Contacts of the helix formed by residues 873 - 890 (chain D) in PDB entry 3BBT
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 THR 873 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815D VAL* 3.7 19.7 - - - +
865D GLU* 4.4 3.8 + - - -
871D LYS* 4.1 30.0 + - + -
872D PHE* 1.3 78.6 - - - +
874D HIS* 1.3 63.1 + - - +
875D GLN* 3.1 12.0 + - - +
876D SER* 3.2 23.7 + - - -
877D ASP* 3.1 21.0 + - - +
936D ALA* 5.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 874 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806D MET* 6.2 1.6 - - - +
810D GLU* 3.7 57.7 + - + +
813D ARG* 4.0 13.0 - - - +
814D LEU 3.9 23.3 + - - -
815D VAL* 3.6 25.0 - - + +
873D THR* 1.3 78.6 - - - +
875D GLN* 1.3 64.4 + - - +
877D ASP* 3.4 13.3 + - - +
878D VAL* 3.1 26.9 + - - +
942D PHE* 3.5 5.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 875 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810D GLU* 4.4 7.1 + - - -
873D THR* 3.1 7.7 + - - +
874D HIS* 1.3 88.8 + - + +
876D SER* 1.3 63.2 + - - +
877D ASP 3.2 0.4 - - - -
878D VAL* 3.3 19.2 + - - +
879D TRP 3.3 6.8 + - - -
936D ALA* 3.4 44.4 - - + +
937D ASP* 4.9 7.0 - - - +
939D ARG* 2.9 25.2 + - - +
940D PRO 3.2 21.3 - - - +
941D LYS* 3.7 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 876 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815D VAL* 5.9 0.2 - - - -
863D ALA* 4.0 5.8 + - - +
865D GLU* 3.4 11.3 + - - -
866D CYS* 3.1 35.0 - - - -
871D LYS 3.1 12.5 + - - -
872D PHE* 4.3 3.8 - - - -
873D THR* 3.2 19.5 + - - -
875D GLN* 1.3 77.6 - - - +
877D ASP* 1.3 62.4 + - - +
879D TRP* 3.2 7.1 + - - +
880D SER* 3.2 22.5 + - - -
939D ARG* 3.8 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 877 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806D MET* 3.7 26.5 - - + +
815D VAL* 3.3 11.7 - - - +
816D HIS* 2.9 28.6 + - - +
817D ARG* 3.2 23.3 + - - -
819D LEU* 3.7 10.2 - - + +
873D THR 3.1 10.6 + - - +
874D HIS* 3.4 14.1 + - - +
875D GLN 3.2 0.2 - - - -
876D SER* 1.3 78.4 - - - +
878D VAL* 1.3 52.4 + - - +
880D SER* 3.2 8.5 + - - -
881D TYR* 2.8 34.5 + - - +
942D PHE* 3.6 6.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 878 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874D HIS 3.1 17.0 + - - +
875D GLN* 3.3 22.0 - - - +
876D SER 3.2 0.4 - - - -
877D ASP* 1.3 73.7 - - - +
879D TRP* 1.3 62.6 + - - +
881D TYR* 3.5 4.4 + - - +
882D GLY 3.1 16.5 + - - -
931D CYS* 3.4 33.7 - - + +
939D ARG* 4.1 8.3 - - + -
940D PRO* 3.4 29.8 - - + +
942D PHE* 3.9 26.5 - - + +
945D LEU* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 879 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860D LYS 5.2 1.2 + - - -
861D TRP 3.8 6.6 - - - -
862D MET 3.2 21.2 + - - -
863D ALA* 3.5 15.3 - - + -
864D LEU* 4.2 16.8 - - + -
875D GLN 3.3 5.1 + - - +
876D SER 3.2 12.2 + - - +
878D VAL* 1.3 77.8 - - - +
880D SER* 1.3 63.3 + - - +
882D GLY 3.0 10.4 + - - -
883D VAL* 3.1 27.4 + - + +
896D TYR* 4.7 6.6 + - - -
908D LEU* 3.7 40.6 - - + -
913D ARG* 4.4 6.1 - - - -
931D CYS 3.3 11.2 + - - +
932D TRP* 3.2 58.0 + + + -
933D MET 3.7 3.4 - - - -
934D ILE* 4.9 1.8 - - - -
939D ARG* 3.3 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 880 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817D ARG 5.7 1.4 - - - -
818D ASP* 5.6 1.0 + - - -
819D LEU* 3.2 34.6 + - - +
861D TRP* 2.9 23.7 + - - +
862D MET* 4.8 1.9 - - - -
863D ALA 5.2 0.2 + - - -
876D SER 3.2 10.8 + - - -
877D ASP* 3.4 14.4 + - - -
879D TRP* 1.3 78.9 - - - +
881D TYR* 1.3 49.8 + - - +
883D VAL* 3.1 6.5 + - - +
884D THR* 2.7 39.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 881 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799D CYS* 2.7 42.9 + - - +
802D ILE* 3.6 30.7 - - + -
803D ALA* 3.6 16.7 - - + +
819D LEU* 3.7 10.0 - - + +
877D ASP 2.8 20.1 + - - +
878D VAL 3.6 4.7 - - - +
879D TRP 3.3 0.2 - - - -
880D SER* 1.3 72.2 - - - +
882D GLY* 1.3 60.4 + - - +
884D THR* 3.4 4.8 - - - -
885D ILE* 2.9 56.0 + - + +
931D CYS* 4.4 2.0 - - - -
942D PHE* 3.6 22.7 - + + -
