Contacts of the helix formed by residues 864 - 889 (chain D) in PDB entry 6X34
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 PRO 864 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863D LEU* 1.3 79.0 - - - +
865D PRO* 1.3 65.2 - - - +
866D HIS* 3.2 9.9 - - + +
867D LEU* 3.2 22.2 + - + +
868D GLU* 3.7 5.0 + - - +
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Residues in contact with PRO 865 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864D PRO* 1.3 71.9 - - - +
866D HIS* 1.3 60.5 + - - +
868D GLU* 3.3 8.4 + - + +
869D ARG* 2.9 28.0 + - - +
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Residues in contact with HIS 866 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864D PRO* 3.2 7.4 - - + +
865D PRO* 1.3 78.5 - - - +
867D LEU* 1.3 57.6 + - - +
869D ARG* 3.7 8.2 - - - +
870D ILE* 2.9 31.4 + - - +
1051D TYR* 4.4 21.9 + - + +
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Residues in contact with LEU 867 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863D LEU* 4.8 6.5 - - - -
864D PRO* 3.2 23.8 + - + +
865D PRO 3.2 0.6 - - - -
866D HIS* 1.3 80.0 - - - +
868D GLU* 1.3 57.2 + - - +
870D ILE* 3.3 4.9 + - - +
871D ARG* 2.9 29.0 + - - +
929D LEU* 5.2 9.7 - - + +
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Residues in contact with GLU 868 (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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864D PRO 3.7 3.9 + - - +
865D PRO* 3.3 10.8 + - + +
867D LEU* 1.3 76.6 - - - +
869D ARG* 1.3 60.5 + - - +
871D ARG* 3.7 7.0 - - - +
872D GLU* 2.9 30.8 + - - +
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Residues in contact with ARG 869 (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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865D PRO 2.9 18.1 + - - +
866D HIS* 3.7 9.9 - - - +
868D GLU* 1.3 78.2 - - - +
870D ILE* 1.3 60.8 + - - +
872D GLU* 3.8 6.2 + - - +
873D LYS* 3.7 16.8 + - - +
1050D GLY* 5.4 6.2 - - - -
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Residues in contact with ILE 870 (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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866D HIS 2.9 17.8 + - - +
867D LEU* 3.9 4.7 - - - +
869D ARG* 1.3 74.6 - - - +
871D ARG* 1.3 61.6 + - - +
873D LYS* 3.4 6.8 + - - +
874D LEU* 2.9 28.3 + - - +
1046D LEU* 4.3 22.9 - - + +
1050D GLY* 4.9 5.6 - - - -
1051D TYR* 4.4 20.4 - - + +
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Residues in contact with ARG 871 (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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867D LEU 2.9 18.8 + - - +
868D GLU* 3.2 8.5 + - - +
870D ILE* 1.3 74.5 - - - +
872D GLU* 1.3 59.9 + - - +
874D LEU* 4.0 7.4 - - - -
875D ALA* 2.9 26.0 + - - +
922D LEU* 6.3 2.0 - - + -
925D SER* 3.2 31.2 - - - +
926D GLY* 5.1 1.6 - - - +
929D LEU* 4.9 8.9 - - + +
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Residues in contact with GLU 872 (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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868D GLU 2.9 16.9 + - - +
869D ARG* 3.9 7.6 - - - +
870D ILE 3.3 0.2 - - - -
871D ARG* 1.3 75.5 - - - +
873D LYS* 1.3 58.0 + - - +
875D ALA* 3.3 7.1 + - - +
876D GLU* 2.9 27.9 + - - +
910D PHE* 4.6 9.5 - - + -
922D LEU* 6.1 3.8 - - - -
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Residues in contact with LYS 873 (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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869D ARG 3.7 9.2 + - - +
870D ILE* 3.4 8.6 + - - +
871D ARG 3.4 0.4 - - - -
872D GLU* 1.3 78.7 - - - +
874D LEU* 1.3 57.8 + - - +
876D GLU* 3.6 7.2 - - - +
877D ASN* 2.9 30.3 + - - +
