Contacts of the helix formed by residues 964 - 973 (chain C) in PDB entry 6DBU
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 HIS 964 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749C CYS* 4.0 5.4 - - - -
751C LEU* 4.2 8.7 - - + +
752C CYS* 3.7 14.6 - - + -
766C HIS* 4.2 14.5 + - + -
767C SER 4.3 5.1 - - - -
768C ILE* 3.7 26.9 + - + +
959C HIS* 2.9 8.3 + + - -
960C LYS* 3.6 22.9 + - - +
963C ALA* 1.3 81.8 - - + +
965C VAL* 1.3 54.6 + - - +
966C PRO* 3.4 3.4 - - - -
967C GLU* 2.9 11.2 + - - +
968C ILE* 2.7 51.8 + - + +
1101C ZN 2.0 38.1 - - - -
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Residues in contact with VAL 965 (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* 4.5 15.3 - - + -
914C VAL* 5.4 2.2 - - + -
915C TRP* 4.5 10.1 - - + -
931C TYR* 3.4 32.3 - - + +
960C LYS 3.3 12.9 + - - +
961C THR* 3.2 30.3 - - - +
963C ALA 3.7 0.6 - - - +
964C HIS* 1.3 74.9 - - - +
966C PRO* 1.3 71.8 - - + +
968C ILE* 3.1 9.0 + - + +
969C VAL* 2.9 30.3 + - + +
975C ILE* 4.1 14.8 - - + -
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Residues in contact with PRO 966 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928C LEU* 4.9 14.0 - - + +
931C TYR* 3.5 31.0 - - + -
932C SER* 4.2 21.8 - - - +
935C SER* 5.5 1.1 - - - +
962C LEU 5.2 2.7 - - - +
963C ALA 4.4 10.1 - - - +
964C HIS 3.6 2.2 - - - +
965C VAL* 1.3 94.7 - - + +
967C GLU* 1.3 63.6 + - + +
969C VAL* 3.4 6.1 + - + +
970C GLU* 3.0 26.0 + - - +
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Residues in contact with GLU 967 (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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768C ILE* 3.6 39.7 - - + +
963C ALA 5.4 0.9 - - - +
964C HIS* 2.9 13.8 + - - +
966C PRO* 1.3 83.4 - - + +
968C ILE* 1.3 57.1 + - - +
970C GLU* 3.4 5.1 + - - +
971C ARG* 2.9 41.4 + - - +
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Residues in contact with ILE 968 (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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751C LEU* 4.3 14.4 - - + -
768C ILE* 4.4 11.4 - - + -
812C THR* 4.2 17.9 - - - +
813C LEU* 4.5 24.2 - - + +
960C LYS* 4.9 5.2 - - + +
964C HIS* 2.7 42.5 + - + +
965C VAL* 3.6 10.5 - - + +
967C GLU* 1.3 71.2 - - - +
969C VAL* 1.3 65.0 + - - +
971C ARG* 2.9 30.7 + - - +
972C ASP* 2.9 17.5 + - + +
974C SER 5.0 3.4 - - - +
975C ILE* 4.5 17.7 - - + -
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Residues in contact with VAL 969 (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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914C VAL* 4.3 12.6 - - + +
920C PRO* 3.7 26.0 - - + -
921C SER* 5.6 2.0 - - - +
928C LEU* 3.9 28.0 - - + -
965C VAL* 2.9 26.6 + - + +
966C PRO* 3.8 4.7 - - + +
968C ILE* 1.3 74.8 - - - +
970C GLU* 1.3 57.5 + - - +
973C GLY* 2.7 33.4 + - - -
974C SER 4.4 8.7 - - - +
975C ILE* 3.5 28.7 - - + -
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Residues in contact with GLU 970 (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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928C LEU* 5.5 2.6 - - + +
966C PRO 3.0 17.2 + - - +
967C GLU* 3.8 5.8 - - - +
969C VAL* 1.3 78.9 - - - +
971C ARG* 1.3 65.4 + - - +
972C ASP 3.4 0.5 + - - -
973C GLY* 4.3 2.3 + - - -
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Residues in contact with ARG 971 (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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725C ARG* 4.7 9.4 + - - +
751C LEU* 5.2 0.2 - - - -
768C ILE* 3.6 33.5 - - - +
770C ARG 5.8 0.2 + - - -
810C GLN* 2.9 47.3 - - - +
811C PRO* 3.9 34.1 + - - +
812C THR* 4.2 6.5 - - - -
967C GLU* 2.9 30.2 + - - +
968C ILE* 2.9 15.4 + - - +
970C GLU* 1.3 82.2 + - - +
972C ASP* 1.3 59.8 + - - +
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Residues in contact with ASP 972 (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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725C ARG* 4.5 11.6 + - - +
810C GLN* 4.5 17.4 + - - +
968C ILE* 2.9 13.9 + - + +
970C GLU 4.6 0.7 - - - -
971C ARG* 1.3 80.9 - - - +
973C GLY* 1.3 56.5 + - - +
974C SER 2.7 28.5 + - - +
978C TRP* 2.7 52.9 + - - -
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Residues in contact with GLY 973 (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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919C CYS* 4.0 7.0 - - - -
920C PRO* 3.6 9.5 - - - +
921C SER* 3.1 25.2 + - - -
969C VAL* 2.7 25.0 + - - -
970C GLU 4.3 2.1 + - - -
971C ARG 3.9 0.2 - - - -
972C ASP* 1.3 72.8 - - - +
974C SER* 1.3 62.6 + - - +
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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