Contacts of the helix formed by residues 765 - 785 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A ILE* 6.0 0.9 - - + -
761A GLN 6.1 0.2 - - - +
763A GLU 3.4 8.2 - - - +
764A ASN* 1.4 91.4 - - - +
766A ALA* 1.3 55.9 + - - +
768A ALA* 4.3 4.7 - - + -
769A PHE* 2.9 58.8 + - + -
813A ASN* 6.1 1.6 - - - +
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Residues in contact with ALA 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A ASN* 3.5 13.4 + - - +
765A PRO* 1.3 80.9 - - - +
767A THR* 1.3 63.2 - - + +
769A PHE* 3.7 12.4 + - - +
770A GLN* 3.7 16.6 + - - +
825A PRO* 5.7 0.3 - - - +
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Residues in contact with THR 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A ASN* 3.0 28.1 + - - +
766A ALA* 1.3 76.4 - - + +
768A ALA* 1.3 67.5 + - - +
769A PHE 3.2 1.6 - - - -
770A GLN* 3.1 28.8 + - - +
771A VAL* 3.3 17.1 + - - +
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Residues in contact with ALA 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A ASN* 3.3 11.7 + - - +
759A ILE* 3.8 20.0 - - + -
763A GLU* 3.2 30.1 - - + +
764A ASN 2.9 22.6 + - - +
765A PRO* 3.7 4.9 - - + +
767A THR* 1.3 76.8 + - - +
769A PHE* 1.3 58.2 + - - +
771A VAL* 3.3 6.1 + - - +
772A GLN* 3.0 24.9 + - - +
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Residues in contact with PHE 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A ILE* 3.7 24.9 - - + -
765A PRO* 2.9 42.3 + - + +
766A ALA* 3.8 9.2 - - - +
767A THR 3.2 0.2 - - - -
768A ALA* 1.3 76.6 - - - +
770A GLN* 1.3 56.6 + - - +
772A GLN* 3.6 8.1 + - - +
773A ALA* 3.0 26.9 + - - +
799A ASP* 4.8 0.9 - - - -
813A ASN* 4.0 23.1 - - + -
818A ASP* 5.5 4.9 - - + -
824A LYS* 3.9 36.8 - - + -
825A PRO* 3.9 28.3 - - + +
826A ALA 4.8 0.9 + - - -
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Residues in contact with GLN 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A ALA 3.7 11.8 + - - +
767A THR* 3.1 27.2 + - - +
769A PHE* 1.3 74.2 - - - +
771A VAL* 1.3 66.0 + - + +
773A ALA* 3.3 7.5 + - - +
774A ASN* 3.1 28.5 + - - +
825A PRO* 4.8 11.4 - - + -
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Residues in contact with VAL 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A ASN* 3.7 16.6 - - - +
727A GLY* 3.7 25.1 - - - +
767A THR* 3.3 14.3 + - - +
768A ALA* 3.3 9.1 + - - +
770A GLN* 1.3 73.8 - - + +
772A GLN* 1.3 67.6 + - - +
774A ASN* 3.1 10.4 + - + +
775A ASN* 3.0 25.7 + - - +
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Residues in contact with GLN 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A ASN* 3.1 19.2 + - - +
757A ILE* 2.9 30.1 + - + -
759A ILE* 3.5 9.8 - - + +
768A ALA 3.0 14.8 + - - +
769A PHE* 3.7 8.5 - - - +
771A VAL* 1.3 77.0 - - - +
773A ALA* 1.3 57.2 + - - +
775A ASN* 3.2 6.3 + - - +
776A TYR* 2.9 49.1 + - + -
813A ASN 3.0 19.8 + - - -
814A PRO 3.6 8.5 + - - -
815A LEU 3.8 3.1 - - - +
824A LYS* 3.1 29.0 + - - +
826A ALA* 4.5 5.8 - - + +
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Residues in contact with ALA 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A PHE 3.0 18.3 + - - +
770A GLN* 3.5 7.0 - - - +
771A VAL 3.2 0.4 - - - -
772A GLN* 1.3 76.3 - - - +
774A ASN* 1.3 59.4 + - - +
776A TYR* 3.4 1.7 + - - +
777A LYS 3.0 23.0 + - - -
825A PRO* 3.6 15.7 - - + +
826A ALA* 3.5 31.8 - - - +
829A ALA* 3.3 17.6 - - + +
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Residues in contact with ASN 774 (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 GLN* 3.1 13.9 + - - +
771A VAL* 3.1 11.6 + - + +
773A ALA* 1.3 77.2 + - - +
775A ASN* 1.3 65.0 + - - +
777A LYS* 3.3 16.4 + - - +
778A GLU* 3.0 36.7 + - + +
829A ALA* 5.5 1.4 - - - +
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Residues in contact with ASN 775 (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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726A ASN* 3.8 5.4 - - - +
727A GLY* 2.8 31.4 + - - -
728A MET* 3.0 42.8 + - - +
733A LEU* 4.9 6.7 - - - +
757A ILE* 3.8 17.7 - - + +
771A VAL* 3.0 19.1 + - - +
772A GLN* 3.2 8.9 + - - +
774A ASN* 1.3 76.7 - - - +
776A TYR* 1.3 65.4 + - - +
778A GLU* 3.3 7.2 + - - +
779A LEU* 3.1 26.0 + - - +
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Residues in contact with TYR 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A ILE* 3.8 23.4 + - + -
756A ASP* 3.8 11.6 - - - -
757A ILE* 3.7 18.8 - - + -
772A GLN* 2.9 43.4 + - + +
773A ALA 3.7 5.2 - - - +
775A ASN* 1.3 76.8 - - - +
777A LYS* 1.3 61.8 + - - +
779A LEU* 3.3 5.7 + - + +
780A MET* 3.1 23.2 + - - +
792A PHE* 4.4 11.2 - + - -
