Contacts of the helix formed by residues 774 - 791 (chain A) in PDB entry 5IXC
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 LYS 774 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ALA* 4.8 2.9 - - - +
772A THR 4.2 1.8 + - - -
773A TYR* 1.3 71.6 - - - +
775A GLU* 1.3 67.5 + - - +
776A GLU* 3.1 23.5 + - + +
777A ASP* 2.8 39.7 + - - +
778A PHE 3.0 10.2 + - - -
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Residues in contact with GLU 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 3.1 34.3 + - - +
390A GLU* 4.3 16.1 - - - +
393A ALA* 3.7 23.3 - - + +
773A TYR 3.4 2.1 + - - -
774A LYS* 1.3 71.1 - - - +
776A GLU* 1.3 62.7 + - - +
778A PHE* 3.3 10.1 + - - +
779A GLU* 3.0 28.2 + - + +
809B LEU* 5.0 8.3 - - + +
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Residues in contact with GLU 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A GLN* 5.2 2.1 - - - +
774A LYS* 4.1 25.0 + - + -
775A GLU* 1.3 78.9 - - - +
777A ASP* 1.3 64.1 + - - +
779A GLU* 3.3 8.4 + - - +
780A ARG* 3.3 55.5 + - - +
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Residues in contact with ASP 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A ASP* 5.8 2.1 - - - +
765A PRO* 3.7 34.3 - - + +
766A TYR* 2.4 39.7 + - + +
773A TYR* 5.0 3.4 - - + -
774A LYS* 2.8 45.6 + - - +
776A GLU* 1.3 77.8 - - - +
778A PHE* 1.3 67.5 + - - +
780A ARG* 3.6 14.7 + - - +
781A LEU 3.5 4.9 + - - -
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Residues in contact with PHE 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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336A THR* 3.6 37.5 + - + -
339A TYR* 5.2 2.0 - + - -
385A ILE* 3.6 41.7 - - + -
388A ALA* 4.2 11.0 - - + -
389A ARG* 3.6 40.4 - - + +
392A LEU* 4.0 13.5 - - + -
773A TYR* 4.3 15.5 - - + +
774A LYS 3.0 9.5 + - - +
775A GLU* 3.4 10.5 - - - +
777A ASP* 1.3 77.8 - - - +
779A GLU* 1.3 69.0 + - - +
781A LEU* 3.4 3.9 + - - +
782A LEU* 2.9 39.8 + - + +
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Residues in contact with GLU 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 5.3 1.2 - - - +
389A ARG* 2.8 40.7 + - - +
775A GLU* 3.0 17.1 + - + +
776A GLU* 3.6 10.3 - - - +
777A ASP 3.2 0.4 - - - -
778A PHE* 1.3 82.7 - - - +
780A ARG* 1.3 65.7 + - + +
782A LEU* 4.3 11.8 - - - +
783A ARG* 2.9 72.4 + - - +
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Residues in contact with ARG 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A PHE* 4.4 1.4 - - - -
753A GLN* 2.7 56.4 + - - +
754A GLY* 3.7 14.6 - - - +
756A GLN* 3.6 23.4 + - - +
757A VAL* 4.2 19.4 - - + +
758A ASP 5.5 1.1 - - - +
766A TYR* 3.8 11.4 - - - +
776A GLU* 3.3 47.6 + - - +
777A ASP* 3.9 14.7 + - - +
778A PHE 3.4 0.2 - - - -
779A GLU* 1.3 76.3 - - + +
781A LEU* 1.3 58.2 + - - +
783A ARG* 3.8 3.5 - - - +
784A LEU* 2.8 32.8 + - - +
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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
----------------------------------------------------------
333A ARG* 3.9 24.2 - - + +
336A THR* 3.3 20.2 - - - +
337A SER* 4.2 7.0 - - - -
732A LEU* 3.8 32.5 - - + -
757A VAL* 4.3 3.6 - - - +
759A LEU* 4.7 12.3 - - + -
766A TYR* 3.5 43.2 + - + -
773A TYR* 4.3 2.0 - - + -
777A ASP 3.5 1.8 + - - -
778A PHE* 3.4 7.2 + - - +
779A GLU 3.3 0.4 - - - -
780A ARG* 1.3 76.0 - - - +
782A LEU* 1.3 64.6 + - - +
784A LEU* 3.4 8.2 + - + +
785A SER* 2.9 31.8 + - - +
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Residues in contact with LEU 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A THR* 3.5 15.4 + - - +
339A TYR* 3.7 12.3 - - + -
340A GLY* 3.2 32.3 - - - +
343A LEU* 4.7 11.2 - - + -
382A GLU* 4.6 10.8 - - - +
385A ILE* 3.7 32.1 - - + -
778A PHE* 2.9 28.7 + - + +
779A GLU* 3.8 19.3 - - - +
781A LEU* 1.3 75.3 - - - +
783A ARG* 1.3 62.7 + - + +
785A SER* 3.1 6.7 + - - -
786A ASP* 2.9 27.5 + - + +
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Residues in contact with ARG 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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382A GLU* 6.0 0.2 + - - -
737A PHE* 3.6 16.8 - - + -
741A SER 6.0 2.2 - - - -
779A GLU* 2.9 57.0 + - - +
