Contacts of the helix formed by residues 797 - 818 (chain A) in PDB entry 5CGD
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 TYR 797 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795A SER* 2.8 9.2 + - - +
796A ASN* 1.3 102.8 - - + +
798A LYS* 1.3 56.4 + - - +
799A ILE 3.4 2.6 + - - -
800A ILE* 3.6 14.3 + - + -
801A THR* 2.7 36.0 + - - +
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Residues in contact with LYS 798 (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 ASN* 4.3 15.4 + - - -
792A TYR* 3.5 67.5 + - + +
793A PHE* 4.3 15.0 + - - +
795A SER* 3.8 17.5 - - - +
796A ASN 3.8 1.2 - - - -
797A TYR* 1.3 73.9 - - - +
799A ILE* 1.3 57.8 + - + +
801A THR* 3.6 3.8 - - - -
802A MET* 2.7 37.0 + - - +
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Residues in contact with ILE 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A LEU* 3.6 38.9 - - + +
636A ILE* 4.2 8.5 - - + -
730A TYR* 4.1 22.2 - - + -
731A LEU 3.2 35.7 - - - +
732A ILE* 3.6 28.0 - - + -
797A TYR 3.4 0.8 - - - -
798A LYS* 1.3 78.0 - - + +
800A ILE* 1.3 58.7 + - - +
802A MET* 3.3 7.6 + - - +
803A CYS* 2.9 32.3 + - - -
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Residues in contact with ILE 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A ALA* 3.8 38.1 - - + +
580A PRO 4.1 1.6 - - - -
583A ALA* 4.9 2.7 - - + -
636A ILE* 4.2 17.0 - - + -
730A TYR* 3.6 36.8 - - + +
797A TYR* 3.6 15.7 + - + +
798A LYS 3.4 0.2 - - - -
799A ILE* 1.3 72.8 - - - +
801A THR* 1.3 66.2 + - - +
803A CYS* 3.1 7.9 + - + +
804A PHE* 3.1 50.7 + - + -
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Residues in contact with THR 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A PHE* 5.1 0.4 - - + -
791A ILE* 3.9 28.2 - - + +
792A TYR* 4.3 19.1 - - + -
795A SER* 3.3 11.3 + - - -
797A TYR* 2.7 25.8 + - - +
798A LYS* 3.7 7.0 - - - -
800A ILE* 1.3 77.4 - - - +
802A MET* 1.3 57.5 + - - +
804A PHE* 4.2 6.4 - - - +
805A SER* 2.6 41.9 + - - +
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Residues in contact with MET 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A LEU* 3.7 13.0 - - + -
651A ILE* 3.7 43.1 - - + -
740A VAL* 4.8 5.6 - - + -
788A PHE* 3.8 12.6 - - + -
792A TYR* 3.6 30.2 - - + +
798A LYS 2.7 21.7 + - - +
799A ILE* 3.5 7.0 - - - +
801A THR* 1.3 73.3 - - - +
803A CYS* 1.3 64.4 + - - +
805A SER* 3.7 2.7 - - - -
806A VAL* 3.0 37.9 + - + +
4005A 51E 3.8 29.6 - - - +
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Residues in contact with CYS 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ALA* 4.0 22.4 - - + -
632A THR* 4.0 21.4 - - + +
635A LEU* 3.6 31.4 - - - -
636A ILE* 4.2 13.9 - - - -
799A ILE* 2.9 26.1 + - - -
800A ILE* 3.1 11.6 + - - +
802A MET* 1.3 76.3 - - - +
804A PHE* 1.3 62.1 + - + +
806A VAL* 3.6 2.6 + - - +
807A SER* 3.1 28.2 + - - -
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Residues in contact with PHE 804 (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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579A ALA* 4.5 6.7 - - + -
582A ALA* 4.5 17.7 - - + -
583A ALA* 4.0 28.5 - - + -
586A PHE* 4.2 24.3 - + + -
800A ILE* 3.1 39.2 + - + +
801A THR* 4.2 6.3 - - - +
