Contacts of the helix formed by residues 74 - 103 (chain 1) in PDB entry 3KMB
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 ILE 74 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731 ALA* 1.3 72.2 - - - +
751 GLU* 1.3 68.0 + - + +
771 LYS* 3.3 8.3 + - + +
781 LEU* 3.0 30.7 + - + +
742 ILE* 3.6 31.4 - - + -
752 GLU* 3.7 30.7 - - + +
782 LEU* 3.4 25.3 - - + +
743 ILE* 3.6 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731 ALA* 3.3 1.9 - - + +
741 ILE* 1.3 90.6 - - + +
761 VAL* 1.3 66.6 + - + +
781 LEU* 3.3 9.1 + - + +
791 ALA* 3.0 24.1 + - - +
743 ILE* 3.9 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731 ALA* 3.3 25.8 + - + +
751 GLU* 1.3 77.1 - - + +
771 LYS* 1.3 59.8 + - + +
791 ALA* 3.3 7.7 + - - +
801 ASN* 3.0 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731 ALA 3.1 25.3 + - - +
741 ILE* 3.6 5.6 - - + +
761 VAL* 1.3 81.0 - - + +
781 LEU* 1.3 56.9 + - - +
801 ASN* 3.4 7.5 + - - +
811 MET* 2.9 32.6 + - - +
752 GLU* 6.3 1.4 - - - +
782 LEU* 3.6 27.1 - - + -
822 GLU* 4.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 ILE* 3.0 23.5 + - + +
751 GLU* 3.3 8.0 + - + +
771 LYS* 1.3 72.7 - - - +
791 ALA* 1.3 61.3 + - - +
811 MET* 3.1 5.8 + - - +
821 GLU* 2.9 32.6 + - + +
782 LEU* 4.0 10.3 - - + -
743 ILE* 3.9 46.2 - - + +
773 LYS* 4.6 17.7 - - + -
783 LEU* 3.6 38.8 - - + +
813 MET* 3.8 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751 GLU 3.0 17.4 + - - +
761 VAL* 3.7 6.7 - - - +
781 LEU* 1.3 72.1 - - - +
801 ASN* 1.3 65.8 + - - +
821 GLU* 3.4 9.6 + - - +
831 ALA* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761 VAL* 3.0 14.9 + - + +
771 LYS* 3.6 11.6 + - - +
781 LEU 3.2 0.2 - - - -
791 ALA* 1.3 73.6 - - - +
811 MET* 1.3 70.5 + - - +
831 ALA* 3.1 9.9 + - - +
841 GLU* 2.8 52.8 + - - +
822 GLU* 5.2 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771 LYS 2.9 18.3 + - - +
781 LEU 3.1 4.5 + - - +
801 ASN* 1.3 84.8 - - - +
821 GLU* 1.3 57.0 + - - +
841 GLU* 3.5 19.4 - - + +
851 ILE* 2.9 36.1 + - - +
782 LEU* 3.8 13.7 - - + -
812 MET 4.2 0.7 - - - -
822 GLU* 3.4 43.1 - - + +
852 ILE* 3.1 33.4 - - + +
862 ASN* 6.0 1.3 - - - +
813 MET* 3.2 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 LEU 2.9 16.5 + - - +
791 ALA* 3.6 11.9 - - - +
801 ASN 3.2 0.4 - - - -
811 MET* 1.3 76.0 - - - +
831 ALA* 1.3 57.4 + - - +
851 ILE* 3.3 8.0 + - - +
861 ASN* 2.9 48.3 + - - +
773 LYS* 5.0 13.1 - - + +
803 ASN* 4.6 11.3 + - - -
813 MET* 3.2 29.5 - - - +
843 GLU* 5.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791 ALA 3.1 13.8 + - - +
801 ASN* 3.4 15.3 - - - +
821 GLU* 1.3 75.1 - - - +
841 GLU* 1.3 53.8 + - + +
861 ASN* 3.4 6.7 + - - +
871 THR* 2.8 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801 ASN* 2.8 43.6 + - - +
811 MET* 3.5 16.4 - - + +
831 ALA* 1.3 76.6 - - + +
851 ILE* 1.3 56.7 + - - +
871 THR* 3.3 9.3 + - - +
881 LEU* 2.9 30.5 + - - +
852 ILE* 4.0 18.9 - - + +
862 ASN* 5.3 2.7 + - - -
