Contacts of the helix formed by residues 917 - 937 (chain C) in PDB entry 3H2U
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 ASN 917 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912C TRP* 5.3 0.2 - - - +
913C SER 3.8 7.1 + - - +
914C SER* 2.7 22.7 + - - +
915C LYS 2.8 1.8 + - - +
916C GLY* 1.3 78.2 - - - +
918C ASP* 1.3 61.5 + - - +
919C ILE* 3.2 10.2 + - - +
920C ILE* 3.1 36.1 + - + +
921C ALA* 3.3 15.4 + - - +
1056C LEU* 3.6 14.0 - - - +
1057C ARG 3.3 28.1 + - - +
1058C TRP* 3.6 29.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 918 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914C SER 5.2 1.6 - - - +
916C GLY 4.0 1.8 - - - -
917C ASN* 1.3 71.6 + - - +
919C ILE* 1.3 58.2 + - - +
920C ILE 3.2 0.9 - - - -
921C ALA* 3.3 9.0 + - - +
922C ALA* 2.8 32.7 + - - +
925C ARG* 6.1 0.2 - - - -
960C GLU* 3.7 15.7 - - - +
963C ARG* 4.8 4.3 + - - -
964C LEU* 3.1 29.5 - - + +
1056C LEU* 3.6 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 919 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917C ASN* 3.2 8.1 + - - +
918C ASP* 1.3 75.9 - - - +
920C ILE* 1.3 58.9 + - + +
922C ALA* 4.0 4.5 - - - +
923C ALA* 3.1 26.9 + - - +
961C VAL* 3.9 22.9 - - + +
964C LEU* 3.1 46.7 - - + +
965C ALA* 3.5 24.7 - - + +
968C VAL* 5.0 0.2 - - + -
1037C THR* 5.0 3.8 - - + +
1038C VAL* 4.0 25.8 - - + -
1041C ALA* 4.7 12.1 - - + -
1056C LEU* 4.1 17.0 - - + +
1058C TRP* 5.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 920 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909C ALA* 3.5 25.5 - - + +
912C TRP* 3.2 36.6 - - + -
913C SER 3.9 2.9 - - - +
914C SER* 3.5 16.8 - - - +
917C ASN* 3.1 35.0 + - - +
919C ILE* 1.3 77.2 - - + +
921C ALA* 1.3 64.4 + - - +
923C ALA* 4.0 2.3 - - - +
924C LYS* 3.1 50.7 + - - +
1038C VAL* 3.9 14.6 - - + -
1058C TRP* 4.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 921 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914C SER* 3.6 26.0 - - - +
917C ASN 3.3 7.6 + - - +
918C ASP* 3.3 13.7 + - - +
920C ILE* 1.3 77.6 - - - +
922C ALA* 1.3 64.3 + - - +
924C LYS* 3.1 7.4 + - - +
925C ARG* 3.1 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 922 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918C ASP 2.8 21.5 + - - +
919C ILE* 4.0 0.4 - - - +
921C ALA* 1.3 73.0 - - - +
923C ALA* 1.3 56.6 + - - +
925C ARG* 3.1 33.8 + - - +
926C MET* 3.0 30.6 + - - +
957C ALA* 4.2 7.0 - - + +
960C GLU* 4.2 11.2 - - + +
961C VAL* 3.4 26.0 - - + +
964C LEU* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 923 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905C LEU* 4.0 9.4 - - + +
909C ALA* 4.3 11.9 - - + -
919C ILE 3.1 18.0 + - - +
920C ILE* 4.0 4.5 - - - +
921C ALA 3.3 0.2 - - - -
922C ALA* 1.3 75.9 - - - +
924C LYS* 1.3 60.8 + - - +
926C MET* 3.1 11.4 + - - +
927C ALA* 3.0 27.2 + - - +
961C VAL* 4.3 2.0 - - + +
1034C VAL* 4.1 24.7 - - + -
1038C VAL* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 924 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883C GLU* 5.3 11.5 - - - +
906C HIS* 5.2 11.8 - - + +
909C ALA* 3.3 28.0 - - + -
910C ARG* 4.5 5.8 + - + +
