2 - - - -
983C ILE* 3.7 25.8 - - - -
984C GLU 4.2 4.0 - - - +
985C GLY* 4.7 3.6 - - - +
986C PRO 4.3 6.1 - - - +
987C ILE* 4.0 11.5 - - - +
942D SER 3.8 0.8 + - - -
943D THR 3.3 8.2 + - - -
944D THR 2.9 4.2 + - - -
945D SER* 1.3 80.2 + - - +
947D ILE* 1.3 63.2 + - - +
948D THR* 3.5 11.5 + - - +
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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