945D LEU* 3.7 30.5 - - + -
949D PHE* 3.6 10.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 882 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878D VAL 3.1 7.3 + - - -
879D TRP 3.0 8.5 + - - -
881D TYR* 1.3 77.3 - - - +
883D VAL* 1.3 59.6 + - - +
885D ILE* 3.3 12.1 - - - +
886D TRP* 3.2 17.3 + - - +
928D MET* 3.8 4.1 - - - +
931D CYS* 3.9 19.5 - - - -
932D TRP* 3.4 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 883 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860D LYS 3.8 19.1 - - - +
861D TRP* 3.6 29.8 - - + +
879D TRP* 3.1 31.7 + - + +
880D SER 3.6 4.7 - - - +
882D GLY* 1.3 72.2 - - - +
884D THR* 1.3 60.3 + - - +
886D TRP* 3.2 5.6 + - + +
887D GLU* 2.9 27.6 + - - +
895D PRO* 4.0 16.6 - - + -
896D TYR* 5.1 1.3 - - - +
914D LEU* 4.1 13.9 - - + -
932D TRP* 3.5 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 884 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802D ILE* 4.4 24.5 - - + -
819D LEU* 3.4 8.6 + - + +
820D ALA* 3.4 23.0 + - - +
821D ALA* 3.5 26.5 - - + +
824D VAL* 4.5 2.7 - - + -
861D TRP* 4.7 0.4 - - - -
880D SER 2.7 27.0 + - - -
881D TYR* 3.4 13.0 - - - -
883D VAL* 1.3 74.0 - - - +
885D ILE* 1.3 59.7 + - + +
887D GLU* 3.0 31.4 + - - +
888D LEU* 3.2 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 885 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799D CYS* 3.7 29.2 - - + -
802D ILE* 5.4 1.6 - - + -
881D TYR* 2.9 48.8 + - + +
882D GLY* 3.3 17.5 - - - +
884D THR* 1.3 76.1 - - + +
886D TRP* 1.3 59.3 - - - +
888D LEU* 3.2 14.1 + - + +
889D MET* 3.0 40.9 + - + +
924D VAL* 5.4 0.7 - - + +
927D VAL* 5.3 1.3 - - + -
928D MET* 3.8 24.9 - - + +
931D CYS* 5.6 0.9 - - - -
949D PHE* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 886 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882D GLY 3.2 14.8 + - - +
883D VAL* 3.3 15.7 - - - +
885D ILE* 1.3 77.7 - - - +
887D GLU* 1.3 65.7 + - + +
889D MET* 4.0 2.5 - - - +
890D THR* 3.0 48.2 + - + +
893D GLY* 3.1 30.3 - - - -
894D LYS 4.0 7.2 - - - -
895D PRO* 3.7 20.6 - - + -
896D TYR 5.0 0.2 - - - -
914D LEU* 3.5 42.9 - - + +
915D PRO* 2.8 35.4 + - + -
917D PRO* 3.9 6.4 - - + +
928D MET* 3.0 37.0 - - + -
932D TRP* 4.0 2.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 887 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780D LEU* 3.5 21.2 - - + +
783D VAL* 5.4 0.4 - - - -
821D ALA* 3.0 33.5 + - + +
861D TRP* 2.9 43.6 + - - +
883D VAL 2.9 15.5 + - - +
884D THR* 3.0 18.2 + - - +
886D TRP* 1.3 78.6 - - + +
888D LEU* 1.3 54.4 + - - +
890D THR* 3.1 11.2 + - - -
892D GLY* 2.7 35.9 + - - -
893D GLY 4.0 14.9 - - - +
895D PRO* 4.3 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 888 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779D LEU* 3.7 28.9 - - + +
783D VAL* 4.4 16.0 - - + +
795D LEU* 3.5 25.5 - - + +
798D TRP* 4.3 26.0 - - + -
799D CYS* 4.7 7.9 - - - -
802D ILE* 4.3 15.9 - - + -
821D ALA* 4.2 15.7 - - + -
884D THR* 3.4 15.7 - - + +
885D ILE* 3.2 21.7 + - + +
887D GLU* 1.3 74.1 - - - +
889D MET* 1.3 61.0 + - + +
891D PHE* 2.8 24.6 + - - -
892D GLY 4.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 889 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795D LEU* 4.3 14.6 - - - +
796D LEU* 4.4 9.4 - - + -
799D CYS* 3.7 29.6 - - - -
885D ILE* 3.0 21.7 + - + +
886D TRP* 4.0 2.2 - - - +
888D LEU* 1.3 75.8 - - - +
890D THR* 1.3 60.7 + - - +
891D PHE* 3.4 9.5 + - - -
917D PRO* 3.8 24.7 - - + +
918D PRO* 5.5 0.7 - - - +
919D ILE* 3.4 27.2 - - + +
920D CYS* 4.5 9.9 - - - -
924D VAL* 3.9 22.7 - - + -
928D MET* 4.8 4.0 - - - -
949D PHE* 4.7 2.0 - - + -
960D LEU* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 890 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787D LYS* 4.7 2.4 + - - -
886D TRP* 3.0 44.5 + - + +
887D GLU 3.1 2.6 + - - -
889D MET* 1.3 75.2 - - - +
891D PHE* 1.3 71.9 + - - +
893D GLY* 3.1 31.4 + - - -
917D PRO* 3.8 25.8 - - + -
918D PRO* 4.6 8.7 - - + -
----------------------------------------------------------
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