Contacts of the helix formed by residues 741 - 755 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736B GLU 3.3 8.4 + - - +
737B ASP* 3.4 20.3 + - - +
738B HIS 4.0 3.8 - - - +
739B LEU 3.3 1.7 - - - +
740B LYS* 1.3 73.9 - - - +
742B LYS* 1.3 60.6 + - - +
743B ASN* 3.2 12.0 + - - +
744B ARG* 3.0 29.2 + - - +
745B LEU* 3.1 19.4 + - - +
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Residues in contact with LYS 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739B LEU* 3.2 28.8 + - - +
740B LYS* 3.2 14.8 + - - +
741B ASN* 1.3 73.2 + - - +
743B ASN* 1.3 57.1 + - - +
745B LEU* 3.3 14.5 - - + +
746B GLU* 2.9 29.9 + - - +
992B LYS* 4.7 2.4 + - - +
996B GLU* 2.5 30.4 + - - -
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Residues in contact with ASN 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B ASN* 3.2 7.7 + - - +
742B LYS* 1.3 77.6 - - - +
744B ARG* 1.3 58.3 + - - +
746B GLU* 3.6 5.7 + - - +
747B LYS* 3.0 27.5 + - - +
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Residues in contact with ARG 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737B ASP* 3.0 54.8 + - - +
738B HIS* 3.7 33.7 + - - -
741B ASN* 3.0 22.4 + - - +
743B ASN* 1.3 75.2 - - - +
745B LEU* 1.3 57.1 + - - +
747B LYS* 3.7 6.9 - - + +
748B GLU* 2.8 52.1 + - - +
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Residues in contact with LEU 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738B HIS 3.6 21.5 + - - +
739B LEU* 4.5 6.1 - - + +
741B ASN 3.1 11.2 + - - +
742B LYS* 3.3 25.4 - - + +
744B ARG* 1.3 75.7 - - - +
746B GLU* 1.3 63.8 + - - +
748B GLU* 3.9 4.9 - - - +
749B TRP* 3.0 20.6 + - - +
992B LYS* 4.2 21.8 - - + -
995B PHE* 3.7 30.7 - - + -
996B GLU* 3.7 44.4 - - + +
999B LEU* 4.6 4.3 - - + -
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Residues in contact with GLU 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742B LYS 2.9 18.9 + - - +
743B ASN* 3.8 6.5 - - - +
744B ARG 3.2 0.2 - - - -
745B LEU* 1.3 71.7 - - - +
747B LYS* 1.3 55.1 + - - +
749B TRP* 3.1 7.8 + - - +
750B GLU* 2.8 44.4 + - + +
992B LYS* 2.5 45.5 + - - +
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Residues in contact with LYS 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743B ASN 3.0 18.7 + - - +
744B ARG* 3.3 9.4 + - + +
746B GLU* 1.3 77.2 - - - +
748B GLU* 1.3 58.6 + - + +
750B GLU* 3.1 9.8 + - - +
751B ALA* 2.8 27.3 + - - +
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Residues in contact with GLU 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734B TYR* 4.1 3.8 + - - -
738B HIS* 3.2 40.4 + - - +
744B ARG* 2.8 35.9 + - - +
745B LEU* 3.9 3.0 - - - +
747B LYS* 1.3 70.2 - - + +
749B TRP* 1.3 61.4 + - - +
751B ALA* 3.0 11.4 + - + +
752B LEU* 2.8 32.5 + - - +
973B ASP* 5.4 1.4 - - - +
975B ALA* 3.7 26.6 - - + +
995B PHE* 4.4 14.4 - - + -
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Residues in contact with TRP 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745B LEU 3.0 17.7 + - - +
746B GLU* 3.7 9.0 - - - +
748B GLU* 1.3 75.7 - - - +
750B GLU* 1.3 62.9 + - - +
752B LEU* 3.3 11.5 + - + +
753B CYS* 3.1 46.5 + - - -
978B LEU* 4.5 3.6 - - + -
982B ARG* 3.6 28.5 - - - -
989B VAL* 3.6 13.9 - - + -
990B GLN 3.6 11.7 - - - -
991B THR* 3.2 33.0 - - - -
992B LYS* 3.4 38.3 - - + +
995B PHE* 3.6 33.5 - + + -
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Residues in contact with GLU 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746B GLU* 2.8 25.8 + - - +
747B LYS* 3.3 13.0 - - - +
749B TRP* 1.3 78.8 - - - +
751B ALA* 1.3 59.4 + - - +
753B CYS* 3.5 9.4 + - - +
754B ALA* 3.3 19.9 + - - +
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Residues in contact with ALA 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747B LYS 2.8 13.2 + - - +
748B GLU* 3.0 13.7 + - + +
750B GLU* 1.3 74.3 - - - +
752B LEU* 1.3 65.9 + - + +
754B ALA* 3.2 17.2 + - - +
755B TYR* 3.2 12.0 + - - +
979B GLU* 5.2 3.9 - - - +
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Residues in contact with LEU 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B GLU 2.8 21.0 + - - +
749B TRP* 3.3 17.9 + - + +
751B ALA* 1.3 73.9 - - + +
753B CYS* 1.3 63.4 + - - +
755B TYR* 2.9 20.1 + - + +
975B ALA* 3.6 32.3 - - + +
978B LEU* 3.7 29.6 - - + -
979B GLU* 3.7 24.0 - - + +
982B ARG* 3.1 27.6 + - - +
995B PHE* 3.9 25.4 - - + -
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Residues in contact with CYS 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749B TRP* 3.1 47.2 + - - -
750B GLU* 3.6 11.2 - - - +
751B ALA 3.3 0.2 - - - -
752B LEU* 1.3 75.6 - - - +
754B ALA* 1.3 61.8 + - - +
755B TYR 3.2 6.8 + - - +
982B ARG* 4.0 4.7 - - - +
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Residues in contact with ALA 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750B GLU 3.3 9.0 + - - +
751B ALA* 3.2 12.5 + - - +
753B CYS* 1.3 75.7 - - - +
755B TYR* 1.3 63.1 + - - +
756B GLN* 3.2 7.4 + - - +
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Residues in contact with TYR 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751B ALA 3.2 8.2 + - - +
752B LEU* 2.9 22.8 + - + +
753B CYS 3.1 6.1 - - - +
754B ALA* 1.3 74.2 - - - +
756B GLN* 1.3 67.5 + - - +
757B ALA* 4.0 12.5 + - - -
979B GLU* 3.5 55.7 + - + +
982B ARG* 4.2 21.7 + - + +
983B ASP* 2.6 34.8 + - - -
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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