Contacts of the helix formed by residues 878 - 898 (chain C) in PDB entry 3U3F
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 ASP 878 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877C ASP* 1.3 76.1 - - - +
879C LEU* 1.3 65.5 + - - +
880C VAL* 3.2 9.7 + - - +
881C TYR* 3.2 35.7 + - + +
882C LEU* 3.1 20.5 + - - +
991C LEU* 4.8 0.7 - - - +
995C ASP* 3.8 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 879 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A ARG* 5.6 12.1 - - - +
877C ASP 4.3 0.4 - - - -
878C ASP* 1.3 70.4 + - - +
880C VAL* 1.3 68.5 + - + +
882C LEU* 3.1 29.6 + - + +
883C ASN* 2.9 42.5 + - - +
923C SER* 4.7 14.1 - - - -
927C LEU* 6.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 880 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878C ASP* 3.2 8.1 + - - +
879C LEU* 1.3 77.1 - - + +
881C TYR* 1.3 59.2 + - - +
883C ASN* 3.3 1.1 + - - -
884C VAL* 2.9 45.2 + - + +
920C LEU* 3.8 4.9 - - + +
923C SER* 3.9 17.0 - - - +
924C VAL* 3.5 36.8 - - + +
927C LEU* 4.1 25.5 - - + +
990C LEU* 4.8 3.6 - - + -
991C LEU* 4.5 13.5 - - + -
994C VAL* 4.5 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 881 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B GLN* 2.9 26.7 + - - -
1000B LEU* 5.7 2.4 - - + +
878C ASP* 3.2 36.3 + - + +
880C VAL* 1.3 78.8 - - - +
882C LEU* 1.3 67.8 + - + +
884C VAL* 3.3 4.2 + - - +
885C MET* 2.9 54.8 + - + +
991C LEU* 3.6 32.1 - - + +
995C ASP* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 882 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A ARG* 6.2 2.2 - - - +
878C ASP 3.1 12.4 + - - +
879C LEU* 3.1 30.0 + - + +
881C TYR* 1.3 84.7 - - + +
883C ASN* 1.3 59.7 + - - +
885C MET* 3.1 8.9 + - + +
886C GLU* 2.8 52.2 + - + +
268E ASP* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 883 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A ARG* 5.3 1.4 - - - +
879C LEU* 2.9 33.4 + - - +
882C LEU* 1.3 74.2 - - - +
884C VAL* 1.3 65.0 + - - +
886C GLU* 3.5 14.3 + - - +
887C LEU* 3.0 22.5 + - - +
916C THR 4.6 3.0 - - - +
919C LYS* 3.0 38.2 - - + +
920C LEU* 3.6 30.7 - - + +
923C SER* 2.9 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 884 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C VAL* 2.9 28.5 + - + +
881C TYR* 3.6 6.5 - - - +
883C ASN* 1.3 73.7 - - - +
885C MET* 1.3 71.1 + - + +
887C LEU* 3.0 4.3 + - - +
888C VAL* 2.8 43.4 + - + +
920C LEU* 3.6 24.7 - - + -
987C ALA* 3.6 33.9 - - + +
988C LYS* 4.4 3.6 - - - +
990C LEU* 4.8 1.6 - - + -
991C LEU* 4.2 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 885 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B GLN* 4.4 11.9 - - - +
999B VAL* 6.4 0.4 - - - -
1000B LEU* 3.9 28.3 - - + -
881C TYR* 2.9 59.6 + - + +
882C LEU* 3.5 13.2 - - + +
884C VAL* 1.3 89.5 - - + +
886C GLU* 1.3 64.4 + - - +
888C VAL* 3.3 13.0 + - + +
889C ARG* 2.9 24.5 + - - +
988C LYS* 6.0 4.0 - - + -
991C LEU* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 886 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A ARG* 5.5 0.9 + - - -
882C LEU* 2.8 42.5 + - + +
883C ASN* 3.5 15.3 + - - +
885C MET* 1.3 72.8 - - - +
887C LEU* 1.3 57.3 + - - +
889C ARG* 3.2 8.8 + - - +
890C ALA* 2.9 27.8 + - - +
916C THR* 4.8 11.6 - - + +
919C LYS* 2.8 44.5 + - - +
268E ASP* 5.1 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 887 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883C ASN 3.0 14.7 + - - +
884C VAL* 3.0 9.6 + - - +
886C GLU* 1.3 73.2 - - - +
888C VAL* 1.3 68.4 + - - +
890C ALA* 3.0 3.9 + - - +
891C VAL* 2.9 38.2 + - + -
913C VAL* 4.6 4.9 - - + +
916C THR* 3.8 18.4 + - - +
917C LEU* 3.4 50.0 - - + -
920C LEU* 3.9 11.9 - - + -
946C LEU* 5.5 0.2 - - + -
983C LEU* 4.3 19.3 - - + +
984C ALA* 4.7 1.3 - - - -
987C ALA* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 888 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999B VAL* 4.0 26.7 - - + -
1000B LEU* 5.8 0.7 - - + -
1003B LEU* 4.1 28.9 - - + -
884C VAL* 2.8 36.4 + - + +