971D ASP* 4.8 5.7 - - + +
1046D LEU* 5.5 1.6 - - - -
1049D TYR* 3.7 30.3 - - + -
1050D GLY 5.2 0.4 - - - +
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Residues in contact with LEU 874 (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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870D ILE 2.9 18.0 + - - +
871D ARG* 3.6 9.9 - - - +
872D GLU 3.2 0.4 - - - -
873D LYS* 1.3 76.4 - - - +
875D ALA* 1.3 57.9 + - - +
877D ASN* 3.3 6.7 + - - +
878D ILE* 2.9 29.7 + - - +
925D SER* 4.3 13.2 - - - +
928D THR* 4.9 9.9 - - + -
1042D ALA* 5.4 3.5 - - + +
1046D LEU* 3.7 26.2 - - + +
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Residues in contact with ALA 875 (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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871D ARG 2.9 16.7 + - - +
872D GLU* 3.7 5.6 - - - +
874D LEU* 1.3 73.2 - - - +
876D GLU* 1.3 61.6 + - - +
878D ILE* 3.3 6.5 + - - +
879D HIS* 2.9 30.3 + - - +
910D PHE* 4.4 10.0 - - + -
921D ASN* 3.5 38.6 - - + +
922D LEU* 4.6 8.7 - - + +
925D SER* 3.7 7.3 - - - +
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Residues in contact with GLU 876 (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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872D GLU 2.9 17.4 + - - +
873D LYS* 3.6 8.7 - - - +
875D ALA* 1.3 76.6 - - - +
877D ASN* 1.3 56.5 + - - +
879D HIS* 3.3 3.3 + - - +
880D GLU* 2.9 28.3 + - - +
910D PHE* 3.7 22.5 - - + -
969D PRO 5.8 0.7 - - - -
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Residues in contact with ASN 877 (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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873D LYS 2.9 17.4 + - - +
874D LEU* 3.8 6.1 - - - +
876D GLU* 1.3 75.8 - - - +
878D ILE* 1.3 56.8 + - - +
880D GLU* 3.3 3.5 + - - +
881D LEU* 2.9 31.0 + - - +
969D PRO* 3.8 28.8 - - + +
971D ASP* 4.2 14.4 - - + -
1042D ALA* 5.7 5.8 - - + +
1045D THR* 4.2 12.1 - - - -
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Residues in contact with ILE 878 (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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874D LEU 2.9 18.0 + - - +
875D ALA* 3.3 8.5 + - - +
877D ASN* 1.3 77.4 - - - +
879D HIS* 1.3 57.5 + - - +
881D LEU* 3.3 6.9 + - - +
882D TRP* 2.9 29.1 + - - +
920D TYR* 6.3 3.8 - - + -
921D ASN* 5.7 3.6 - - + +
924D MET* 4.9 16.8 - - + -
925D SER 6.0 0.2 - - - +
1042D ALA* 6.0 7.8 - - + +
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Residues in contact with HIS 879 (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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875D ALA 2.9 17.1 + - - +
876D GLU 3.7 4.5 - - - +
878D ILE* 1.3 76.3 - - - +
880D GLU* 1.3 58.2 + - - +
882D TRP* 3.3 13.5 + - + +
883D ALA* 2.9 28.4 + - - +
907D LEU 4.6 3.1 - - - +
908D VAL 5.0 2.2 - - - +
909D ASP* 4.2 27.8 - - + -
910D PHE* 4.3 15.0 - - + +
921D ASN* 5.2 5.3 - - + +
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Residues in contact with GLU 880 (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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876D GLU 2.9 17.1 + - - +
877D ASN 3.7 0.9 - - - +
878D ILE 3.3 0.2 - - - -
879D HIS* 1.3 77.7 - - - +
881D LEU* 1.3 55.8 + - - +
883D ALA* 3.3 2.9 + - - +
884D LEU 2.9 22.9 + - - -
909D ASP* 6.0 0.4 - - - +
966D LYS* 3.9 22.9 - - + +
967D PRO 3.3 11.2 - - - +
968D ALA 3.3 32.3 - - - +
969D PRO* 3.6 10.1 - - + +
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Residues in contact with LEU 881 (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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877D ASN 2.9 17.5 + - - +
878D ILE* 3.8 7.0 - - - +
880D GLU* 1.3 73.3 - - - +
882D TRP* 1.3 61.4 + - - +