912C TRP 2.7 23.6 + - - -
913C SER* 4.2 0.8 - - - +
914C SER* 2.9 28.5 + - - +
920C ILE* 3.1 35.6 + - - +
921C ALA* 3.1 8.1 + - - +
923C ALA* 1.3 72.3 - - - +
925C ARG* 1.3 68.7 + - - +
927C ALA* 3.4 6.9 + - - +
928C LEU* 3.0 36.4 + - + +
1061C LYS* 4.9 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 925 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918C ASP* 6.0 0.6 + - - -
921C ALA* 3.1 19.3 + - - +
922C ALA* 3.1 38.5 - - - +
924C LYS* 1.3 78.6 - - - +
926C MET* 1.3 52.2 + - + +
928C LEU* 3.1 9.2 + - + +
929C LEU* 2.7 42.3 + - + +
957C ALA* 4.1 19.6 - - + +
960C GLU* 3.1 33.5 + - - -
69D ASP* 3.7 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 926 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905C LEU* 4.3 4.5 - - + -
922C ALA 3.0 17.3 + - - +
923C ALA* 3.1 11.2 + - - +
925C ARG* 1.3 73.8 - - - +
927C ALA* 1.3 59.7 + - - +
929C LEU* 3.4 7.6 + - + +
930C MET* 2.8 31.4 + - - +
954C ILE* 4.2 13.1 - - + +
957C ALA* 3.4 18.4 - - + +
958C SER* 3.6 32.1 - - - -
961C VAL* 4.6 7.4 - - - -
1030C LEU* 4.3 14.1 - - + -
1031C MET* 3.6 27.6 - - + +
1034C VAL* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 927 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C PHE* 4.5 2.0 - - + -
902C ALA* 3.7 15.4 - - - +
905C LEU* 4.2 3.1 - - + +
906C HIS* 3.7 42.2 - - + +
923C ALA 3.0 12.6 + - - +
924C LYS* 3.7 8.1 - - - +
926C MET* 1.3 76.4 - - - +
928C LEU* 1.3 59.7 + - - +
930C MET* 3.2 7.3 + - - +
931C ALA* 2.9 29.3 + - - +
1031C MET* 4.5 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 928 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883C GLU* 3.7 31.0 - - - +
885C PHE* 4.0 23.6 - - + -
906C HIS* 4.7 5.8 - - + +
924C LYS* 3.0 26.1 + - + +
925C ARG* 3.4 8.3 - - + +
927C ALA* 1.3 81.6 - - - +
929C LEU* 1.3 57.9 + - - +
931C ALA* 3.7 5.4 - - - +
932C GLU 3.4 12.3 + - - -
935C ARG* 5.2 0.7 + - - -
68D GLY* 3.2 36.1 - - - +
69D ASP* 5.3 0.9 - - - -
91D LYS* 3.8 40.2 - - + +
92D TYR* 4.6 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 929 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925C ARG* 2.7 25.9 + - + +
926C MET* 3.7 3.8 - - - +
928C LEU* 1.3 71.3 - - - +
930C MET* 1.3 57.4 + - - +
931C ALA 3.2 1.8 - - - -
932C GLU* 3.1 14.4 - - - +
933C MET 2.8 22.2 + - - -
950C CYS* 3.3 11.2 - - - -
953C ASP* 3.6 26.7 - - + +
954C ILE* 3.5 30.1 - - + +
957C ALA* 5.2 4.5 - - + -
69D ASP* 3.5 37.5 - - + +
121D ARG* 3.2 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 930 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898C MET* 3.7 34.9 - - - +
902C ALA* 3.9 4.0 - - + +
926C MET 2.8 18.4 + - - +
927C ALA 3.2 4.7 + - - +
929C LEU* 1.3 74.9 - - - +
931C ALA* 1.3 59.3 + - - +
933C MET* 3.4 12.1 + - - -
934C SER* 2.9 26.7 + - - -
954C ILE* 4.0 19.3 - - + +
995C LEU* 4.6 2.9 - - + -
1027C ALA* 3.4 39.0 - - + -
1030C LEU* 4.4 8.5 - - + -
1031C MET* 3.8 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 931 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C PHE* 3.7 16.6 - - + -
899C MET* 3.7 29.4 - - + +
902C ALA* 4.1 2.2 - - + +
927C ALA 2.9 15.5 + - - +