885C MET* 3.3 18.8 + - + +
887C LEU* 1.3 75.0 - - - +
889C ARG* 1.3 63.5 + - - +
891C VAL* 3.2 7.4 + - - +
892C LEU* 3.0 28.3 + - + +
984C ALA* 4.6 14.1 - - + +
987C ALA* 4.8 2.7 - - + -
988C LYS* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 889 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C MET 2.9 13.1 + - - +
886C GLU* 3.3 11.7 - - - +
888C VAL* 1.3 76.4 - - - +
890C ALA* 1.3 51.3 + - - +
892C LEU* 2.8 16.6 + - + +
893C GLU* 2.7 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 890 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886C GLU 2.9 16.2 + - - +
887C LEU 3.0 7.6 + - - +
889C ARG* 1.3 71.9 - - - +
891C VAL* 1.3 61.3 + - - +
893C GLU* 3.4 18.0 + - - +
894C LEU* 3.1 21.3 + - - +
897C GLU* 4.8 0.2 - - - +
909C VAL* 5.3 0.7 - - - +
912C ASN* 4.8 4.0 - - + +
913C VAL* 3.8 21.0 - - + +
916C THR* 3.9 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 891 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887C LEU* 2.9 36.0 + - + +
888C VAL 3.5 7.4 - - - +
890C ALA* 1.3 73.9 - - - +
892C LEU* 1.3 61.7 + - + +
894C LEU* 3.1 8.2 + - - +
895C LYS* 2.9 42.5 + - - +
913C VAL* 4.4 15.5 - - + -
980C SER* 3.3 46.4 - - - +
983C LEU* 4.6 3.1 - - + -
984C ALA* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 892 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999B VAL* 4.0 36.3 - - + -
1002B ASN* 5.2 6.5 - - - +
1003B LEU* 6.4 1.8 - - + -
888C VAL* 3.0 24.1 + - + +
889C ARG* 2.8 14.4 + - - +
891C VAL* 1.3 76.7 - - + +
893C GLU* 1.3 63.1 + - + +
895C LYS* 3.2 34.8 + - + +
896C ASN* 3.0 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 893 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A LYS* 3.0 41.8 + - - +
889C ARG* 2.7 28.3 + - + +
890C ALA* 3.4 17.7 + - - +
892C LEU* 1.3 72.5 - - + +
894C LEU* 1.3 62.0 + - - +
896C ASN* 2.9 17.4 + - - +
897C GLU* 2.8 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 894 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890C ALA 3.1 8.8 + - - +
891C VAL* 3.1 10.0 + - - +
893C GLU* 1.3 76.7 - - - +
895C LYS* 1.3 68.2 + - - +
896C ASN 3.0 0.7 + - - -
897C GLU* 3.1 11.3 + - - -
898C LEU* 3.1 37.0 + - + +
909C VAL* 3.4 26.5 - - + -
910C VAL* 4.2 19.3 - - + -
913C VAL* 3.9 16.2 - - + -
953C LEU* 4.6 9.4 - - + -
976C MET* 4.5 9.6 - - + -
977C LEU* 3.6 22.7 - - + -
980C SER* 4.0 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 895 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002B ASN* 3.8 16.2 - - - +
1003B LEU* 5.5 3.2 - - - +
891C VAL* 2.9 38.0 + - + +
892C LEU* 3.4 29.5 - - + +
894C LEU* 1.3 73.3 - - - +
896C ASN* 1.3 61.2 + - + +
898C LEU* 4.1 7.1 + - - +
899C SER* 4.7 3.8 + - - -
977C LEU* 3.5 38.4 - - + +
980C SER* 4.7 1.8 - - - +
981C HIS* 3.1 42.6 + - - +
984C ALA* 5.9 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 896 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892C LEU 3.0 11.3 + - - +
893C GLU* 2.9 12.0 + - - +
895C LYS* 1.3 79.6 - - + +
897C GLU* 1.3 60.2 + - - +
898C LEU 3.6 0.2 - - - -
899C SER* 2.9 19.1 + - - -
900C GLN* 4.0 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 897 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A GLY* 6.1 0.7 - - - -
908A VAL* 4.4 18.2 + - - +
890C ALA 4.8 0.2 - - - +
893C GLU* 2.8 45.8 + - - +
894C LEU* 3.1 11.7 + - - +
896C ASN* 1.3 78.3 - - - +
898C LEU* 1.3 67.5 + - - +
899C SER 3.1 1.8 - - - -
900C GLN* 3.3 21.7 + - + +
901C LEU* 3.1 32.2 + - + +
909C VAL* 3.8 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 898 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894C LEU* 3.1 30.9 + - + +
895C LYS 4.3 4.7 - - - +
896C ASN 3.6 0.2 - - - -
897C GLU* 1.3 77.6 - - - +
899C SER* 1.3 63.6 + - - +
901C LEU* 3.1 22.4 + - - +
906C TYR* 3.6 39.6 + - + +
909C VAL* 5.5 6.5 - - + -
973C LYS* 4.4 22.4 + - + +
976C MET* 4.1 27.6 - - + -
977C LEU* 3.3 38.8 - - + -
----------------------------------------------------------
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