Contacts of the helix formed by residues 930 - 946 (chain C) in PDB entry 6DBV
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 GLN 930 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910C GLN* 5.9 1.6 - - - +
926C ASP 3.2 17.1 + - - +
927C GLN* 3.1 8.5 + - - +
929C CYS* 1.3 81.5 + - + +
931C TYR* 1.3 58.2 + - - +
932C SER 3.5 1.6 - - - -
933C TYR* 3.3 35.9 + - + +
934C ASN* 2.8 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 931 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911C MET* 3.2 61.9 + - + +
914C VAL* 3.5 30.7 - - + -
915C TRP* 3.8 16.2 - + - -
927C GLN* 2.6 15.8 + - + +
928C LEU* 3.1 19.5 + - + +
929C CYS 3.5 0.6 - - - -
930C GLN* 1.3 71.4 - - - +
932C SER* 1.3 61.0 + - - +
934C ASN* 3.2 4.6 + - + +
935C SER* 2.7 45.0 + - - -
961C THR* 4.0 15.4 + - - -
962C LEU* 5.9 0.2 - - - -
965C VAL* 4.4 22.2 - - + +
966C PRO* 4.5 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 932 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928C LEU 4.5 1.6 + - - -
929C CYS 5.4 0.6 + - - -
931C TYR* 1.3 79.3 - - - +
933C TYR* 1.3 58.2 + - - +
935C SER* 2.8 19.2 + - - -
936C GLN* 2.9 20.8 + - - +
966C PRO* 4.2 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 933 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930C GLN* 3.3 30.1 + - + +
931C TYR 3.2 0.6 - - - -
932C SER* 1.3 80.5 - - - +
934C ASN* 1.3 60.9 + - + +
936C GLN* 3.2 9.2 + - + +
937C GLN* 2.4 72.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 934 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907C LEU* 3.5 39.8 - - - +
910C GLN* 3.0 34.8 + - - +
911C MET* 4.2 14.0 - - + +
927C GLN* 6.2 1.4 - - - +
930C GLN* 2.8 24.1 + - + +
931C TYR* 3.2 8.5 + - + +
933C TYR* 1.3 79.2 - - + +
935C SER* 1.3 57.9 + - - +
937C GLN* 3.3 11.1 + - - +
938C PHE* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 935 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764C VAL* 4.4 13.1 - - - +
911C MET* 3.8 24.6 - - - +
931C TYR* 2.7 33.5 + - - -
932C SER* 2.8 17.0 + - - -
934C ASN* 1.3 72.3 + - - +
936C GLN* 1.3 59.0 + - - +
938C PHE* 3.2 5.1 + - - +
939C ALA* 2.9 29.5 + - - +
962C LEU* 4.9 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 936 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762C ASN* 5.6 0.2 - - - +
764C VAL* 3.3 33.5 - - - +
932C SER 2.9 20.0 + - - +
933C TYR* 3.2 10.7 + - + +
935C SER* 1.3 73.7 + - - +
937C GLN* 1.3 61.5 + - - +
938C PHE 3.2 0.2 + - - -
939C ALA* 3.2 7.7 + - - +
940C ASP* 2.6 50.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 937 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903C LYS* 3.3 22.4 + - - +
907C LEU* 4.0 24.7 - - + +
933C TYR* 2.4 61.7 + - + +
934C ASN* 3.6 11.1 - - - +
936C GLN* 1.3 76.0 - - - +
938C PHE* 1.3 56.8 + - - +
940C ASP* 3.4 11.1 + - - +
941C LEU 3.0 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 938 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826C PHE* 5.1 5.8 - + - -
904C LEU* 3.5 47.1 - - + +
907C LEU* 4.1 14.8 - - + +
908C TYR* 4.6 21.3 - + + -
911C MET* 4.2 16.2 - - - -
934C ASN 2.9 14.3 + - - +
935C SER* 3.3 14.1 - - - +
936C GLN 3.1 0.2 - - - -
