Contacts of the helix formed by residues 775 - 786 (chain A) in PDB entry 1N54
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 775 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722A THR* 5.0 12.9 - - + +
725A LEU* 3.5 38.2 - - + +
726A VAL* 5.9 1.9 - - - +
773A GLU 3.4 4.7 + - - -
774A LEU* 1.3 76.0 - - - +
776A PRO* 1.3 76.2 - - - +
777A HIS* 2.9 41.5 + - - +
778A ILE* 3.3 11.2 + - + +
779A LEU 3.2 17.3 + - - -
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Residues in contact with PRO 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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774A LEU 3.4 4.2 - - - +
775A ASP* 1.3 92.0 - - - +
777A HIS* 1.3 72.6 + - + +
779A LEU* 4.5 6.5 - - + -
780A ALA* 2.9 31.5 + - - +
783A GLN* 5.3 0.3 - - - +
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Residues in contact with HIS 777 (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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725A LEU* 3.9 21.1 - - + +
735A VAL* 4.4 15.9 - - + +
740A TYR* 3.3 28.3 + + - +
744A ILE* 4.2 12.3 - - - +
775A ASP* 2.9 16.9 + - - +
776A PRO* 1.3 88.3 - - + +
778A ILE* 1.3 62.9 + - + +
780A ALA* 3.5 12.0 - - - +
781A VAL* 4.2 3.5 + - - +
784A GLN* 5.3 0.2 + - - -
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Residues in contact with ILE 778 (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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718A ILE* 4.3 12.6 - - + -
721A LEU* 3.8 26.2 - - + -
722A THR* 3.6 23.6 - - - +
725A LEU* 3.8 26.7 - - + -
744A ILE* 4.5 8.1 - - + -
747A LEU* 4.5 11.9 - - + -
770A PHE* 4.2 21.4 - - + -
774A LEU* 4.3 13.5 - - + -
775A ASP* 3.3 16.5 + - + +
776A PRO 3.2 0.4 - - - -
777A HIS* 1.3 73.7 - - - +
779A LEU* 1.3 70.2 + - - +
780A ALA 2.6 3.4 + - - -
781A VAL* 2.7 22.2 + - - +
782A PHE 3.8 1.6 + - - -
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Residues in contact with LEU 779 (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 PHE* 4.1 27.1 - - + +
771A THR 3.0 32.3 - - - +
772A ALA* 3.8 9.0 - - - +
774A LEU* 3.7 17.2 - - + +
775A ASP 3.2 11.4 + - - +
776A PRO* 4.2 6.1 - - + +
778A ILE* 1.3 79.4 - - - +
780A ALA* 1.3 63.5 + - - +
782A PHE* 2.9 26.2 + - + +
783A GLN* 3.0 42.9 + - + +
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Residues in contact with ALA 780 (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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209A THR* 5.1 0.2 - - - +
776A PRO 2.9 20.8 + - - +
777A HIS* 3.5 13.0 - - - +
778A ILE 2.6 3.8 + - - -
779A LEU* 1.3 74.3 - - - +
781A VAL* 1.3 57.4 + - - +
783A GLN* 3.1 15.3 + - - +
784A GLN* 2.8 45.1 + - + +
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Residues in contact with VAL 781 (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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213A MET* 3.2 8.1 - - + +
744A ILE* 4.7 19.7 - - + +
747A LEU* 4.4 11.2 - - + -
748A GLN* 4.1 28.7 - - + +
751A PHE* 3.1 31.2 - - + -
777A HIS 4.7 3.8 - - - +
778A ILE 2.7 16.5 + - - +
780A ALA* 1.3 74.6 - - - +
782A PHE* 1.3 54.3 + - - +
784A GLN* 3.4 24.2 - - - +
785A PHE* 2.8 25.5 + - - +
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Residues in contact with PHE 782 (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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751A PHE* 3.8 24.0 - + - -
762A MET* 4.5 6.3 - - + -
765A LEU* 3.6 21.1 - - + -
766A GLU* 3.5 44.2 - - + -
770A PHE* 3.4 43.5 - + + -
778A ILE 3.8 0.8 + - - -
779A LEU* 2.9 19.5 + - + +
781A VAL* 1.3 78.2 - - - +
783A GLN* 1.3 60.3 + - + +
785A PHE* 3.1 25.4 + + - +
786A CYS* 2.9 46.9 + - - -
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Residues in contact with GLN 783 (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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209A THR* 3.2 22.6 - - + +
779A LEU* 3.0 37.6 + - + +
780A ALA* 3.5 20.0 + - - +
782A PHE* 1.3 74.1 - - + +
784A GLN* 1.3 65.8 + - - +
786A CYS* 3.6 12.7 + - - +
787A ALA* 3.5 9.7 + - - +
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Residues in contact with GLN 784 (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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209A THR* 3.8 28.3 - - + +
210A HIS* 4.7 1.9 - - - -
212A PRO* 4.4 10.8 - - + +
213A MET* 3.0 42.4 + - + +
748A GLN* 4.6 2.4 - - - +
780A ALA* 2.8 25.3 + - - +
781A VAL* 3.2 45.7 - - - +
783A GLN* 1.3 75.7 - - - +
785A PHE* 1.3 58.4 + - - +
786A CYS 2.9 1.1 - - - -
787A ALA* 2.5 35.0 + - - +
788A LEU* 3.8 4.3 + - - +
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Residues in contact with PHE 785 (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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213A MET* 3.2 17.2 - - + +
751A PHE* 3.8 33.9 - + + -
755A HIS* 3.8 27.4 - - + -
758A ILE* 3.5 29.4 - - + -
759A GLN* 4.0 22.0 - - + -
762A MET* 4.3 15.5 - - - -
781A VAL 2.8 14.1 + - - +
782A PHE* 3.2 30.3 - + - +
784A GLN* 1.3 76.8 - - - +
786A CYS* 1.3 70.5 + - - -
787A ALA 3.2 0.3 + - - -
788A LEU* 3.3 28.1 + - + +
789A GLN* 4.5 1.2 + - - +
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Residues in contact with CYS 786 (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 MET* 4.4 15.9 - - + -
782A PHE* 2.9 45.8 + - - +
783A GLN* 3.8 11.2 - - - +
784A GLN 2.8 0.6 + - - -
785A PHE* 1.3 92.0 - - - +
787A ALA* 1.3 60.7 + - - +
788A LEU 3.1 2.1 + - - -
789A GLN* 3.4 12.5 + - - +
790A ALA* 3.4 17.7 - - + +
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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