Contacts of the helix formed by residues 765 - 785 (chain B) in PDB entry 1XYZ
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 PRO 765 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759B ILE* 6.1 0.7 - - + -
762B SER* 5.5 1.1 - - - -
763B GLU 3.0 11.9 - - - +
764B ASN* 1.4 89.3 - - - +
766B ALA* 1.3 55.4 + - - +
768B ALA* 4.2 5.8 - - + -
769B PHE* 3.0 56.6 + - + -
813B ASN* 6.1 1.3 - - - +
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Residues in contact with ALA 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B ASN* 3.1 21.4 + - - +
765B PRO* 1.3 81.6 - - - +
767B THR* 1.3 63.2 + - + +
769B PHE* 3.5 8.9 + - - +
770B GLN* 3.5 18.5 + - - +
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Residues in contact with THR 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B ASN* 3.3 26.8 + - - +
766B ALA* 1.3 77.3 - - + +
768B ALA* 1.3 67.7 + - - +
770B GLN* 3.1 11.3 + - + +
771B VAL* 3.1 29.1 + - - +
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Residues in contact with ALA 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B ASN* 3.4 12.5 + - - +
759B ILE* 3.9 13.9 - - + -
763B GLU* 3.0 35.0 - - + +
764B ASN 2.9 21.6 + - - +
765B PRO* 4.0 4.5 - - + +
767B THR* 1.3 78.6 + - - +
769B PHE* 1.3 63.0 + - - +
771B VAL* 3.3 5.0 + - - +
772B GLN* 3.0 20.8 + - - +
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Residues in contact with PHE 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759B ILE* 3.7 26.2 - - + -
765B PRO* 3.0 43.7 + - + +
766B ALA* 3.8 5.2 - - - +
767B THR 3.3 0.4 - - - -
768B ALA* 1.3 74.5 - - - +
770B GLN* 1.3 57.9 + - - +
772B GLN* 3.7 11.9 + - - +
773B ALA* 3.1 25.1 + - - +
799B ASP* 5.0 0.9 - - - -
813B ASN* 4.1 23.6 - - + -
818B ASP* 5.6 5.2 - - + -
824B LYS* 4.1 25.1 - - + -
825B PRO* 3.7 33.5 - - + +
826B ALA 4.7 0.7 + - - -
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Residues in contact with GLN 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B ALA 3.5 14.4 + - - +
767B THR* 3.1 12.1 + - - +
769B PHE* 1.3 75.7 - - - +
771B VAL* 1.3 67.7 + - + +
773B ALA* 3.2 6.5 + - - +
774B ASN* 3.1 31.4 + - - +
825B PRO* 4.1 25.2 - - - +
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Residues in contact with VAL 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B ASN* 3.9 7.2 - - - +
727B GLY* 3.6 34.5 - - - +
767B THR* 3.1 17.7 + - - +
768B ALA* 3.3 7.4 + - - +
770B GLN* 1.3 75.3 - - + +
772B GLN* 1.3 58.7 + - - +
774B ASN* 3.1 14.0 + - + +
775B ASN* 2.9 32.0 + - - +
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Residues in contact with GLN 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B ASN* 3.0 19.7 + - - +
757B ILE* 2.9 30.7 + - + -
759B ILE* 3.7 10.6 - - + +
768B ALA 3.0 14.6 + - - +
769B PHE* 3.8 9.0 - - - +
771B VAL* 1.3 78.2 - - - +
773B ALA* 1.3 56.7 + - - +
775B ASN* 3.1 5.9 + - - +
776B TYR* 2.9 49.2 + - + -
813B ASN 3.0 19.7 + - - -
814B PRO 3.6 8.7 + - - -
815B LEU 3.9 1.3 - - - +
824B LYS* 3.1 28.0 + - - -
825B PRO* 6.0 0.2 - - - +
826B ALA* 4.3 6.8 + - + +
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Residues in contact with ALA 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B PHE 3.1 15.4 + - - +
770B GLN* 3.5 13.0 - - - +
771B VAL 3.2 0.2 - - - -
772B GLN* 1.3 78.0 - - - +
774B ASN* 1.3 58.5 + - - +
776B TYR* 3.4 1.4 + - - +
777B LYS* 2.9 29.8 + - - +
825B PRO* 3.7 14.4 - - + +
826B ALA* 3.7 30.7 - - - +
829B ALA* 3.4 12.7 - - + +
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Residues in contact with ASN 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B GLN* 3.1 24.0 + - - +
771B VAL* 3.5 14.7 - - + +
773B ALA* 1.3 76.9 - - - +
775B ASN* 1.3 62.6 + - - +
777B LYS* 3.4 10.9 + - - +
778B GLU* 2.9 37.5 + - + +
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Residues in contact with ASN 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B ASN* 3.7 4.7 - - - +
727B GLY 2.8 28.0 + - - -
728B MET* 2.9 55.2 + - + +
733B LEU* 5.0 4.8 - - - +
757B ILE* 3.8 11.3 - - + +
771B VAL* 2.9 21.7 + - - +
772B GLN* 3.1 10.3 + - - +
774B ASN* 1.3 77.7 - - - +
776B TYR* 1.3 63.3 + - - +
778B GLU* 3.4 6.0 + - - +
779B LEU* 3.1 22.7 + - - +
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Residues in contact with TYR 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B ILE* 3.7 23.4 + - + -
756B ASP* 3.8 6.9 - - - -
757B ILE* 3.7 25.0 + - + +
