Contacts of the helix formed by residues 768 - 776 (chain A) in PDB entry 3NC0
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 ASP 768 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A HIS* 4.5 4.9 - - + +
766A SER* 3.9 2.4 + - - -
767A ASN* 1.3 80.1 - - - +
769A PRO* 1.3 75.2 - - - +
770A GLN* 3.1 5.0 + - - +
771A MET* 2.9 42.3 + - + +
772A VAL* 3.1 20.2 + - - +
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Residues in contact with PRO 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766A SER* 5.7 0.9 - - - +
767A ASN* 4.1 6.1 - - - +
768A ASP* 1.3 87.0 - - - +
770A GLN* 1.3 59.8 + - - +
772A VAL* 2.9 8.7 + - + +
773A ALA* 2.8 26.9 + - - +
810A LYS* 5.4 11.0 - - + +
811A LEU* 3.6 24.1 - - + +
814A HIS* 3.4 31.2 - - + +
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Residues in contact with GLN 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A ASP* 3.1 5.5 + - - +
769A PRO* 1.3 79.0 - - - +
771A MET* 1.3 65.0 + - - +
773A ALA* 2.8 14.7 + - + +
774A GLU* 2.9 52.5 + - + +
814A HIS* 3.5 33.4 + - + +
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Residues in contact with MET 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704A HIS* 4.1 16.8 - - + +
707A VAL* 5.3 4.7 - - + -
762A TRP* 4.5 4.3 - - + -
768A ASP* 2.9 45.9 + - + +
770A GLN* 1.3 77.8 - - - +
772A VAL* 1.3 83.1 + - + +
774A GLU* 4.9 3.6 - - - -
775A ASN* 3.1 42.3 + - - +
776A PHE* 3.8 23.8 - - - -
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Residues in contact with VAL 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762A TRP* 3.6 37.9 - - + -
763A VAL* 4.1 17.3 - - + -
766A SER* 3.8 16.8 - - - +
768A ASP 3.1 15.6 + - - +
769A PRO* 2.9 11.0 + - + +
771A MET* 1.3 87.8 - - + +
773A ALA* 1.3 56.0 + - - +
776A PHE* 3.3 22.1 + - + -
777A VAL* 3.2 15.6 + - + +
811A LEU* 3.6 21.8 - - + -
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Residues in contact with ALA 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769A PRO 2.8 10.6 + - - +
770A GLN* 2.8 9.4 + - + +
772A VAL* 1.3 76.7 - - - +
774A GLU* 1.3 62.2 + - + +
775A ASN 3.5 0.4 - - - -
777A VAL* 3.7 16.2 - - + +
778A PRO* 3.5 17.3 - - - +
811A LEU* 4.2 10.8 - - + -
814A HIS* 3.7 33.7 - - + +
815A ILE* 5.4 1.8 - - + -
818A GLU* 5.7 4.4 - - + +
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Residues in contact with GLU 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770A GLN* 2.9 54.6 + - + +
771A MET* 4.4 4.4 - - - +
773A ALA* 1.3 84.5 - - + +
775A ASN* 1.3 72.5 + - - +
778A PRO* 4.1 13.4 - - - +
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Residues in contact with ASN 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714A TYR* 4.8 1.0 - - - -
771A MET* 3.1 32.1 + - - +
773A ALA 3.5 0.2 - - - -
774A GLU* 1.3 95.0 + - - +
776A PHE* 1.3 75.1 + - + +
777A VAL 3.3 1.8 - - - -
778A PRO* 4.0 1.1 - - - +
779A PRO* 3.1 26.3 - - - +
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Residues in contact with PHE 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A VAL* 3.6 26.2 - - + -
710A LEU* 3.7 30.5 - - + -
711A GLY* 4.1 18.2 - - - -
714A TYR* 2.7 56.3 + + + +
762A TRP* 4.0 24.2 - + + -
763A VAL* 5.6 3.4 - - + +
771A MET* 3.8 26.7 - - - -
772A VAL* 3.3 12.0 + - + +
775A ASN* 1.3 89.6 - - + +
777A VAL* 1.3 60.4 + - - +
779A PRO* 4.0 1.1 - - - +
780A LEU* 3.5 9.9 - - - +
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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