Contacts of the helix formed by residues 775 - 793 (chain A) in PDB entry 5E3H
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 VAL 775 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771A TRP* 5.7 9.2 - - + -
772A ASP* 3.5 38.1 - - + +
773A GLU 2.8 5.6 + - - +
774A ALA* 1.3 76.2 - - + +
776A PHE* 1.3 61.5 + - - +
777A ARG 3.4 0.2 - - - -
778A GLU* 3.3 14.7 + - - +
779A LYS* 3.1 23.4 + - - +
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Residues in contact with PHE 776 (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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428A CYS* 3.9 24.5 - - - -
431A CYS* 3.9 25.6 - - + -
436A ALA 3.3 22.4 - - - -
437A SER* 3.2 30.7 - - - +
438A VAL* 4.3 2.5 - - - -
439A ILE* 5.2 3.6 - - + -
768A LEU* 4.0 18.8 - - + +
771A TRP* 3.8 31.1 - + + +
772A ASP 3.6 11.5 + - - +
773A GLU* 4.9 4.9 - - + -
774A ALA 4.0 0.2 - - - +
775A VAL* 1.3 75.7 - - - +
777A ARG* 1.3 63.6 + - - +
778A GLU 3.0 1.6 - - - -
779A LYS* 2.9 18.4 + - + +
780A ILE* 3.0 28.7 + - + +
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Residues in contact with ARG 777 (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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257A GLY 5.7 0.6 + - - -
258A LYS* 4.7 9.9 - - - +
259A ASN* 4.6 15.8 + - - +
435A ASP* 5.9 0.4 + - - -
437A SER* 3.2 34.1 + - - -
773A GLU* 3.1 23.4 + - - +
774A ALA* 3.8 22.7 - - - +
776A PHE* 1.3 80.0 - - - +
778A GLU* 1.3 58.1 + - - +
780A ILE* 3.0 29.6 - - + +
781A LEU* 3.5 10.2 + - - +
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Residues in contact with GLU 778 (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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774A ALA 3.5 16.7 + - - +
775A VAL* 3.3 17.4 + - - +
776A PHE 3.0 0.4 - - - -
777A ARG* 1.3 78.5 - - - +
779A LYS* 1.3 64.5 + - - +
781A LEU* 3.3 9.7 + - + +
782A HIS* 2.9 54.2 + - + -
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Residues in contact with LYS 779 (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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424A LEU* 3.9 9.7 - - - +
425A ASP* 4.1 11.5 + - - -
428A CYS* 3.6 28.2 - - - -
771A TRP* 3.7 32.5 - - + -
775A VAL 3.1 11.9 + - - +
776A PHE* 2.9 13.9 + - + +
778A GLU* 1.3 75.0 - - - +
780A ILE* 1.3 60.9 + - + +
782A HIS* 3.0 12.4 + - + +
783A ILE* 2.9 42.3 + - + +
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Residues in contact with ILE 780 (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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428A CYS 4.6 3.1 - - - +
431A CYS* 4.3 1.3 - - + -
432A ALA* 4.3 22.2 - - + +
435A ASP* 4.0 22.4 - - - +
436A ALA 3.6 32.5 - - - +
437A SER* 4.3 6.1 - - - +
776A PHE* 3.0 31.6 + - + +
777A ARG* 3.0 38.1 - - + +
779A LYS* 1.3 76.1 - - + +
781A LEU* 1.3 52.7 + - - +
783A ILE* 3.0 10.6 + - + +
784A GLN* 2.7 43.7 + - - +
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Residues in contact with LEU 781 (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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395A LEU* 3.4 30.7 - - + -
777A ARG 3.7 10.1 - - - +
778A GLU* 3.3 14.8 + - + +
779A LYS 3.2 0.6 - - - -
780A ILE* 1.3 83.1 - - + +
782A HIS* 1.3 63.9 + - + +
784A GLN* 3.6 11.6 - - - +
785A THR* 2.5 42.4 + - - +
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Residues in contact with HIS 782 (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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778A GLU* 2.9 46.5 + - + -
779A LYS* 3.0 14.4 + - + +
781A LEU* 1.3 88.4 - - + +
783A ILE* 1.3 61.0 + - + +
785A THR* 4.0 4.7 - - - -
786A HIS* 3.5 22.2 + - - +
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Residues in contact with ILE 783 (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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428A CYS* 3.6 37.2 - - + +
429A LYS* 4.2 14.8 - - + +
432A ALA* 3.3 18.4 - - + -
779A LYS* 2.9 36.6 + - + +
780A ILE* 3.0 14.1 + - + +
782A HIS* 1.3 76.5 - - + +
784A GLN* 1.3 63.4 + - - +
786A HIS* 3.6 3.9 + - - +
787A GLU* 3.1 42.6 + - + +
