Contacts of the helix formed by residues 741 - 755 (chain A) in PDB entry 2QEP
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 ASN 741 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736A GLU 3.4 9.2 + - - +
737A ASP* 3.7 18.1 + - - +
738A HIS 4.2 4.5 - - - +
739A LEU 4.1 1.0 - - - +
740A LYS* 1.3 74.7 - - - +
742A LYS* 1.3 63.1 + - - +
743A ASN* 2.8 33.6 + - - +
744A ARG* 3.1 17.8 + - - +
745A LEU* 3.1 19.1 + - - +
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Residues in contact with LYS 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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739A LEU 4.7 2.5 - - - -
740A LYS 3.0 9.8 + - - +
741A ASN* 1.3 70.9 + - - +
743A ASN* 1.3 68.8 + - - +
745A LEU* 3.3 12.6 + - + +
746A GLU* 3.0 23.6 + - - +
992A LYS* 5.5 0.9 - - - -
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Residues in contact with ASN 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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741A ASN* 2.8 22.7 + - - +
742A LYS* 1.3 80.6 - - - +
744A ARG* 1.3 55.4 + - - +
746A GLU* 3.3 7.9 + - - +
747A LYS* 2.9 29.0 + - - +
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Residues in contact with ARG 744 (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 ASP 3.2 26.5 - - - +
738A HIS* 4.0 21.8 - - + +
741A ASN* 3.1 19.6 + - - +
743A ASN* 1.3 74.1 - - - +
745A LEU* 1.3 65.8 + - - +
747A LYS* 4.3 7.2 - - + -
748A GLU* 2.8 35.6 + - + +
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Residues in contact with LEU 745 (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 HIS 3.6 17.3 + - - +
739A LEU* 3.7 27.1 - - + +
741A ASN 3.1 9.7 + - - +
742A LYS* 3.4 15.0 - - + +
744A ARG* 1.3 77.3 - - - +
746A GLU* 1.3 63.9 + - - +
748A GLU* 3.6 4.6 - - - +
749A TRP* 2.8 23.1 + - + +
992A LYS* 4.1 29.8 - - + -
995A PHE* 4.3 22.5 - - + -
996A GLU* 4.0 38.8 - - + +
999A LEU* 4.7 3.8 - - + -
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Residues in contact with GLU 746 (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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742A LYS 3.0 13.0 + - - +
743A ASN* 3.6 9.6 - - - +
745A LEU* 1.3 73.6 - - - +
747A LYS* 1.3 55.7 + - - +
749A TRP* 2.9 10.2 + - - -
750A GLU* 2.7 50.2 + - - +
992A LYS* 3.8 30.4 - - - +
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Residues in contact with LYS 747 (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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743A ASN 2.9 17.7 + - - +
744A ARG* 3.8 9.6 - - + +
746A GLU* 1.3 78.0 - - - +
748A GLU* 1.3 60.2 + - + +
750A GLU* 3.1 7.8 + - - +
751A ALA* 2.8 28.6 + - - +
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Residues in contact with GLU 748 (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 TYR* 3.7 9.9 + - - -
738A HIS* 3.1 44.5 + - + +
744A ARG* 2.8 23.9 + - + +
745A LEU* 3.6 3.9 - - - +
747A LYS* 1.3 78.6 - - + +
749A TRP* 1.3 50.7 + - - +
751A ALA* 3.1 10.6 + - - +
752A LEU* 2.7 39.7 + - + +
973A ASP* 4.6 2.4 - - - +
975A ALA* 3.6 27.4 - - + +
995A PHE* 4.4 14.8 - - + -
999A LEU* 5.6 0.3 - - - +
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Residues in contact with TRP 749 (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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745A LEU 2.8 13.8 + - - +
746A GLU* 3.6 11.4 - - - +
748A GLU* 1.3 76.7 - - - +
750A GLU* 1.3 55.1 + - - +
752A LEU* 3.1 15.7 + - + +
753A CYS* 2.7 59.0 + - - -
978A LEU* 4.6 0.9 - - + -
982A ARG* 3.7 15.5 - - - -
989A VAL* 3.7 26.9 - - + -
990A GLN 3.9 5.6 - - - -
991A THR* 3.3 20.9 - - - -
992A LYS* 3.2 48.9 - - + +
995A PHE* 3.6 41.0 - + + -
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Residues in contact with GLU 750 (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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746A GLU* 2.7 30.8 + - - +
747A LYS* 3.3 12.1 - - - +
749A TRP* 1.3 71.9 - - - +
751A ALA* 1.3 65.3 + - - +
753A CYS* 3.3 8.9 + - - +
754A ALA* 3.3 22.0 + - - +
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Residues in contact with ALA 751 (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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747A LYS 2.8 16.1 + - - +
748A GLU* 3.1 14.1 - - - +
750A GLU* 1.3 72.7 - - - +
752A LEU* 1.3 64.7 + - + +
754A ALA* 3.4 5.1 + - - +
755A TYR* 3.0 21.5 + - - +
979A GLU* 5.7 4.5 - - - +
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Residues in contact with LEU 752 (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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748A GLU 2.7 19.0 + - - +
749A TRP* 3.1 20.4 + - + +
751A ALA* 1.3 73.4 - - + +
753A CYS* 1.3 62.2 + - - +
755A TYR* 3.0 20.7 + - + +
975A ALA* 3.9 18.8 - - + +
978A LEU* 3.6 34.1 - - + -
979A GLU* 3.9 32.3 - - + +
982A ARG* 3.0 29.4 + - - +
995A PHE* 4.0 24.9 - - + -
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Residues in contact with CYS 753 (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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749A TRP* 2.7 65.5 + - - +
750A GLU* 3.3 7.6 + - - +
752A LEU* 1.3 73.3 - - - +
754A ALA* 1.3 60.8 + - - +
755A TYR 4.1 3.5 - - - +
982A ARG* 4.3 6.6 + - - +
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Residues in contact with ALA 754 (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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750A GLU 3.3 12.6 + - - +
751A ALA* 4.0 4.3 - - - +
752A LEU 3.3 0.6 - - - -
753A CYS* 1.3 76.7 - - - +
755A TYR* 1.3 66.5 + - - +
756A GLN* 3.3 12.0 + - - +
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Residues in contact with TYR 755 (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 ALA 3.0 12.7 + - - +
752A LEU* 3.0 24.2 + - + +
753A CYS 4.1 3.3 - - - +
754A ALA* 1.3 76.5 - - - +
756A GLN* 1.3 73.5 + - - +
757A ALA* 4.1 11.2 + - - -
979A GLU* 3.6 55.4 + - + +
982A ARG* 4.3 22.7 + - + -
983A ASP* 2.7 35.0 + - - -
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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