Contacts of the helix formed by residues 769 - 781 (chain A) in PDB entry 6A69
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 SER 769 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740A ASN* 5.6 2.8 + - - -
768A SER* 1.3 98.3 + - - +
770A PRO* 1.3 69.1 - - - +
771A THR* 3.1 14.2 + - - -
772A ASP* 2.5 45.4 + - - +
773A LYS* 3.0 5.2 + - - +
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Residues in contact with PRO 770 (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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769A SER* 1.3 86.0 - - - +
771A THR* 1.3 57.6 + - - +
773A LYS* 3.5 7.6 + - + +
774A HIS* 2.9 27.9 + - - +
798A GLY* 6.5 1.1 - - - -
800A ASN* 3.8 42.6 - - + +
801A ASP* 4.0 16.6 - - - +
804A ALA* 4.6 4.2 - - - +
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Residues in contact with THR 771 (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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749A GLU* 6.1 0.9 - - - +
769A SER* 3.1 10.1 + - - -
770A PRO* 1.3 80.5 - - - +
772A ASP* 1.3 52.8 + - - +
774A HIS* 3.5 11.0 - - + +
775A THR* 2.7 42.6 + - - +
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Residues in contact with ASP 772 (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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736A GLY 5.8 4.3 - - - +
739A PHE* 3.8 14.4 - - + -
740A ASN* 5.4 11.4 - - - +
765A LEU* 4.7 12.3 - - + +
768A SER* 3.3 20.2 - - - +
769A SER* 2.5 23.8 + - - +
771A THR* 1.3 70.8 - - - +
773A LYS* 1.3 61.4 + - - +
775A THR* 3.2 8.8 + - - -
776A LEU* 3.0 27.5 + - - +
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Residues in contact with LYS 773 (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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473A CYS* 5.3 2.5 - - + -
474A SER 5.2 0.7 - - - -
475A ASP* 3.0 37.6 + - - -
707A VAL* 4.3 26.2 - - + -
768A SER* 3.7 5.6 + - - +
769A SER 3.0 11.8 + - - +
770A PRO* 3.8 9.0 - - + +
772A ASP* 1.3 76.3 - - - +
774A HIS* 1.3 57.8 + - - +
776A LEU* 3.3 6.8 + - + +
777A VAL* 2.9 45.9 + - + +
794A VAL* 3.8 20.0 - - + -
795A THR 3.4 14.3 + - - +
796A GLY* 4.0 4.8 - - - -
801A ASP* 4.5 16.7 + - - +
804A ALA* 4.4 10.8 - - + -
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Residues in contact with HIS 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 PRO 2.9 18.1 + - - +
771A THR* 3.5 13.2 - - + +
772A ASP 3.2 0.2 - - - -
773A LYS* 1.3 76.8 - - - +
775A THR* 1.3 61.5 + - - +
777A VAL* 4.1 1.2 - - - +
778A LYS* 2.9 38.8 + - + +
803A PRO* 3.9 24.3 - - + +
804A ALA* 3.5 32.9 + - + +
807A LYS* 3.2 32.2 + - + +
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Residues in contact with THR 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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739A PHE* 3.9 21.2 - - + +
740A ASN* 5.0 7.6 + - - +
749A GLU* 4.7 29.6 + - + +
754A ARG* 6.4 1.8 - - + -
771A THR* 2.7 26.7 + - - +
772A ASP* 3.2 9.6 + - - -
774A HIS* 1.3 79.7 - - - +
776A LEU* 1.3 59.3 + - - +
778A LYS* 3.5 4.7 + - - +
779A GLY* 2.9 24.9 + - - -
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Residues in contact with LEU 776 (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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473A CYS* 4.0 23.1 - - - -
705A ARG* 5.4 9.6 - - + -
707A VAL* 4.1 22.0 - - + -
739A PHE* 3.9 28.2 - - + -
759A TRP* 5.7 4.5 - - + -
762A LEU* 4.8 14.8 - - + +
765A LEU* 5.0 9.9 - - + -
772A ASP 3.0 13.1 + - - +
773A LYS* 3.6 9.9 - - + +
774A HIS 3.3 0.2 - - - -
775A THR* 1.3 76.5 - - - +
777A VAL* 1.3 60.0 + - + +
779A GLY* 2.9 4.9 + - - -
780A ILE* 2.9 44.9 + - + +
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Residues in contact with VAL 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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473A CYS* 4.1 17.9 - - - -
773A LYS* 2.9 27.5 + - + +
774A HIS* 4.3 2.5 - - - +
776A LEU* 1.3 76.9 - - + +
778A LYS* 1.3 61.4 + - - +
780A ILE* 3.1 15.5 + - + +
781A ILE* 3.3 22.4 + - + +
792A VAL* 5.0 4.9 - - + -
794A VAL* 3.7 33.7 - - + -
804A ALA* 4.4 12.1 - - + +
807A LYS* 4.7 3.8 - - + +
808A ALA* 3.9 21.5 - - + +
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Residues in contact with LYS 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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774A HIS* 2.9 27.8 + - + +
775A THR* 3.8 4.7 - - - +
777A VAL* 1.3 77.0 - - - +
779A GLY* 1.3 59.4 + - - +
781A ILE 3.8 4.3 - - - +
782A ASP* 2.8 23.6 - - - +
807A LYS* 3.8 35.2 - - + +
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Residues in contact with GLY 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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751A GLU* 6.1 2.2 - - - -
754A ARG* 5.8 10.1 - - - -
755A ILE* 3.8 15.3 - - - +
759A TRP* 4.2 8.7 - - - -
775A THR 2.9 16.2 + - - -
776A LEU* 2.9 5.5 + - - -
778A LYS* 1.3 77.9 - - - +
780A ILE* 1.3 64.5 + - - +
782A ASP* 3.3 18.3 - - - +
784A THR* 4.3 0.7 - - - +
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Residues in contact with ILE 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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471A ALA* 5.4 4.5 - - + -
473A CYS* 4.0 27.1 - - - -
705A ARG* 5.3 9.2 - - - +
759A TRP* 3.4 34.5 - - + -
776A LEU* 2.9 32.0 + - + +
777A VAL* 3.1 11.3 + - - +
779A GLY* 1.3 76.1 - - - +
781A ILE* 1.3 62.4 + - - +
782A ASP 2.8 9.7 + - - +
784A THR* 3.8 12.0 + - - +
789A ARG* 5.5 1.2 - - - +
790A GLN* 3.5 23.5 + - + +
792A VAL* 3.6 27.1 - - + -
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Residues in contact with ILE 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 VAL* 3.3 14.2 + - + +
778A LYS* 3.8 3.6 - - - +
780A ILE* 1.3 71.2 - - + +
782A ASP* 1.3 69.8 + - - +
790A GLN 4.5 16.2 - - - +
792A VAL* 3.8 27.4 - - + -
807A LYS* 4.3 12.5 - - + +
808A ALA* 3.8 31.2 - - + -
809A ASP* 3.9 29.2 - - - +
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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
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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