892 LYS* 3.0 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811 MET 2.9 21.7 + - - +
821 GLU* 3.6 9.9 - - - +
841 GLU* 1.3 76.3 - - - +
861 ASN* 1.3 62.9 + - - +
881 LEU* 3.2 9.1 + - + +
891 LYS* 2.9 50.1 + - - +
852 ILE* 3.8 18.6 - - + -
813 MET* 3.6 51.1 - - + +
843 GLU* 4.2 17.0 - - + +
853 ILE* 4.3 7.0 - - + -
883 LEU* 4.2 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821 GLU* 2.9 33.7 + - - +
831 ALA* 3.8 6.7 - - - +
851 ILE* 1.3 84.8 - - - +
871 THR* 1.3 64.1 + - - +
891 LYS* 3.3 18.7 + - - +
901 SER* 3.0 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831 ALA* 2.8 23.7 + - - +
841 GLU* 3.5 11.0 - - - +
861 ASN* 1.3 75.3 - - - +
881 LEU* 1.3 58.2 + - - +
901 SER* 3.3 7.6 + - - -
911 LYS* 3.0 58.3 + - + +
892 LYS* 6.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841 GLU 2.9 11.7 + - - +
851 ILE* 3.4 11.0 - - + +
871 THR* 1.3 78.2 - - - +
891 LYS* 1.3 57.2 + - - +
911 LYS* 3.2 7.3 + - + +
921 LEU* 2.9 32.8 + - + +
852 ILE* 4.4 13.9 - - + +
882 LEU* 4.0 30.3 - - + +
892 LYS* 3.8 37.7 - - + +
922 LEU* 4.0 21.5 - - + -
883 LEU* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851 ILE* 2.9 26.1 + - - +
861 ASN* 3.5 23.7 - - - +
881 LEU* 1.3 75.5 - - - +
901 SER* 1.3 62.7 + - - +
921 LEU* 3.5 3.0 + - - +
931 GLU* 3.1 23.6 + - - +
843 GLU* 2.9 34.3 + - - -
873 THR* 6.4 1.6 - - - -
883 LEU* 3.9 27.8 - - + -
913 LYS* 6.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861 ASN* 3.0 15.0 + - - +
871 THR* 3.6 9.7 - - - -
891 LYS* 1.3 77.8 - - - +
911 LYS* 1.3 58.5 + - - +
931 GLU* 3.3 7.7 + - - +
941 LEU* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41 CA 4.5 17.8 - - - -
871 THR* 3.0 43.0 + - + +
881 LEU* 3.8 5.2 - - + +
901 SER* 1.3 74.3 - - - +
921 LEU* 1.3 60.9 + - - +
941 LEU* 3.2 14.3 + - + +
951 THR* 2.9 31.8 + - - +
892 LYS* 6.2 1.6 - - - +
922 LEU* 3.7 20.2 - - + -
962 ASN* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881 LEU* 2.9 18.3 + - + +
891 LYS* 3.9 5.2 - - - +
911 LYS* 1.3 76.9 - - - +
931 GLU* 1.3 58.4 + - - +
951 THR* 3.1 4.2 + - - -
961 ASN* 2.9 37.2 + - - +
922 LEU* 3.7 29.7 - - + +
883 LEU* 4.0 20.2 - - + +
913 LYS* 3.6 35.2 - - + -
923 LEU* 4.1 16.6 - - + +
953 THR* 3.6 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891 LYS 3.1 17.2 + - - +
901 SER* 3.6 7.4 - - - +
911 LYS 3.2 0.2 - - - -
921 LEU* 1.3 78.4 - - - +
941 LEU* 1.3 56.9 + - + +
961 ASN* 3.2 18.0 + - - +
971 LYS* 2.9 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 SER* 3.0 22.5 + - - +
911 LYS* 3.2 17.7 + - + +
931 GLU* 1.3 73.0 - - + +
951 THR* 1.3 61.1 + - - +
971 LYS* 3.4 13.2 + - + +
981 LEU* 2.9 30.3 + - - +
1302 GLU 3.2 28.0 - - - +
1312 LEU* 4.2 11.8 - - - +
1322 ARG* 3.3 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911 LYS 2.9 15.9 + - - -
921 LEU 3.4 9.6 - - - -
941 LEU* 1.3 77.2 - - - +
961 ASN* 1.3 57.7 + - - +
981 LEU* 3.4 6.7 + - - +
991 HIS* 2.9 27.9 + - - +
922 LEU* 3.7 14.2 - - + +
