Contacts of the helix formed by residues 776 - 792 (chain A) in PDB entry 5Y36
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 776 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770A THR* 2.8 24.6 + - - +
771A GLN* 2.8 51.0 - - - +
772A LYS 4.5 1.4 + - - -
773A GLY 2.9 4.9 + - - +
774A GLN 3.2 0.8 - - - -
775A LYS* 1.3 89.5 - - - +
777A SER* 1.4 61.6 + - - +
778A ARG 3.3 0.4 - - - -
779A GLU* 2.9 17.8 + - - +
780A ARG 3.3 2.4 + - - -
924A THR* 5.2 8.6 + - - -
1035A LYS* 3.4 14.1 + - - +
32C G 4.5 7.7 + - - -
33C A 3.6 24.1 + - - -
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Residues in contact with SER 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A THR 5.5 0.4 - - - -
771A GLN 3.0 8.7 + - - -
772A LYS* 3.2 2.6 - - - -
773A GLY 2.4 35.4 + - - -
774A GLN* 5.1 1.1 - - - -
776A ASN* 1.4 69.6 - - - +
778A ARG* 1.4 55.7 + - - -
780A ARG* 2.9 24.6 + - - +
781A MET* 3.2 4.9 + - - +
806A LEU 4.4 0.2 - - - -
807A GLN* 2.8 31.5 + - - -
812A TYR* 2.6 32.9 + - - -
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Residues in contact with ARG 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A GLY 3.4 1.8 + - - -
774A GLN* 2.7 56.3 + - - +
775A LYS* 4.4 17.6 + - - +
776A ASN 3.1 0.4 + - - -
777A SER* 1.4 76.2 - - - +
779A GLU* 1.4 98.6 + - - +
781A MET* 3.4 27.2 - - - +
782A LYS* 4.3 10.0 + - - +
803A ASN* 4.4 14.4 - - - +
1029A ILE* 4.8 9.6 + - - +
1030A GLY* 4.1 9.5 + - - -
1031A LYS* 2.8 45.6 + - - +
1032A ALA* 4.8 6.9 - - - +
1035A LYS* 5.9 2.8 - - - +
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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
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770A THR* 4.9 9.6 - - + +
775A LYS 5.0 5.4 - - - +
776A ASN 2.9 10.6 + - - +
778A ARG* 1.4 109.1 + - - +
780A ARG* 1.4 64.6 + - - +
781A MET 3.1 1.8 - - - -
782A LYS* 2.9 61.4 + - - +
783A ARG* 4.0 2.1 + - - +
920A GLN* 4.8 8.7 - - - +
1032A ALA* 5.9 1.0 - - - +
1035A LYS* 5.4 9.6 - - + +
1036A TYR* 5.7 3.5 - - - -
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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
----------------------------------------------------------
768A GLN 2.9 24.7 + - - -
769A THR* 3.2 26.7 + - - +
770A THR* 4.0 16.0 + - - +
776A ASN 3.3 4.4 + - - -
777A SER* 2.9 12.4 + - - +
779A GLU* 1.4 75.0 - - - +
781A MET* 1.4 62.0 + - - +
782A LYS 3.2 0.9 + - - -
783A ARG* 3.3 52.6 + - - +
784A ILE* 3.6 7.6 + - + +
812A TYR* 3.6 31.6 - - + -
816A LEU* 3.9 15.6 - - - +
852A ILE* 3.4 21.1 - - + +
853A ASP* 2.8 25.5 + - - -
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Residues in contact with MET 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A SER 3.2 3.0 + - - +
778A ARG* 3.4 27.1 - - - +
780A ARG* 1.4 76.3 - - - +
782A LYS* 1.4 55.3 + - + +
784A ILE* 3.1 10.5 + - - +
785A GLU* 2.8 52.4 + - + +
801A VAL* 5.3 8.3 - - + +
802A GLU 5.3 1.1 - - - +
803A ASN* 3.5 39.7 - - - +
806A LEU* 4.0 33.4 - - + +
812A TYR* 3.5 29.1 + - + +
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Residues in contact with LYS 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 ARG* 4.6 6.7 - - - +
779A GLU* 2.9 57.5 + - - +
781A MET* 1.4 75.3 - - - +
783A ARG* 1.4 56.7 + - - +
785A GLU* 3.7 16.5 - - - +
786A GLU* 3.0 33.6 + - - +
918A LYS* 5.0 6.7 - - - +
920A GLN* 4.4 19.8 + - - +
1029A ILE* 5.3 17.6 - - - +
1036A TYR* 5.0 16.6 - - - -
30D G 5.5 1.2 + - - -
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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
----------------------------------------------------------
768A GLN 3.9 1.6 + - - -
779A GLU 4.0 1.4 + - - +
780A ARG* 3.3 45.4 + - - +
782A LYS* 1.4 77.9 - - - +
784A ILE* 1.4 58.1 + - - +
786A GLU* 4.2 6.1 + - - +
787A GLY 3.9 6.2 + - - -
816A LEU* 4.0 8.7 - - + +
853A ASP* 2.8 42.6 + - - -
889A ALA 4.2 6.3 - - - +
890A LYS* 3.0 26.3 + - + +
891A LEU* 2.9 44.5 + - - +
892A ILE* 3.6 11.1 - - - +