937C GLN* 1.3 76.6 - - - +
939C ALA* 1.3 56.6 + - - +
941C LEU* 3.2 6.6 + - + +
942C LEU* 2.9 48.4 + - + +
958C LEU* 4.4 8.7 - - + -
962C LEU* 3.5 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 939 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763C MET* 4.4 20.9 - - + -
764C VAL* 4.3 19.3 - - + -
935C SER 2.9 16.8 + - - +
936C GLN* 3.8 8.5 - - - +
938C PHE* 1.3 79.9 - - - +
940C ASP* 1.3 59.1 + - - +
942C LEU* 3.6 6.8 - - - +
943C SER* 2.9 33.6 + - - -
962C LEU* 4.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 940 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903C LYS* 5.7 0.4 - - - +
936C GLN* 2.6 50.7 + - - +
937C GLN* 3.5 11.9 + - - +
939C ALA* 1.3 74.2 - - - +
941C LEU* 1.3 65.8 + - - +
943C SER* 3.7 1.6 - - - -
944C SER* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 941 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900C ALA* 3.3 37.2 - - + +
903C LYS* 3.5 39.2 - - + +
904C LEU* 3.6 30.5 - - + +
907C LEU* 5.6 1.8 - - + -
937C GLN 3.0 10.0 + - - +
938C PHE* 3.7 4.3 - - - +
940C ASP* 1.3 76.0 - - - +
942C LEU* 1.3 58.3 + - - +
944C SER* 2.7 17.4 + - - +
945C MET* 2.9 38.9 + - + +
946C PHE* 4.1 5.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 942 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763C MET* 4.5 10.3 - - + -
829C ILE* 5.9 2.0 - - + -
904C LEU* 4.5 12.1 - - + -
938C PHE* 2.9 42.6 + - + +
939C ALA* 3.6 7.0 - - - +
940C ASP 3.1 0.2 - - - -
941C LEU* 1.3 76.8 - - - +
943C SER* 1.3 59.4 + - - +
944C SER 3.0 0.2 + - - -
946C PHE* 2.8 61.2 + - + +
950C TYR* 3.3 41.7 - - + +
958C LEU* 3.9 14.6 - - + -
962C LEU* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 943 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760C SER 4.5 8.8 + - - -
761C GLN 5.0 3.8 + - - -
763C MET* 3.7 23.6 - - - +
939C ALA 2.9 16.9 + - - -
940C ASP* 3.7 1.8 - - - -
942C LEU* 1.3 71.1 - - - +
944C SER* 1.3 56.5 + - - +
947C LYS* 3.1 48.6 + - - +
950C TYR* 5.6 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 944 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940C ASP 2.9 16.9 + - - -
941C LEU* 2.7 26.2 + - - +
943C SER* 1.3 79.9 - - - +
945C MET* 1.3 83.1 + - - +
946C PHE 3.5 0.2 - - - -
947C LYS* 4.4 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 945 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896C GLU* 4.9 16.4 - - + +
897C ARG* 2.4 68.6 + - - +
900C ALA* 4.4 9.4 - - + -
941C LEU* 2.9 26.2 + - + +
944C SER* 1.3 101.5 + - - +
946C PHE* 1.3 76.1 + - + +
947C LYS 3.8 0.4 - - - -
948C TYR* 4.4 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 946 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829C ILE* 3.5 31.9 - - + -
833C GLU* 3.8 26.9 - - - -
838C TYR* 6.5 0.2 - + - -
897C ARG* 4.1 7.6 - - - -
900C ALA* 5.0 11.0 - - + -
901C LEU* 5.0 17.0 - - + -
904C LEU* 5.0 12.1 - - + -
941C LEU* 4.2 9.9 - - + -
942C LEU* 2.8 37.7 + - + +
945C MET* 1.3 97.4 - - + +
947C LYS* 1.3 60.3 + - - +
948C TYR* 3.1 26.2 - + + -
949C ARG* 2.8 28.6 + - + +
950C TYR* 3.3 8.2 + - + -
----------------------------------------------------------
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