952 THR* 4.1 11.7 - - + -
962 ASN* 2.7 36.6 + - - +
992 HIS* 5.7 2.5 + - + +
953 THR* 4.4 5.8 - - + -
993 HIS* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921 LEU* 2.9 25.7 + - - +
931 GLU* 3.2 24.7 + - - +
951 THR* 1.3 77.3 - - - +
971 LYS* 1.3 57.5 + - - +
991 HIS* 3.4 6.1 + - - +
1001 ALA* 3.0 30.0 + - - +
953 THR* 3.1 40.3 + - - +
983 LEU* 5.8 4.8 - - - +
993 HIS* 4.5 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931 GLU* 2.9 47.7 + - - +
941 LEU* 3.6 13.7 - - + +
961 ASN* 1.3 74.3 - - - +
981 LEU* 1.3 65.2 + - - +
1001 ALA* 3.5 6.0 + - - +
1011 PHE* 3.1 24.8 + - - +
1302 GLU* 3.7 44.4 - - + +
1312 LEU* 3.8 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941 LEU 2.9 17.6 + - - +
951 THR* 3.8 7.0 - - - +
971 LYS* 1.3 75.4 - - - +
991 HIS* 1.3 64.4 + - - +
1011 PHE* 3.3 3.9 + - + +
1021 SER* 2.9 22.0 + - - -
962 ASN* 6.0 3.8 - - - +
992 HIS* 3.9 22.9 - - + +
1112 PHE* 4.5 9.9 - - + -
1132 VAL* 4.2 13.5 - - + -
1312 LEU* 3.9 19.4 - - + +
2192 PHE* 3.7 45.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 99 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951 THR 2.9 14.4 + - - +
961 ASN* 3.7 5.5 + - - +
971 LYS 3.3 0.2 - - - -
981 LEU* 1.3 76.3 - - - +
1001 ALA* 1.3 65.5 + - - +
1021 SER* 2.8 20.7 + - - -
1031 MET* 2.9 30.7 + - + +
1111 PHE* 5.1 5.0 - + - -
1131 VAL* 5.4 0.2 - - + -
992 HIS* 3.7 25.7 - + + +
983 LEU* 3.7 29.1 - - + +
993 HIS* 3.2 42.7 + + + +
1023 SER* 2.9 38.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961 ASN 3.0 17.2 + - - +
971 LYS* 3.7 6.5 - - - +
991 HIS* 1.3 76.1 + - - +
1011 PHE* 1.3 58.9 + - - +
1031 MET* 2.9 18.4 + - - +
1041 GLY 3.3 0.3 + - - -
1051 LYS* 3.0 45.9 + - + +
1111 PHE* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971 LYS 3.1 18.2 + - - +
981 LEU* 3.5 8.1 - - + +
1001 ALA* 1.3 76.3 - - - +
1021 SER* 1.3 58.6 + - - +
1041 GLY 3.0 15.4 + - - -
1051 LYS* 4.2 9.2 - - - +
1132 VAL* 3.5 34.3 - - + -
1142 THR* 3.7 12.1 - - - -
1152 ASN* 3.1 63.8 - - + +
1272 LEU* 3.7 27.1 - - + -
1312 LEU* 3.7 27.4 - - + -
2152 ALA* 3.9 8.1 - - + -
2172 CYS* 3.9 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981 LEU* 2.9 12.5 + - - -
991 HIS 2.8 11.4 + - - -
1011 PHE* 1.3 76.4 - - - +
1031 MET* 1.3 67.2 + - - +
1041 GLY 3.2 2.0 + - - -
992 HIS* 2.6 34.0 + - - -
1032 MET* 3.7 21.5 - - - +
1132 VAL* 3.6 30.1 - - - -
1142 THR 4.3 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 103 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991 HIS* 2.9 36.9 + - + +
1001 ALA 2.9 13.2 + - - +
1021 SER* 1.3 88.9 - - - +
1041 GLY* 1.3 58.7 + - - +
1051 LYS 3.5 0.4 + - - -
1111 PHE* 4.1 15.3 - - + +
1121 PHE 4.3 11.1 - - - +
1131 VAL* 4.4 15.5 - - + -
1501 VAL* 6.0 0.7 - - - +
992 HIS* 5.2 1.3 - - + +
1032 MET* 4.0 21.3 - - - -
1023 SER* 3.7 31.9 - - - +
----------------------------------------------------------
Back to top of page
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