Contacts of the helix formed by residues 744 - 759 (chain A) in PDB entry 2N8Z
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 744 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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742A SER 3.7 0.7 + - - -
743A ILE* 1.3 89.0 - - - +
745A GLN* 1.3 66.6 + - - +
746A GLU* 3.2 16.3 - - - -
747A GLN* 3.0 28.0 + - - +
748A MET* 3.1 4.2 + - - +
825A THR* 2.7 36.6 + - - +
827A ASP* 3.4 15.9 - - - -
828A GLN* 4.2 5.5 - - - +
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Residues in contact with GLN 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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744A SER* 1.3 71.7 - - - +
746A GLU* 1.3 61.6 + - - +
748A MET* 3.4 18.6 - - + +
749A ASN* 3.3 19.9 + - - +
827A ASP* 2.8 36.3 + - - +
831A ALA* 5.2 11.2 - - + +
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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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744A SER* 4.0 15.5 - - - -
745A GLN* 1.3 77.5 - - - +
747A GLN* 1.3 71.2 + - + +
749A ASN* 3.1 30.9 + - - +
750A GLU* 3.4 8.6 + - - +
825A THR* 6.5 0.4 - - - -
827A ASP* 4.5 14.2 - - - +
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Residues in contact with GLN 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 ILE* 3.9 9.5 - - + +
744A SER* 3.0 34.4 + - - +
746A GLU* 1.3 78.3 - - + +
748A MET* 1.3 65.2 + - - +
749A ASN 3.0 4.5 + - - -
750A GLU* 3.0 32.1 + - - +
751A PHE* 3.0 58.8 + - + -
816A MET* 4.2 9.7 - - - +
820A THR* 5.3 2.9 + - - -
825A THR* 5.7 2.7 - - + -
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Residues in contact with MET 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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743A ILE* 3.5 29.7 - - + +
744A SER 3.1 7.6 + - - +
745A GLN* 3.4 21.1 - - + +
747A GLN* 1.3 78.3 - - - +
749A ASN* 1.3 60.5 + - - +
751A PHE* 3.9 11.7 - - - -
752A ARG* 2.9 66.5 + - + +
809A PHE* 5.6 3.6 - - + -
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Residues in contact with ASN 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 GLN 3.3 12.1 + - - +
746A GLU* 3.1 23.9 + - - +
747A GLN 3.0 0.2 - - - -
748A MET* 1.3 84.3 - - - +
750A GLU* 1.3 73.9 + - - +
752A ARG* 3.9 5.0 - - - +
753A ALA* 2.9 32.6 + - - +
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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 3.5 8.2 - - - +
747A GLN* 3.0 40.8 + - - +
749A ASN* 1.3 86.5 - - - +
751A PHE* 1.3 59.8 + - + +
753A ALA* 3.8 6.2 - - - +
754A SER* 2.8 33.8 + - - -
778A LEU* 4.2 25.0 - - + +
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Residues in contact with PHE 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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743A ILE* 3.4 33.9 - - + -
747A GLN* 3.0 55.4 + - - +
748A MET* 3.7 5.2 - - - +
750A GLU* 1.3 76.7 - - - +
752A ARG* 1.3 60.1 + - - +
754A SER* 3.0 16.6 + - - -
755A PHE* 3.3 13.3 + - - +
778A LEU* 3.6 32.1 - - + -
780A TYR* 4.9 8.5 - + - -
809A PHE* 3.7 11.0 - - + -
812A PHE* 3.4 37.9 - + + -
813A ILE* 4.2 2.5 - - + -
816A MET* 3.7 20.9 - - + -
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Residues in contact with ARG 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 MET* 2.9 52.3 + - - +
749A ASN* 3.9 4.3 - - - +
751A PHE* 1.3 75.7 - - - +
753A ALA* 1.3 59.4 + - - +
755A PHE* 3.4 8.3 - - + -
756A ASN* 3.0 30.0 + - - +
809A PHE* 3.5 30.8 - - + -
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Residues in contact with ALA 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 ASN* 2.9 24.6 + - - +
750A GLU* 3.8 7.6 - - - +
752A ARG* 1.3 78.1 - - - +
754A SER* 1.3 57.1 + - - +
756A ASN* 3.3 14.3 + - - +
757A HIS* 2.8 30.2 + - - +
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Residues in contact with SER 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 2.8 21.8 + - - -
751A PHE* 3.0 15.4 + - - -
753A ALA* 1.3 69.3 - - - +
755A PHE* 1.3 64.3 + - - +
757A HIS* 3.1 15.0 + - - -
758A PHE* 3.1 22.9 + - - -
774A CYS* 3.6 26.7 - - - -
777A SER* 4.6 12.1 - - - -
778A LEU* 4.0 13.4 - - - +
812A PHE* 5.5 1.0 - - - -
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Residues in contact with PHE 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 PHE 3.3 11.3 + - - +
752A ARG* 3.4 13.7 - - + -
754A SER* 1.3 80.7 + - - +
756A ASN* 1.3 72.9 + - + +
758A PHE* 4.0 1.9 - - - +
759A ASP* 2.8 62.8 + - + +
762A HIS* 5.6 6.7 - - - -
764A GLY* 3.7 28.9 - - - -
765A THR 4.2 0.4 - - - -
766A LEU* 4.3 0.2 - - - +
771A PHE* 4.0 30.7 - + + -
774A CYS* 3.7 10.4 - - - -
809A PHE* 3.9 33.0 - + + -
812A PHE* 4.9 2.5 - - + -
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Residues in contact with ASN 756 (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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752A ARG 3.0 20.4 + - - +
753A ALA* 3.5 13.3 + - - +
754A SER 3.2 0.2 - - - -
755A PHE* 1.3 86.8 - - + +
757A HIS* 1.3 67.8 + - - +
759A ASP 3.3 12.3 - - - +
760A ARG* 2.9 45.3 + - - +
762A HIS* 3.3 15.7 - - + +
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Residues in contact with HIS 757 (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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753A ALA 2.8 17.2 + - - +
754A SER* 3.1 10.0 + - - +
756A ASN* 1.3 81.0 - - - +
758A PHE* 1.3 81.3 + + + +
760A ARG* 3.1 26.4 - - - +
777A SER* 6.0 0.4 - - - -
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Residues in contact with PHE 758 (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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754A SER* 3.1 22.1 + - - +
757A HIS* 1.3 101.2 - + + +
759A ASP* 1.3 57.3 + - - +
760A ARG* 3.2 8.5 + - - +
766A LEU* 3.4 26.2 - - + +
770A GLU* 3.7 24.7 - - + -
773A ALA* 3.7 30.5 - - + -
774A CYS* 3.7 25.6 - - + -
777A SER* 4.3 18.6 - - - -
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Residues in contact with ASP 759 (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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755A PHE* 2.8 35.2 + - + +
756A ASN* 3.3 13.2 - - - +
758A PHE* 1.3 74.2 - - - +
760A ARG* 1.3 59.5 + - - +
761A ASP* 3.2 10.2 + - - +
762A HIS* 2.9 32.8 + - - -
763A SER* 3.0 11.0 + - - -
764A GLY* 2.7 30.7 + - - -
765A THR 3.5 11.5 + - - +
766A LEU* 3.8 19.8 - - + +
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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