928C LEU* 3.7 9.6 - - + +
930C MET* 1.3 73.3 - - - +
932C GLU* 1.3 67.7 + - - +
934C SER* 3.3 15.9 + - - -
935C ARG* 3.5 27.3 + - - +
92D TYR* 4.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 932 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928C LEU 3.4 10.5 + - - +
929C LEU* 3.1 12.8 + - - +
931C ALA* 1.3 79.0 - - - +
933C MET* 1.3 53.2 + - - +
935C ARG* 2.7 48.0 + - + +
936C LEU* 3.0 35.3 + - + +
950C CYS* 3.4 3.0 - - - -
65D GLY 4.7 0.3 - - - +
66D LEU 3.8 6.3 - - - +
67D PRO* 3.8 1.8 - - - +
68D GLY* 3.1 22.2 + - - +
121D ARG* 2.8 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 933 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898C MET* 3.5 25.1 - - + -
929C LEU 2.8 14.3 + - - +
930C MET* 3.5 23.3 - - - +
931C ALA 3.3 0.2 - - - -
932C GLU* 1.3 75.0 - - - +
934C SER* 1.3 56.9 + - - +
935C ARG 3.0 0.2 + - - -
936C LEU* 4.3 4.7 - - - -
937C VAL* 2.9 37.4 + - + +
947C LEU* 3.6 20.9 - - + -
950C CYS* 4.0 7.7 - - - -
951C ALA* 3.4 38.1 - - + +
954C ILE* 3.6 19.1 - - + -
995C LEU* 3.9 15.7 - - + -
999C SER* 3.5 10.3 - - - +
1023C LEU* 4.5 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 934 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894C ILE* 3.4 10.2 - - - +
895C ASN* 2.9 44.6 + - - +
898C MET* 3.9 14.3 - - - -
899C MET* 3.4 34.8 - - - +
930C MET 2.9 14.8 + - - -
931C ALA 3.4 10.5 - - - -
932C GLU 3.1 0.6 + - - -
933C MET* 1.3 75.7 - - - +
935C ARG* 1.3 57.4 + - - +
937C VAL* 4.0 1.8 - - - +
938C ARG* 4.0 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 935 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893C VAL* 4.3 9.1 - - - +
894C ILE* 4.0 18.8 - - + +
899C MET* 4.2 10.3 - - - +
928C LEU 5.2 0.8 + - - -
931C ALA* 3.5 32.4 + - - +
932C GLU* 2.7 35.3 + - + +
934C SER* 1.3 80.3 - - - +
936C LEU* 1.3 68.1 + - + +
937C VAL 3.2 0.9 - - - -
938C ARG* 3.1 17.9 + - - +
939C GLY 4.0 5.4 - - - +
943C THR* 5.3 0.3 - - - +
66D LEU 5.4 0.4 + - - -
68D GLY* 5.7 1.4 - - - -
91D LYS 4.8 1.6 + - - -
92D TYR* 2.3 33.2 + - - -
93D LYS* 3.9 22.3 + - - +
94D GLY* 4.5 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 936 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932C GLU* 3.0 45.4 + - + +
933C MET* 3.9 3.4 - - - +
935C ARG* 1.3 80.8 - - + +
937C VAL* 1.3 64.3 + - - +
938C ARG 3.0 3.0 + - - -
939C GLY* 3.0 14.0 + - - +
943C THR* 3.7 22.7 - - + +
946C ALA* 4.0 20.0 - - + -
947C LEU* 4.0 27.4 - - + +
950C CYS* 3.9 22.9 - - + -
1006C LEU* 3.6 15.0 - - - +
121D ARG* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 937 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C ASN* 3.8 33.0 - - + +
898C MET* 4.3 10.8 - - + -
933C MET 2.9 17.3 + - - +
934C SER 4.0 2.9 - - - +
935C ARG 3.2 0.2 - - - -
936C LEU* 1.3 77.8 - - - +
938C ARG* 1.3 63.7 + - + +
939C GLY 3.0 5.7 + - - -
947C LEU* 4.6 12.0 - - + +
1002C LYS* 4.1 24.4 + - + -
1006C LEU* 3.9 10.2 - - - +
1020C THR* 5.4 11.0 - - + +
1023C LEU* 3.8 29.8 - - + -
1024C VAL* 6.2 0.7 - - + -
----------------------------------------------------------
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