794A MET* 4.0 17.9 - - + +
814A PRO 2.8 26.2 + - - -
815A LEU* 3.9 10.1 - - - +
816A ILE* 4.2 9.5 - - + +
826A ALA* 3.7 22.4 - - + -
830A ILE* 4.0 28.1 - - + +
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Residues in contact with LYS 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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773A ALA 3.0 17.1 + - - +
774A ASN* 3.5 17.4 - - - +
775A ASN 3.3 0.2 - - - -
776A TYR* 1.3 76.5 - - - +
778A GLU* 1.3 63.4 + - - +
780A MET* 3.3 8.2 + - - +
781A LYS* 3.0 41.1 + - + +
829A ALA* 3.9 32.9 - - + +
830A ILE 5.0 0.4 - - - +
832A GLU* 3.4 28.1 + - - +
833A ALA* 4.0 13.3 - - + +
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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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733A LEU* 3.8 31.2 - - + +
774A ASN* 3.0 24.0 + - + +
775A ASN* 3.3 4.0 + - - +
777A LYS* 1.3 81.9 - - - +
779A LEU* 1.3 62.2 + - - +
781A LYS* 3.1 42.4 + - - +
782A ILE* 3.1 29.0 + - + +
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Residues in contact with LEU 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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722A CYS* 4.7 2.7 - - + -
724A PHE* 3.9 33.4 - - + -
728A MET* 5.0 2.9 - - - -
733A LEU* 4.3 16.7 - - + +
736A ILE* 4.5 9.0 - - + -
752A PHE* 3.7 27.3 - - + -
755A ILE* 3.8 40.8 - - + -
757A ILE* 4.7 7.0 - - + -
775A ASN 3.1 15.8 + - - +
776A TYR* 3.6 9.9 - - + +
777A LYS 3.3 0.2 - - - -
778A GLU* 1.3 74.7 - - - +
780A MET* 1.3 62.9 + - - +
782A ILE* 3.2 11.5 + - + +
783A CYS* 3.1 17.8 + - - +
792A PHE* 4.0 8.7 - - + -
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Residues in contact with MET 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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522A ALA* 6.0 0.2 - - + -
527A ILE* 4.7 6.1 - - + -
529A ILE* 4.1 9.0 - - + -
776A TYR 3.1 13.1 + - - +
777A LYS* 3.3 8.5 + - - +
779A LEU* 1.3 76.2 - - - +
781A LYS* 1.3 58.4 + - - +
783A CYS* 3.1 12.9 + - - +
784A LEU* 2.9 39.7 + - + +
792A PHE* 3.7 45.8 - - + -
830A ILE* 3.9 25.6 - - + +
833A ALA* 3.8 21.3 - - + -
834A LEU* 4.0 26.0 - - + -
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Residues in contact with LYS 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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777A LYS* 3.0 32.2 + - + +
778A GLU* 3.1 43.1 + - - +
780A MET* 1.3 76.0 - - - +
782A ILE* 1.3 62.9 + - + +
784A LEU* 3.4 11.3 + - + +
785A ALA* 3.1 24.4 + - - +
833A ALA* 4.3 13.2 - - + +
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Residues in contact with ILE 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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733A LEU* 3.5 47.6 - - + +
736A ILE* 4.6 9.2 - - + -
737A ASP* 4.1 16.4 - - + +
740A ILE* 3.5 28.9 - - + -
752A PHE* 4.2 7.0 - - + -
778A GLU* 3.1 16.0 + - + +
779A LEU* 3.2 11.4 + - + +
781A LYS* 1.3 73.3 - - + +
783A CYS* 1.3 67.8 + - - +
785A ALA* 3.3 7.5 + - - -
786A ASN* 3.0 32.3 + - - +
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Residues in contact with CYS 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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527A ILE* 3.8 32.6 - - - +
752A PHE* 4.2 12.1 - - + -
779A LEU 3.1 12.5 + - - +
780A MET* 3.1 11.2 + - - +
782A ILE* 1.3 78.1 - - - +
784A LEU* 1.3 64.0 + - - +
785A ALA 3.2 0.9 + - - -
786A ASN* 3.3 9.9 + - - +
789A CYS* 3.2 48.6 - - - +
790A ASN* 4.3 3.9 - - - +
791A THR 4.6 1.6 - - - -
792A PHE* 4.3 19.1 - - + -
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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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525A ARG* 4.0 43.4 + - + +
527A ILE* 3.8 29.4 - - + -
780A MET* 2.9 31.3 + - + +
781A LYS* 3.8 11.2 - - + +
782A ILE 3.3 0.2 - - - -
783A CYS* 1.3 74.4 - - - +
785A ALA* 1.3 59.1 + - - +
786A ASN 3.4 2.4 + - - -
833A ALA* 3.4 31.2 - - + +
834A LEU* 4.2 8.7 - - + -
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Residues in contact with ALA 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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737A ASP* 4.8 4.5 - - - +
741A LYS* 4.7 6.0 + - - +
781A LYS 3.1 16.7 + - - +
782A ILE* 3.3 6.3 + - - +
783A CYS 3.2 0.4 - - - -
784A LEU* 1.3 77.3 - - - +
786A ASN* 1.3 67.0 + - - +
787A PRO* 3.8 8.0 - - - +
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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
------------------------------------------------------------
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