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Residues in contact with GLN 784 (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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391A LEU* 3.5 23.6 - - + +
394A LYS* 5.7 2.4 - - - +
395A LEU* 3.6 18.6 - - + +
432A ALA* 3.2 33.8 + - + +
435A ASP* 2.6 39.4 + - - +
780A ILE* 2.7 24.4 + - - +
781A LEU* 3.6 24.0 - - - +
783A ILE* 1.3 74.1 - - - +
785A THR* 1.3 61.9 + - - +
787A GLU* 3.3 5.9 + - - +
788A LYS* 3.0 24.6 + - - +
791A ARG* 5.1 2.1 + - - -
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Residues in contact with THR 785 (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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395A LEU* 3.7 17.4 - - + +
781A LEU* 2.5 35.9 + - - +
782A HIS* 4.3 5.3 - - - -
783A ILE 3.3 0.2 - - - -
784A GLN* 1.3 78.5 - - - +
786A HIS* 1.3 62.5 + - - +
788A LYS* 3.3 11.0 + - + +
789A PHE* 3.6 15.7 + - + +
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Residues in contact with HIS 786 (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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782A HIS 3.5 17.0 + - - +
783A ILE* 4.1 4.3 - - - +
785A THR* 1.3 78.8 - - - +
787A GLU* 1.3 76.2 + - + +
789A PHE* 3.1 58.2 - + + -
790A ILE* 3.3 17.4 - - + +
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Residues in contact with GLU 787 (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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391A LEU* 6.1 2.0 - - + -
429A LYS* 5.7 5.5 - - + +
783A ILE* 3.1 34.4 + - + +
784A GLN* 3.8 6.1 - - - +
786A HIS* 1.3 88.0 - - + +
788A LYS* 1.3 59.2 + - - +
790A ILE* 3.0 26.2 - - - +
791A ARG* 3.2 29.0 + - - +
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Residues in contact with LYS 788 (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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391A LEU 4.7 0.2 - - - +
392A ASP* 3.0 46.4 + - - +
395A LEU* 3.7 32.1 - - + -
396A GLY* 4.9 5.6 - - - +
784A GLN 3.0 16.9 + - - +
785A THR* 3.6 6.5 - - - +
786A HIS 3.2 0.8 - - - -
787A GLU* 1.3 76.3 - - - +
789A PHE* 1.3 61.8 + - + +
791A ARG* 3.0 17.9 + - - +
792A ASP* 2.9 52.0 + - - +
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Residues in contact with PHE 789 (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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785A THR* 3.6 11.9 + - + +
786A HIS* 3.1 57.0 - + - -
788A LYS* 1.3 81.0 - - + +
790A ILE* 1.3 64.6 + - + +
792A ASP* 3.8 7.8 - - - +
793A SER* 2.5 44.2 + - - +
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Residues in contact with ILE 790 (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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786A HIS* 3.3 22.0 - - + +
787A GLU* 3.0 37.7 - - - +
789A PHE* 1.3 92.5 - - + +
791A ARG* 1.3 62.5 + - - +
793A SER* 3.4 15.4 + - - -
794A GLN* 3.4 17.0 + - + +
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Residues in contact with ARG 791 (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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388A PHE* 3.5 62.3 - - - +
391A LEU* 3.9 27.7 - - - +
392A ASP* 3.7 22.0 + - - -
784A GLN 5.1 0.6 + - - -
787A GLU* 3.2 41.7 + - - +
788A LYS* 3.0 21.5 + - - +
790A ILE* 1.3 84.0 - - + +
792A ASP* 1.3 62.0 + - - +
794A GLN* 2.7 40.2 + - - +
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Residues in contact with ASP 792 (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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392A ASP* 5.0 5.6 - - - +
788A LYS* 2.9 50.0 + - - +
789A PHE* 3.5 7.6 + - - +
790A ILE 3.3 0.2 - - - -
791A ARG* 1.3 82.6 + - - +
793A SER* 1.3 60.6 + - - +
794A GLN* 3.4 5.4 + - - +
795A GLU* 4.3 8.8 + - - +
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Residues in contact with SER 793 (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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789A PHE* 2.5 30.4 + - - +
790A ILE* 3.4 13.2 + - - -
791A ARG 3.3 0.4 - - - -
792A ASP* 1.3 77.0 - - - +
794A GLN* 1.3 61.7 + - - +
795A GLU 3.3 5.5 + - - -
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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