772B GLN* 2.9 40.5 + - + +
773B ALA 3.8 3.8 - - - +
775B ASN* 1.3 73.2 - - - +
777B LYS* 1.3 63.4 + - - +
779B LEU* 3.3 6.4 + - + +
780B MET* 3.0 23.7 + - - +
792B PHE* 4.4 11.1 - + - -
794B MET* 4.1 18.5 - - + +
814B PRO 2.7 30.1 + - - -
815B LEU* 3.9 9.5 - - - +
816B ILE* 4.2 8.1 - - + +
826B ALA* 3.6 25.6 - - + +
830B ILE* 4.0 28.5 - - + +
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Residues in contact with LYS 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B ALA 2.9 18.4 + - - +
774B ASN* 3.6 11.2 - - - +
775B ASN 3.3 0.2 - - - -
776B TYR* 1.3 77.3 - - - +
778B GLU* 1.3 65.6 + - - +
780B MET* 3.3 4.1 + - - +
781B LYS* 3.0 36.3 + - + +
829B ALA* 3.8 24.6 - - + +
830B ILE 5.0 0.2 - - - +
832B GLU* 2.9 42.7 + - - +
833B ALA* 3.9 20.0 - - + +
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Residues in contact with GLU 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B LEU* 3.6 34.4 - - + +
774B ASN* 2.9 26.1 + - + +
775B ASN* 3.9 3.8 - - - +
776B TYR 3.3 0.2 - - - -
777B LYS* 1.3 81.3 - - - +
779B LEU* 1.3 62.9 + - - +
781B LYS* 3.2 31.5 + - - +
782B ILE* 3.0 29.9 + - + +
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Residues in contact with LEU 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B CYS* 5.0 1.1 - - + -
724B PHE* 3.8 32.8 - - + -
728B MET* 4.4 2.7 - - + -
733B LEU* 4.2 19.3 - - + -
736B ILE* 4.5 8.1 - - + -
752B PHE* 3.6 31.2 - - + -
755B ILE* 3.9 34.3 - - + -
757B ILE* 4.4 13.5 - - + -
775B ASN 3.1 9.0 + - - +
776B TYR* 3.5 10.3 - - - +
778B GLU* 1.3 77.1 - - - +
780B MET* 1.3 62.0 + - - +
782B ILE* 3.3 12.2 + - + +
783B CYS 3.1 17.0 + - - -
792B PHE* 4.0 7.6 - - + -
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Residues in contact with MET 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ILE* 3.7 32.3 - - + -
529B ILE* 4.1 6.5 - - + -
776B TYR 3.0 16.7 + - - +
777B LYS* 3.8 4.3 - - - +
779B LEU* 1.3 76.5 - - - +
781B LYS* 1.3 58.3 + - - +
783B CYS* 3.3 5.1 + - - -
784B LEU* 3.0 33.9 + - + +
792B PHE* 3.7 39.6 - - + -
830B ILE* 3.8 24.7 - - + +
833B ALA* 3.9 20.6 - - + -
834B LEU* 3.8 21.1 - - + -
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Residues in contact with LYS 781 (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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777B LYS* 3.0 39.9 + - + +
778B GLU* 3.2 35.2 + - - +
780B MET* 1.3 73.8 - - - +
782B ILE* 1.3 61.3 + - + +
784B LEU* 3.3 12.5 + - + +
785B ALA* 2.9 30.9 + - - +
833B ALA* 4.4 12.3 - - + +
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Residues in contact with ILE 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B LEU* 3.6 46.4 - - + +
736B ILE* 4.6 9.4 - - + -
737B ASP* 4.1 17.5 - - + +
740B ILE* 3.5 29.6 - - + +
752B PHE* 4.2 7.0 - - + -
778B GLU* 3.0 20.2 + - + +
779B LEU* 3.3 12.3 + - + +
781B LYS* 1.3 75.4 - - + +
783B CYS* 1.3 63.8 + - - +
785B ALA* 3.3 3.8 + - - -
786B ASN* 2.9 37.9 + - - +
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Residues in contact with CYS 783 (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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527B ILE* 4.3 27.2 - - - +
752B PHE* 4.1 10.5 - - + -
779B LEU 3.1 12.8 + - - +
780B MET* 3.4 12.3 - - - +
782B ILE* 1.3 78.3 - - - +
784B LEU* 1.3 60.6 + - - +
786B ASN 3.3 11.3 - - - +
789B CYS* 3.2 51.6 - - - +
790B ASN* 4.4 4.5 + - - -
791B THR 4.6 2.7 - - - -
792B PHE* 4.3 19.5 - - + -
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Residues in contact with LEU 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ARG* 3.8 53.7 + - + +
527B ILE* 4.4 16.2 - - + -
780B MET* 3.0 32.0 + - + +
781B LYS* 3.7 10.5 - - + +
782B ILE 3.3 0.2 - - - -
783B CYS* 1.3 76.2 - - - +
785B ALA* 1.3 60.6 + - - +
786B ASN 3.6 2.3 + - - +
833B ALA 3.3 29.6 - - - +
834B LEU* 4.2 9.4 - - + -
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Residues in contact with ALA 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B ASP* 4.7 4.5 - - - +
741B LYS* 4.9 5.5 + - - +
781B LYS 2.9 16.9 + - - +
782B ILE* 3.3 8.9 + - - +
784B LEU* 1.3 78.3 - - - +
786B ASN* 1.3 63.9 + - - +
787B PRO* 3.6 8.3 - - - +
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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
------------------------------------------------------------
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