Contacts of the helix formed by residues 737 - 743 (chain A) in PDB entry 1DQA
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 LEU 737 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732A ASN* 3.5 8.9 + - - +
733A ILE* 3.2 25.1 + - + +
735A LYS 3.3 0.2 - - - -
736A ASN* 1.3 84.7 - - - +
738A VAL* 1.3 66.3 + - - +
739A GLY 3.4 0.2 - - - -
740A SER 3.5 0.9 + - - -
741A ALA* 3.0 24.7 + - - +
749A TYR* 3.8 12.7 - - + -
778A ILE* 4.0 29.2 - - + -
779A THR 4.8 2.5 - - - +
780A LEU* 4.1 14.8 - - + -
733C ILE* 4.4 11.0 - - + -
737C LEU* 4.2 28.3 - - + -
738C VAL* 3.9 26.5 - - + +
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Residues in contact with VAL 738 (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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733A ILE* 2.9 20.9 + - + +
734A ASN* 3.8 13.9 - - - +
737A LEU* 1.3 70.8 - - - +
739A GLY* 1.3 57.9 + - - +
741A ALA* 3.1 7.2 + - - +
742A MET* 2.9 34.0 + - + +
639B ALA* 3.9 22.4 - - + -
642B ASN* 4.5 1.3 - - - +
644B TYR* 3.1 23.6 - - + +
737C LEU* 3.9 16.2 - - + -
778C ILE* 4.0 13.5 - - + -
780C LEU* 3.9 26.7 - - + -
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Residues in contact with GLY 739 (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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734A ASN 3.0 11.7 + - - -
735A LYS 3.2 5.7 + - - -
738A VAL* 1.3 75.0 - - - +
740A SER* 1.3 60.3 + - - +
742A MET* 3.2 5.1 + - - +
743A ALA* 3.1 22.9 + - - +
644B TYR* 3.6 16.4 - - - -
685B GLY 3.2 26.0 - - - -
686B ASN* 3.9 4.8 - - - +
687B TYR* 4.6 1.2 - - - -
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Residues in contact with SER 740 (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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735A LYS 3.1 4.4 + - - -
736A ASN 3.5 17.4 + - - -
737A LEU 3.5 0.4 + - - -
738A VAL 3.4 0.4 - - - -
739A GLY* 1.3 75.3 - - - +
741A ALA* 1.3 62.4 + - - +
743A ALA* 3.3 6.3 + - - +
744A GLY 3.2 4.5 + - - -
745A SER* 3.0 34.0 + - - -
748A GLY 2.8 28.0 + - - -
749A TYR* 3.7 12.8 - - - -
686B ASN* 3.0 23.4 + - - +
689B THR* 5.9 1.5 - - - +
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Residues in contact with ALA 741 (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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737A LEU 3.0 19.0 + - - +
738A VAL* 3.1 8.0 + - - +
740A SER* 1.3 76.6 - - - +
742A MET* 1.3 63.3 + - - +
744A GLY* 3.0 10.2 + - - -
749A TYR* 4.0 3.3 - - - +
698C TRP* 2.9 18.4 + - - -
737C LEU* 5.5 1.1 - - + -
746C ILE* 6.0 0.3 - - - -
749C TYR* 3.5 50.9 + - + -
778C ILE* 4.4 7.9 - - + -
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Residues in contact with MET 742 (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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738A VAL* 2.9 21.2 + - + +
739A GLY* 3.2 7.4 + - - +
741A ALA* 1.3 78.6 - - - +
743A ALA* 1.3 59.0 + - - +
744A GLY 3.2 1.3 + - - -
637B SER* 2.8 29.8 + - - +
638B ILE 3.3 24.9 - - - +
639B ALA* 4.1 12.6 - - + -
644B TYR* 3.9 22.4 - - + -
687B TYR* 3.8 23.8 - - + -
698C TRP* 3.6 31.1 + - + +
699C ILE* 3.8 12.6 - - - +
778C ILE* 4.5 12.8 - - + -
796C THR* 5.8 0.2 - - + -
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Residues in contact with ALA 743 (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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739A GLY 3.1 9.5 + - - +
740A SER* 3.7 7.9 - - - +
741A ALA 3.2 0.2 - - - -
742A MET* 1.3 76.2 - - - +
744A GLY* 1.3 61.1 + - - +
745A SER* 5.1 0.7 - - - -
686B ASN 3.5 13.0 - - - +
687B TYR* 4.0 10.5 - - + -
689B THR* 3.2 28.0 - - + +
694B ALA* 3.7 6.2 - - + +
695B ALA 3.2 2.4 + - - -
696B ILE* 3.0 36.1 + - + -
699C ILE* 3.7 4.3 - - - +
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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