Contacts of the helix formed by residues 777 - 781 (chain B) in PDB entry 6CNC
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 SER 777 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774B ASN* 2.2 40.6 + - - -
775B LYS 2.7 2.2 + - - -
776B SER* 1.3 75.5 - - - +
778B ILE* 1.3 59.8 + - - +
779B ASP 3.0 1.4 - - - +
780B ARG* 2.6 32.2 + - - +
781B GLY 3.5 0.5 + - - -
782B PHE* 3.8 9.1 + - - +
928B GLN* 3.2 7.4 + - - -
941B ASP* 3.2 14.1 - - - -
8J PHE* 3.0 26.6 + - - +
9J SER* 4.6 0.5 - - - -
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Residues in contact with ILE 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B LEU* 4.5 13.5 - - + -
774B ASN 2.9 19.4 + - - +
775B LYS* 3.7 17.0 - - + +
777B SER* 1.3 74.7 - - - +
779B ASP* 1.3 63.2 + - - +
781B GLY* 3.2 11.4 + - - -
782B PHE* 3.5 24.0 + - + +
784B ARG* 4.3 9.2 + - - +
905B ARG* 4.1 25.1 + - + +
906B PRO* 3.1 57.2 - - + +
907B GLU* 5.4 0.4 - - - -
925B ILE* 4.7 12.3 - - + -
941B ASP* 4.5 0.8 + - - -
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Residues in contact with ASP 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776B SER* 4.1 17.3 - - - +
777B SER 3.0 1.2 - - - +
778B ILE* 1.3 80.4 - - - +
780B ARG* 1.3 56.5 + - - +
781B GLY 3.1 4.5 + - - -
784B ARG* 5.2 4.4 + - - +
905B ARG* 3.8 13.7 + - - +
99C HIS* 3.7 17.0 + - - -
103C LEU* 4.6 3.6 - - - +
216C HIS* 2.9 54.0 + - - +
217C ALA* 3.4 10.7 + - - +
218C LYS* 4.0 9.9 + - - +
70L ARG* 3.9 20.3 - - - -
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Residues in contact with ARG 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730B TYR* 4.8 3.1 - - - -
776B SER* 2.7 26.4 + - - +
777B SER* 2.6 20.0 + - - +
779B ASP* 1.3 71.4 - - - +
781B GLY* 1.3 56.4 + - - -
928B GLN* 4.8 1.8 - - - +
99C HIS* 4.7 4.3 - - - -
103C LEU* 4.7 13.7 - - + +
217C ALA* 2.7 39.6 + - + +
218C LYS 5.0 0.4 - - - +
220C SER* 4.0 11.5 + - - -
222C VAL 5.1 2.4 + - - -
223C SER 5.2 1.4 + - - -
4J PRO* 5.0 3.1 - - - +
6J ARG* 2.2 55.4 + - + +
7J CYS 3.3 27.4 - - - +
8J PHE* 3.2 22.8 - - - -
9J SER 4.4 4.8 + - - -
11J GLY* 3.8 18.7 + - - -
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Residues in contact with GLY 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730B TYR* 3.2 24.6 - - - +
778B ILE 3.2 1.0 + - - -
779B ASP 3.1 7.1 + - - -
780B ARG* 1.3 80.4 - - - +
782B PHE* 1.3 61.9 + - - +
783B GLY 3.8 1.6 + - - -
784B ARG* 3.5 26.5 + - - +
99C HIS* 4.3 2.2 - - - -
8J PHE* 3.1 21.2 - - - -
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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