Contacts of the helix formed by residues 742 - 754 (chain N) in PDB entry 6AH0
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 742 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739N CYS 3.9 6.7 + - - +
740N PRO* 5.5 0.7 - - - +
741N HIS* 1.3 76.9 + - - +
743N THR* 1.4 64.5 + - - +
744N PRO 3.2 4.6 - - - -
745N LEU* 4.0 7.2 + - - -
746N TRP 4.6 4.0 + - - -
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Residues in contact with THR 743 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741N HIS 3.5 4.2 + - - -
742N SER* 1.4 71.5 - - - +
744N PRO* 1.3 65.8 - - - +
745N LEU 3.2 1.1 - - - -
746N TRP* 3.7 3.4 + - - +
747N LEU* 3.2 19.8 + - - -
778N GLY 5.8 4.2 - - - +
779N LEU* 5.8 8.3 - - - +
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Residues in contact with PRO 744 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742N SER* 3.2 3.0 - - - -
743N THR* 1.3 80.5 - - - +
745N LEU* 1.3 59.6 + - - +
747N LEU* 3.5 1.2 + - - -
748N LEU* 3.2 17.3 + - - -
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Residues in contact with LEU 745 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736N LEU* 6.4 2.5 - - - +
742N SER 4.0 6.0 + - - -
743N THR 3.2 0.6 - - - -
744N PRO* 1.3 71.8 - - - +
746N TRP* 1.3 56.5 + - - +
747N LEU 3.0 1.1 - - - -
748N LEU* 2.7 24.9 + - - -
749N LEU* 2.9 10.7 + - - -
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Residues in contact with TRP 746 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736N LEU* 6.1 2.2 - - - +
742N SER 4.6 4.0 + - - -
743N THR* 3.7 5.1 + - - +
745N LEU* 1.3 73.6 - - - +
747N LEU* 1.3 61.1 + - - +
749N LEU* 4.4 2.9 - - - +
750N SER* 3.0 20.6 + - - -
765N ILE 5.4 7.2 - - - +
766N LEU* 5.4 6.6 + - - -
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Residues in contact with LEU 747 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743N THR 3.2 14.0 + - - -
744N PRO* 3.8 4.3 - - - -
745N LEU 3.0 1.4 - - - -
746N TRP* 1.3 77.8 - - - +
748N LEU* 1.3 57.2 + - - +
750N SER* 3.9 0.9 - - - -
751N ARG* 3.0 23.9 + - - -
782N GLU* 6.2 4.5 - - - +
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Residues in contact with LEU 748 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744N PRO 3.2 9.3 + - - -
745N LEU* 2.7 14.3 + - - +
747N LEU* 1.3 70.7 - - - +
749N LEU* 1.3 56.6 + - - +
751N ARG* 3.2 3.8 + - - +
752N LEU* 2.9 24.6 + - - -
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Residues in contact with LEU 749 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729N ARG* 6.5 0.7 - - - +
732N TYR* 5.8 8.5 - - - +
745N LEU 2.9 11.9 + - - -
746N TRP* 4.1 2.2 - - - +
748N LEU* 1.3 76.3 - - - +
750N SER* 1.3 57.5 + - - +
752N LEU* 2.9 16.3 + - - +
753N GLU* 3.1 12.1 + - - -
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Residues in contact with SER 750 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746N TRP 3.0 16.5 + - - -
747N LEU 3.9 0.9 - - - -
749N LEU* 1.3 78.6 - - - +
751N ARG* 1.3 56.1 + - - +
752N LEU 3.1 0.4 - - - -
753N GLU* 4.6 0.7 - - - +
754N GLU* 3.2 23.9 + - - -
762N ALA* 4.5 23.7 - - - +
765N ILE* 5.8 2.9 - - - +
766N LEU 5.6 2.9 - - - +
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Residues in contact with ARG 751 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747N LEU 3.0 16.7 + - - -
748N LEU* 3.2 6.9 + - - +
750N SER* 1.3 74.1 - - - +
752N LEU* 1.3 60.1 + - - +
754N GLU* 4.2 2.0 - - - +
755N LYS* 4.1 8.9 + - - -
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Residues in contact with LEU 752 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748N LEU 2.9 11.6 + - - -
749N LEU* 2.9 5.0 + - - +
751N ARG* 1.3 75.7 - - - +
753N GLU* 1.3 66.8 + - - +
754N GLU 3.0 2.6 + - - -
755N LYS* 3.0 12.6 + - - -
756N ILE 3.7 5.0 + - - -
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Residues in contact with GLU 753 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749N LEU 3.1 12.5 + - - -
750N SER* 4.3 1.8 - - - +
752N LEU* 1.3 74.6 - - - +
754N GLU* 1.3 63.1 + - - +
756N ILE* 3.1 23.6 + - - +
762N ALA* 5.5 6.1 - - - +
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Residues in contact with GLU 754 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750N SER 3.2 16.5 + - - -
751N ARG* 4.7 2.0 - - - +
752N LEU 3.0 1.4 - - - -
753N GLU* 1.3 78.1 - - - +
755N LYS* 1.3 61.0 - - - +
756N ILE 3.2 4.2 + - - -
762N ALA* 5.1 9.0 - - - +
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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