803A CYS* 1.3 74.4 - - - +
805A SER* 1.3 60.6 + - - +
807A SER* 4.0 2.6 - - - +
808A LEU* 2.8 34.8 + - - +
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Residues in contact with SER 805 (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* 4.7 5.3 - - - +
788A PHE* 3.4 33.6 - - - -
791A ILE* 6.0 0.3 - - - +
801A THR* 2.6 28.7 + - - +
802A MET 3.4 3.8 + - - -
804A PHE* 1.3 78.0 - - - +
806A VAL* 1.3 56.7 + - - +
808A LEU* 3.9 5.9 - - - +
809A SER* 2.9 30.7 + - - -
4005A 51E 3.8 14.8 - - - +
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Residues in contact with VAL 806 (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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628A GLY 3.1 30.7 - - - +
631A CYS* 4.2 10.8 - - + -
632A THR* 5.3 1.8 - - + -
635A LEU* 5.4 0.7 - - + -
651A ILE* 4.8 3.4 - - + -
802A MET* 3.0 39.0 + - + +
803A CYS* 3.9 4.7 - - - +
805A SER* 1.3 76.3 - - - +
807A SER* 1.3 58.9 + - - +
809A SER* 3.3 4.2 + - - -
810A ALA* 2.9 27.0 + - - +
4005A 51E 3.3 51.3 - - + +
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Residues in contact with SER 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ALA 5.0 0.2 + - - -
586A PHE* 3.8 34.2 - - - +
587A ALA* 4.7 3.1 + - - -
629A TYR* 3.8 23.2 - - - -
632A THR* 3.7 17.7 - - - +
803A CYS 3.1 16.5 + - - -
804A PHE* 4.0 0.4 - - - -
806A VAL* 1.3 79.1 - - - +
808A LEU* 1.3 54.0 + - - +
810A ALA* 3.3 2.2 + - - +
811A THR* 2.6 38.4 + - - -
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Residues in contact with LEU 808 (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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586A PHE* 4.2 10.5 - - + -
784A ILE* 3.8 32.3 - - + -
804A PHE 2.8 22.8 + - - +
805A SER* 3.9 5.2 - - - +
807A SER* 1.3 70.0 - - - +
809A SER* 1.3 65.1 + - - +
811A THR* 3.2 9.8 + - + -
812A VAL* 3.0 42.0 + - + +
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Residues in contact with SER 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR* 3.0 16.5 + - - -
781A THR* 4.8 3.9 + - - +
784A ILE* 4.7 11.6 - - - +
785A TRP* 3.0 19.9 + - - -
805A SER 2.9 18.2 + - - -
806A VAL 3.3 4.9 + - - -
808A LEU* 1.3 76.5 - - - +
810A ALA* 1.3 61.0 + - - +
812A VAL* 4.1 2.7 - - - +
813A ALA* 3.6 14.9 + - - +
4005A 51E 3.0 37.7 + - - -
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Residues in contact with ALA 810 (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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625A ILE* 3.6 29.6 - - + +
628A GLY* 4.9 3.8 - - - -
629A TYR* 3.5 16.6 - - + -
806A VAL 2.9 16.6 + - - +
807A SER* 3.8 4.3 - - - +
809A SER* 1.3 76.0 - - - +
811A THR* 1.3 64.0 + - - +
813A ALA* 3.7 1.6 + - - +
814A LEU* 3.2 23.6 + - - +
4005A 51E 3.8 20.8 - - + +
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Residues in contact with THR 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A PHE* 3.4 22.1 - - + -
629A TYR* 2.9 16.8 + - - +
807A SER 2.6 24.6 + - - -
808A LEU* 3.2 12.5 + - + -
810A ALA* 1.3 75.2 - - - +
812A VAL* 1.3 55.6 + - + +
814A LEU* 3.2 3.9 + - + +
815A GLY* 2.7 34.3 + - - -
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Residues in contact with VAL 812 (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 THR* 4.0 19.7 - - + +