780A ARG* 3.9 2.9 - - - +
782A LEU* 1.3 78.8 - - + +
784A LEU* 1.3 60.5 + - - +
786A ASP* 3.5 12.4 + - - +
787A TYR* 2.9 30.5 + - - +
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Residues in contact with LEU 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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732A LEU* 4.6 11.2 - - + -
733A VAL 3.5 26.0 - - - +
734A ASN* 3.9 6.7 - - - +
737A PHE* 3.5 44.5 - - + -
757A VAL* 4.0 26.7 - - + -
759A LEU* 4.1 15.7 - - + -
780A ARG 2.8 18.1 + - - +
781A LEU* 3.6 7.6 - - + +
783A ARG* 1.3 76.7 - - - +
785A SER* 1.3 64.6 + - - +
787A TYR* 3.4 1.7 + - - +
788A ASN* 3.0 39.3 + - - +
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Residues in contact with SER 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER* 2.6 49.3 + - - -
340A GLY* 4.1 2.0 - - - -
341A HIS* 3.3 26.9 - - - -
732A LEU* 4.5 3.9 - - - +
781A LEU* 2.9 18.2 + - - +
782A LEU 3.5 7.2 - - - -
784A LEU* 1.3 73.3 - - - +
786A ASP* 1.3 66.9 + - - +
788A ASN* 3.2 16.2 + - - +
789A VAL* 3.3 6.2 + - - +
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Residues in contact with ASP 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLY* 3.2 17.8 + - - +
343A LEU* 4.1 17.2 - - + +
344A ALA* 3.3 20.5 + - - +
347A LYS* 4.1 11.8 + - - -
782A LEU* 2.9 16.9 + - + +
783A ARG* 3.6 12.7 - - + +
785A SER* 1.3 76.2 - - - +
787A TYR* 1.3 56.2 + - - +
790A GLN* 2.9 54.5 + - - +
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Residues in contact with TYR 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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712A GLU* 4.1 1.8 - - - -
736A SER* 2.6 29.7 + - - -
737A PHE* 3.3 38.4 - + + -
740A HIS* 3.5 28.4 + - + +
741A SER 5.7 0.2 - - - +
742A ALA* 3.7 29.4 - - - -
743A PRO* 3.7 21.0 - - + +
744A GLY 5.1 0.5 + - - -
783A ARG 2.9 18.6 + - - +
784A LEU 3.5 1.8 - - - +
785A SER 3.2 0.2 - - - -
786A ASP* 1.3 79.3 + - - +
788A ASN* 1.3 71.3 + - - +
790A GLN* 4.5 6.5 - - - -
791A THR* 2.8 51.3 + - + +
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Residues in contact with ASN 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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341A HIS* 5.0 7.1 + - - +
712A GLU* 3.3 34.7 - - + +
730A PHE* 4.3 6.0 - - + -
731A PRO 4.4 8.1 + - - +
732A LEU* 5.3 3.6 - - - +
733A VAL* 3.1 30.0 + - - +
734A ASN 4.3 0.5 - - - +
784A LEU* 3.0 36.0 + - - +
785A SER* 3.2 8.7 + - - +
787A TYR* 1.3 85.4 - - - +
789A VAL* 1.3 56.1 + - + +
791A THR* 3.4 10.0 - - - +
792A SER* 2.7 28.9 + - - -
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Residues in contact with VAL 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A HIS* 3.3 34.8 - - + +
344A ALA* 3.4 25.4 - - + -
345A LEU* 3.9 28.0 - - + +
348A LEU* 4.3 3.5 - - + +
672A PHE* 3.8 19.5 - - + -
730A PHE* 4.1 13.2 - - + -
785A SER 3.3 2.2 + - - +
786A ASP 4.0 0.7 - - - +
788A ASN* 1.3 77.4 - - + +
790A GLN* 1.3 66.7 + - - +
792A SER* 3.0 17.3 + - - -
793A GLN 3.6 3.3 + - - -
796A ILE* 4.1 12.7 - - + +
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Residues in contact with GLN 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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344A ALA* 3.7 16.8 - - + +
347A LYS* 3.4 41.8 - - - +
348A LEU* 4.1 19.6 - - + +
743A PRO* 3.8 31.5 - - + +
786A ASP* 2.9 40.9 + - - +
787A TYR* 4.0 2.4 + - - +
789A VAL* 1.3 76.9 - - - +
791A THR* 1.3 56.8 - - - +
792A SER 3.1 4.7 + - - -
793A GLN* 3.1 21.3 + - - +
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Residues in contact with THR 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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712A GLU* 3.8 24.2 - - + -
736A SER* 5.0 0.7 + - - +
743A PRO* 4.0 15.4 - - - +
744A GLY 4.9 2.4 + - - -
787A TYR* 2.8 52.3 + - + +
788A ASN 3.4 13.7 - - - +
790A GLN* 1.3 71.7 - - - +
792A SER* 1.3 56.6 + - - +
793A GLN* 3.4 2.3 + - - -
794A GLY 5.2 0.3 + - - -
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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
------------------------------------------------------------
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