Contacts of the helix formed by residues 955 - 964 (chain C) in PDB entry 6DBT
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 955 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756C ARG* 5.5 1.6 - - - +
821C GLY* 4.2 27.1 + - - -
822C ASN* 5.9 0.4 - - - +
824C THR* 5.9 1.8 - - + +
825C GLU* 3.6 24.6 + - - -
954C ILE* 1.3 84.8 - - - +
956C ASN* 1.3 70.9 + - + +
957C TYR* 3.9 12.1 - - + +
958C LEU* 3.1 19.8 + - + +
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Residues in contact with ASN 956 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735C ARG* 4.0 15.5 - - - +
743C SER 5.2 1.2 + - - -
748C ILE* 3.1 59.0 + - + +
756C ARG* 5.6 0.2 - - - +
954C ILE 3.7 2.7 + - - -
955C THR* 1.3 74.6 - - + +
957C TYR* 1.3 74.7 + - + +
958C LEU 2.9 1.7 + - - -
959C HIS* 3.0 19.4 + - - +
960C LYS* 3.3 28.5 + - - +
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Residues in contact with TYR 957 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731C GLU* 3.2 21.1 + - + +
813C LEU* 5.6 9.4 - - + -
814C ASP* 5.4 3.4 - - + +
817C HIS* 2.2 42.5 + - + -
818C CYS* 3.2 40.4 - - - +
819C ASP 4.4 0.7 - - - -
820C ILE* 5.3 0.9 - - + -
821C GLY* 4.2 19.5 - - - -
822C ASN* 4.0 13.0 - - - +
955C THR* 3.4 9.8 - - + +
956C ASN* 1.3 86.1 - - + +
958C LEU* 1.3 61.9 + - - +
959C HIS 3.4 0.2 + - - -
960C LYS* 3.4 17.9 + - + +
961C THR* 3.0 26.9 + - - +
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Residues in contact with LEU 958 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763C MET* 4.8 6.3 - - + -
822C ASN* 4.5 12.0 + - + +
825C GLU* 5.2 12.3 - - + -
938C PHE* 5.3 4.9 - - + -
942C LEU* 4.3 22.0 - - + -
950C TYR* 4.8 13.7 - - + -
954C ILE* 3.8 15.5 - - + -
955C THR* 3.1 21.0 + - + +
956C ASN 2.9 0.4 + - - -
957C TYR* 1.3 79.2 - - - +
959C HIS* 1.3 63.9 + - - +
961C THR* 3.1 17.6 - - + +
962C LEU* 2.9 48.6 + - + +
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Residues in contact with HIS 959 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748C ILE* 4.8 13.0 - - + -
749C CYS* 2.9 29.4 - - + +
752C CYS* 4.1 4.3 - - + -
754C SER* 6.1 0.7 - - - -
759C ALA* 4.6 13.8 - - + +
763C MET* 4.8 2.7 + - - +
766C HIS* 3.8 32.0 + + - -
954C ILE* 4.2 15.3 - - + +
955C THR 3.8 1.4 + - - -
956C ASN* 3.0 10.0 + - - +
958C LEU* 1.3 80.1 - - - +
960C LYS* 1.3 68.0 + - + +
962C LEU* 3.8 3.1 - - - +
963C ALA* 2.9 30.6 + - + +
964C HIS* 2.8 7.6 + - - -
1101C ZN 2.1 38.6 - - - -
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Residues in contact with LYS 960 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731C GLU* 5.5 11.9 - - - +
748C ILE 4.0 6.1 + - - -
749C CYS* 4.5 2.0 - - - +
750C THR* 3.0 32.6 + - - +
751C LEU* 5.5 5.6 - - + -
813C LEU* 5.5 25.9 - - + +
956C ASN* 3.3 34.0 + - - +
957C TYR* 3.4 15.9 + - + +
958C LEU 3.4 0.4 - - - -
959C HIS* 1.3 86.4 - - + +
961C THR* 1.3 62.0 + - - +
964C HIS* 3.4 36.9 + - + +
965C VAL* 3.7 9.7 + - - +
968C ILE* 5.5 3.8 - - + +
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Residues in contact with THR 961 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813C LEU* 5.4 7.7 - - - +
818C CYS 5.5 2.0 - - - -
822C ASN* 4.7 11.4 - - - +
911C MET* 6.0 0.3 - - - +
915C TRP* 3.6 32.2 - - + -
931C TYR* 3.0 26.7 + - - -
957C TYR* 3.0 19.1 + - - +
958C LEU* 3.1 37.2 - - + +
960C LYS* 1.3 78.2 - - - +
962C LEU* 1.3 64.4 + - + +
965C VAL* 3.2 15.1 - - - +
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Residues in contact with LEU 962 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763C MET* 3.8 40.6 - - + +
764C VAL* 3.7 30.8 - - + +
911C MET* 4.5 21.1 - - + -
931C TYR* 5.4 1.0 - - - -
935C SER* 4.6 13.6 + - - +
938C PHE* 4.7 10.5 - - + -
939C ALA* 4.5 4.7 - - + -
942C LEU* 4.5 9.0 - - + -
958C LEU* 2.9 37.2 + - + +
959C HIS* 4.0 2.7 - - - +
961C THR* 1.3 95.5 - - + +
963C ALA* 1.3 60.5 + - - +
965C VAL* 5.1 1.6 - - - -
966C PRO* 5.3 3.3 - - - +
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Residues in contact with ALA 963 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763C MET 4.0 3.6 - - - +
764C VAL* 4.7 5.9 - - - +
766C HIS* 3.7 42.3 - - + +
959C HIS* 2.9 26.7 + - + +
962C LEU* 1.3 80.8 - - - +
964C HIS* 1.3 71.1 + - + +
965C VAL 3.5 1.8 + - - -
966C PRO* 3.8 11.6 - - - +
967C GLU* 5.8 0.3 - - - +
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Residues in contact with HIS 964 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749C CYS* 3.2 4.5 - - - -
751C LEU* 3.8 16.6 - - + -
752C CYS* 3.6 14.6 - - + -
766C HIS* 4.4 7.6 + - + -
767C SER 4.8 2.6 - - - -
768C ILE* 3.4 35.6 + - + +
959C HIS* 2.8 13.4 + + - -
960C LYS* 3.4 24.0 + - + +
963C ALA* 1.3 81.9 + - + +
965C VAL* 1.3 59.6 + - - +
966C PRO* 3.3 3.0 - - - -
967C GLU* 3.4 6.0 + - - +
968C ILE* 2.8 40.9 + - + +
1101C ZN 1.9 38.6 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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