780A THR* 4.1 26.2 - - + +
781A THR* 4.5 4.7 - - - +
784A ILE* 3.7 21.1 - - + -
808A LEU* 3.0 30.5 + - + +
809A SER* 4.1 4.7 - - - +
811A THR* 1.3 78.7 - - + +
813A ALA* 1.3 62.7 + - - +
816A CYS* 3.1 41.6 + - - +
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Residues in contact with ALA 813 (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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625A ILE* 4.2 3.8 - - + -
659A TYR* 5.4 4.9 - - + -
777A THR* 3.8 17.9 - - + +
781A THR* 5.7 1.3 - - - +
809A SER 3.6 9.3 + - - +
810A ALA 4.1 1.1 - - - +
812A VAL* 1.3 79.5 - - - +
814A LEU* 1.3 59.9 + - - +
816A CYS 4.4 0.2 - - - -
817A MET* 3.3 43.0 - - + +
818A PHE* 3.4 3.3 - - - -
4005A 51E 3.2 32.3 - - + -
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Residues in contact with LEU 814 (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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590A GLY 4.4 0.2 - - - +
593A ALA* 4.0 24.5 - - + -
594A THR* 3.4 26.0 - - - +
597A VAL* 4.3 14.4 - - + -
622A LEU* 4.2 17.7 - - + -
625A ILE* 4.1 9.4 - - + +
629A TYR* 4.2 14.1 - - + +
810A ALA 3.2 17.5 + - - +
811A THR* 3.7 5.2 - - + +
812A VAL 3.2 0.6 - - - -
813A ALA* 1.3 80.2 - - - +
815A GLY* 1.3 60.9 + - - +
818A PHE* 3.4 28.6 + - + +
819A VAL* 3.3 23.6 + - + +
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Residues in contact with GLY 815 (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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811A THR* 2.7 21.1 + - - -
812A VAL 4.0 0.2 - - - -
814A LEU* 1.3 76.1 - - - +
816A CYS* 1.3 60.9 + - - +
817A MET 3.5 0.2 - - - -
819A VAL* 3.3 31.6 - - - +
820A PRO* 3.4 6.8 - - - +
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Residues in contact with CYS 816 (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 TYR* 3.3 36.5 - - + +
776A PHE* 4.0 28.9 - - + -
777A THR* 3.2 20.4 - - - +
812A VAL* 3.1 32.5 + - - +
815A GLY* 1.3 78.8 - - - +
817A MET* 1.3 60.4 + - - +
820A PRO* 3.5 6.7 - - - +
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Residues in contact with MET 817 (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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621A ILE* 4.2 13.5 - - + -
662A LEU* 4.0 38.4 - - + -
773A TYR* 4.4 9.9 - - - +
774A ILE* 4.4 20.2 - - + -
777A THR* 3.5 21.8 - - + +
813A ALA* 3.3 34.5 + - + +
816A CYS* 1.3 80.9 - - - +
818A PHE* 1.3 78.3 + - + +
820A PRO* 3.8 4.0 - - - +
821A LYS* 3.5 26.2 - - - +
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Residues in contact with PHE 818 (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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597A VAL* 3.8 18.6 - - + -
601A PHE* 3.4 26.9 - + + -
618A CYS* 4.4 18.6 - - + -
621A ILE* 3.5 34.1 - - + -
622A LEU* 3.8 23.6 - - + -
625A ILE* 4.0 8.7 - - + -
813A ALA 3.4 21.1 - - - -
814A LEU* 3.4 20.0 + - + +
817A MET* 1.3 95.9 - - + +
819A VAL* 1.3 60.3 + - - +
820A PRO 3.3 1.8 - - - -
821A LYS* 3.0 12.5 + - - +
822A VAL* 2.8 32.1 + - - +
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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