893A THR* 3.8 10.8 - - - +
896A LYS* 5.5 2.6 - - - +
918A LYS* 5.1 4.2 - - - +
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Residues in contact with ILE 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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780A ARG* 3.6 7.8 + - + +
781A MET* 3.1 10.3 + - - +
783A ARG* 1.4 74.3 - - - +
785A GLU* 1.4 67.5 + - + +
787A GLY* 3.1 13.9 + - - -
788A ILE* 3.1 26.8 + - + +
806A LEU* 5.5 5.8 - - + -
812A TYR* 3.3 56.1 - - + +
815A TYR* 3.3 33.7 - - + +
816A LEU* 3.5 23.1 - - + +
891A LEU* 3.8 8.4 - - - +
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Residues in contact with GLU 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A MET* 2.8 47.3 + - + +
782A LYS* 3.7 18.6 - - - +
784A ILE* 1.4 73.8 - - + +
786A GLU* 1.3 57.2 + - - +
788A ILE* 3.3 14.3 + - + +
789A LYS* 2.9 53.6 + - - +
796A LEU* 5.3 14.6 - - + +
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Residues in contact with GLU 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 LYS 3.0 14.8 + - - +
783A ARG* 4.2 5.9 - - - +
785A GLU* 1.3 75.5 - - - +
787A GLY* 1.4 55.6 + - - +
789A LYS* 3.4 8.5 + - - +
790A GLU* 2.8 32.6 + - + +
889A ALA* 3.9 10.5 - - - +
890A LYS* 2.9 37.3 + - - +
918A LYS* 2.6 35.9 + - - +
29D C 4.9 10.1 - - - +
30D G 3.3 10.5 + - - -
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Residues in contact with GLY 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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783A ARG 3.9 4.6 + - - -
784A ILE 3.1 8.8 + - - -
786A GLU* 1.4 76.3 - - - +
788A ILE* 1.3 55.4 + - - +
790A GLU* 3.4 1.6 + - - +
791A LEU* 3.1 38.8 + - - +
889A ALA* 3.9 15.2 + - - +
891A LEU* 3.8 25.6 - - - -
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Residues in contact with ILE 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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784A ILE* 3.1 33.9 + - + +
785A GLU* 3.4 14.6 - - + +
787A GLY* 1.3 74.9 - - - +
789A LYS* 1.3 56.4 + - - +
791A LEU* 3.4 8.8 + - + +
792A GLY* 2.9 28.2 + - - -
793A SER* 4.3 16.9 + - - +
795A ILE* 6.5 0.2 - - + -
796A LEU* 3.7 30.5 - - + -
815A TYR* 4.4 22.7 - - + +
818A ASN* 6.0 2.2 - - - +
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Residues in contact with LYS 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 GLU* 2.9 41.2 + - - +
786A GLU* 3.9 7.6 - - - +
788A ILE* 1.3 70.1 - - - +
790A GLU* 1.3 62.3 - - - +
792A GLY* 3.7 10.7 + - - +
793A SER 5.6 0.7 - - - +
796A LEU* 3.9 27.1 - - + -
28D T 3.1 36.4 + - - +
29D C 5.0 10.7 + - - +
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Residues in contact with GLU 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 GLU* 2.8 24.5 + - + +
787A GLY* 3.6 8.5 - - - +
788A ILE 3.4 0.2 - - - -
789A LYS* 1.3 73.5 - - - +
791A LEU* 1.4 62.7 + - + +
885A GLN 5.8 0.9 - - - +
888A ASN* 5.9 2.0 - - + -
889A ALA* 4.2 19.1 - - + +
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Residues in contact with LEU 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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787A GLY 3.1 22.3 + - - +
788A ILE* 3.8 7.0 - - + +
790A GLU* 1.4 79.3 - - + +
792A GLY* 1.3 62.4 + - - +
818A ASN* 4.2 27.1 - - - +
882A TYR* 6.1 5.4 - - + -
885A GLN* 5.8 8.1 - - + +
886A LEU* 6.1 1.1 - - + -
891A LEU* 5.4 7.9 - - + -
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Residues in contact with GLY 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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788A ILE 2.9 12.4 + - - -
789A LYS* 3.7 9.1 + - - -
790A GLU 3.5 2.2 - - - -
791A LEU* 1.3 82.2 - - - +
793A SER* 1.3 63.0 + - - -
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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
------------------------------------------------------------
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