Contacts of the helix formed by residues 872 - 880 (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 ASN 872 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820C ILE* 4.7 9.8 - - - +
868C VAL* 5.7 2.2 - - - +
870C ARG* 3.6 20.7 + - + +
871C MET* 1.3 77.1 - - - +
873C GLY* 1.3 62.5 + - - +
874C ASN* 2.4 54.4 + - - +
875C TYR* 3.6 18.6 - - - +
876C ALA* 3.7 16.1 + - - +
17G C 3.8 10.9 + - - +
18G A 3.3 31.1 + - - -
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Residues in contact with GLY 873 (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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820C ILE* 5.3 4.8 - - - +
872C ASN* 1.3 75.7 + - - +
874C ASN* 1.3 63.6 + - - -
876C ALA* 3.0 8.4 + - - +
877C ARG* 2.9 30.1 + - - +
916C ARG* 6.4 0.2 - - - -
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Residues in contact with ASN 874 (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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872C ASN* 2.4 38.7 + - - +
873C GLY* 1.3 69.0 - - - -
875C TYR* 1.3 69.0 + - - +
877C ARG* 3.3 31.6 + - - +
878C ARG* 2.9 36.4 + - + +
18G A 3.0 39.0 + - - +
19G C 4.9 2.9 + - - +
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Residues in contact with TYR 875 (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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827C TYR* 4.2 16.6 - + - -
856C ASP* 5.0 2.4 + - - -
859C LEU* 4.4 16.7 - - + +
865C LEU* 4.7 20.9 - - + +
866C LYS* 3.3 27.6 + - - -
867C PRO* 4.3 6.9 - - - +
868C VAL* 3.5 36.8 - - + +
871C MET* 3.8 24.0 - - + -
872C ASN* 3.1 26.0 + - - +
874C ASN* 1.3 85.1 + - - +
876C ALA* 1.3 63.6 + - - +
878C ARG* 3.4 5.6 + - - +
879C LEU* 2.9 48.9 + - + +
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Residues in contact with ALA 876 (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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819C ASP* 3.3 26.0 - - + +
820C ILE* 5.4 1.8 - - + -
823C ALA* 3.7 25.8 - - + -
871C MET* 5.3 0.6 - - + +
872C ASN 3.7 12.5 + - - +
873C GLY* 3.0 10.4 + - - +
875C TYR* 1.3 81.2 - - - +
877C ARG* 1.3 63.0 + - - +
879C LEU* 2.8 18.0 + - - +
880C MET* 2.9 18.9 + - - +
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Residues in contact with ARG 877 (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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819C ASP* 4.4 1.6 + - - +
873C GLY* 2.9 13.2 + - - +
874C ASN* 3.3 40.9 + - - +
876C ALA* 1.3 77.8 - - - +
878C ARG* 1.3 62.1 + - - +
879C LEU 3.0 4.7 + - - -
880C MET* 3.2 28.0 + - + +
881C THR* 3.6 9.0 - - - +
912C LYS* 5.2 6.1 - - - +
916C ARG* 4.0 26.1 - - - +
19G C 5.9 0.6 + - - -
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Residues in contact with ARG 878 (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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859C LEU* 6.0 0.3 - - - +
863C MET* 3.6 37.1 + - - +
864C LYS* 3.4 11.5 + - - +
865C LEU* 3.2 54.1 - - + +
866C LYS* 5.8 0.8 - - - +
874C ASN* 2.9 21.7 + - + +
875C TYR* 3.6 4.9 - - - +
877C ARG* 1.3 79.0 - - + +
879C LEU* 1.3 58.1 + - - +
881C THR* 3.3 21.2 + - - +
884C ALA* 4.8 2.8 - - - +
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Residues in contact with LEU 879 (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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823C ALA* 4.7 18.4 - - + +
826C PHE* 5.8 6.1 - - + -
827C TYR* 4.5 20.2 - - + +
830C PHE* 5.0 16.6 - - + -
859C LEU* 3.7 28.7 - - + -
865C LEU* 6.0 1.3 - - + -
871C MET* 5.5 0.9 - - + -
875C TYR* 2.9 42.0 + - + +
876C ALA* 2.8 11.9 + - - +
878C ARG* 1.3 78.1 - - - +
880C MET* 1.3 57.9 + - + +
881C THR 2.9 12.6 + - - +
884C ALA* 3.9 17.7 - - + +
885C VAL* 5.1 1.7 - - - +
905C MET* 4.5 4.0 - - - +
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Residues in contact with MET 880 (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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819C ASP* 3.1 40.4 - - - +
823C ALA* 5.6 2.9 - - - -
826C PHE* 4.5 15.9 - - + -
876C ALA* 2.9 15.9 + - + +
877C ARG* 3.2 19.9 + - + +
879C LEU* 1.3 74.9 - - + +
881C THR* 1.3 61.7 + - - +
905C MET* 3.6 22.0 - - + -
908C TYR* 3.4 22.2 - - + -
909C LEU* 3.4 27.0 - - + +
912C LYS* 3.7 24.7 - - + +
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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