884D LEU* 3.5 11.1 - - - +
885D THR* 2.9 31.9 + - - +
969D PRO* 5.0 5.3 - - + -
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Residues in contact with TRP 882 (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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878D ILE 2.9 17.6 + - - +
879D HIS* 3.3 11.6 + - + +
881D LEU* 1.3 77.0 - - - +
883D ALA* 1.3 57.9 + - - +
885D THR* 3.1 15.7 - - + +
886D ARG* 2.9 33.7 + - + +
906D CYS* 3.8 27.6 - - + -
907D LEU* 4.8 15.2 - - + +
908D VAL 5.6 2.2 - - - -
917D GLU* 5.0 10.8 - - + -
920D TYR* 4.2 36.6 - + + -
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Residues in contact with ALA 883 (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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879D HIS 2.9 17.3 + - - +
880D GLU* 3.6 4.3 - - - +
882D TRP* 1.3 75.0 - - - +
884D LEU* 1.3 58.0 + - - +
886D ARG* 3.3 6.7 + - - +
887D ILE* 2.9 31.7 + - - +
907D LEU* 3.8 20.7 + - - +
908D VAL 5.9 0.4 - - - -
963D ASN* 5.2 9.0 - - + -
965D TYR* 4.9 11.2 - - + -
966D LYS 3.9 15.7 - - - +
967D PRO* 4.8 1.6 - - + -
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Residues in contact with LEU 884 (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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880D GLU 2.9 12.0 + - - +
881D LEU* 3.5 10.8 - - + +
882D TRP 3.2 0.2 - - - -
883D ALA* 1.3 77.2 - - - +
885D THR* 1.3 62.9 + - - +
887D ILE* 3.3 5.9 + - - +
888D GLU* 2.9 35.6 + - + +
967D PRO* 3.2 24.7 + - - +
968D ALA* 4.0 19.1 - - + -
969D PRO 5.3 0.7 - - - -
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Residues in contact with THR 885 (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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881D LEU 2.9 17.5 + - - +
882D TRP* 3.1 30.7 - - + +
884D LEU* 1.3 80.6 - - - +
886D ARG* 1.3 57.2 + - - +
888D GLU* 3.9 7.2 - - - +
889D GLN* 2.9 32.4 + - - +
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Residues in contact with ARG 886 (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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882D TRP* 2.9 24.4 + - + +
883D ALA* 3.7 7.2 - - - +
885D THR* 1.3 80.1 - - - +
887D ILE* 1.3 59.0 + - - +
889D GLN* 3.7 3.6 + - - +
890D GLY 3.5 1.9 + - - -
891D TRP* 3.0 48.1 + - + +
892D THR* 4.7 2.2 - - - -
893D TYR 5.4 0.2 - - - +
904D HIS* 5.0 2.7 - - + -
907D LEU* 4.4 17.0 - - + -
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Residues in contact with ILE 887 (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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883D ALA 2.9 17.0 + - - +
884D LEU* 3.8 5.4 - - - +
886D ARG* 1.3 76.5 - - - +
888D GLU* 1.3 63.0 + - - +
890D GLY* 3.4 11.1 + - - -
892D THR* 4.4 20.8 - - + +
958D THR* 5.4 12.8 - - - -
961D MET* 5.7 6.5 - - + -
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Residues in contact with GLU 888 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884D LEU* 2.9 23.1 + - + +
885D THR* 3.9 8.1 - - - +
887D ILE* 1.3 74.8 - - - +
889D GLN* 1.3 57.9 + - - +
890D GLY 3.1 8.1 + - - -
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Residues in contact with GLN 889 (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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885D THR* 2.9 20.4 + - - +
886D ARG* 4.2 5.4 - - - +
887D ILE 3.4 0.4 - - - -
888D GLU* 1.3 75.0 - - - +
890D GLY* 1.3 56.5 + - - +
891D TRP* 3.2 13.6 + - + +
902D ARG* 5.7 0.2 - - - +
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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) + - + + + + + -
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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