Contacts of the helix formed by residues 786 - 797 (chain A) in PDB entry 3BK0
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 786 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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657A VAL* 4.1 20.9 - - + -
661A LEU* 5.1 0.4 - - + -
754A PHE* 4.0 13.2 - - + -
784A LEU 3.3 9.4 - - - +
785A CYS* 1.3 85.2 - - - +
787A ASP* 1.3 65.8 + - - +
788A ALA* 4.4 2.9 - - + +
789A VAL* 3.0 40.0 + - + +
790A PHE* 3.0 10.6 + - - +
817A ILE* 4.6 6.1 - - + -
820A ARG* 5.4 2.9 - - - +
821A HIS* 4.1 19.1 - - + +
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Residues in contact with ASP 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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781A CYS* 5.5 4.8 - - - -
785A CYS 4.6 3.5 - - - +
786A PRO* 1.3 71.5 - - - +
788A ALA* 1.3 58.1 + - - +
790A PHE* 3.2 8.1 + - - +
791A ARG* 2.9 48.3 + - + +
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Residues in contact with ALA 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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786A PRO* 3.2 1.8 - - + +
787A ASP* 1.3 78.9 - - - +
789A VAL* 1.3 63.3 + - - +
791A ARG* 3.6 30.3 + - - +
792A LEU* 3.2 21.1 + - - +
813A GLU* 4.2 7.9 - - - +
817A ILE* 3.6 30.5 - - + +
820A ARG* 3.9 21.1 - - - +
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Residues in contact with VAL 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A LEU* 3.8 23.1 - - + -
750A LEU* 4.2 14.5 - - + +
754A PHE* 3.8 22.4 - - + -
785A CYS* 3.7 17.3 - - - -
786A PRO* 3.0 28.3 + - + +
788A ALA* 1.3 79.4 - - - +
790A PHE* 1.3 57.3 + - - +
792A LEU* 3.2 6.7 + - - +
793A MET* 2.9 33.1 + - + +
814A LEU* 4.6 4.5 - - + -
817A ILE* 3.8 20.4 - - + -
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Residues in contact with PHE 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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778A ARG* 6.4 0.4 - - + -
779A LEU 3.9 17.3 - - - -
780A PRO* 4.0 1.1 - - + -
781A CYS* 3.6 59.5 - - + -
782A PRO* 4.7 0.7 - - + -
785A CYS* 3.7 4.8 - - - -
786A PRO 3.0 9.7 + - - +
787A ASP* 3.6 8.7 - - - +
789A VAL* 1.3 78.3 - - - +
791A ARG* 1.3 57.7 + - + +
793A MET* 3.2 28.0 + - + +
794A GLU* 2.9 66.3 + - + +
797A TRP* 4.4 3.1 - + - -
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Residues in contact with ARG 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 ASP* 2.9 45.2 + - + +
788A ALA* 3.6 28.1 - - - +
789A VAL 3.3 0.2 - - - -
790A PHE* 1.3 76.2 - - + +
792A LEU* 1.3 62.0 + - - +
794A GLU* 3.3 15.7 + - - +
795A GLN* 3.1 31.4 + - + +
813A GLU* 5.2 3.2 + - - -
820A ARG* 5.1 4.8 - - - +
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Residues in contact with LEU 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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750A LEU* 4.3 11.0 - - + -
788A ALA 3.2 11.5 + - - +
789A VAL* 3.4 9.4 - - - +
790A PHE 3.2 0.2 - - - -
791A ARG* 1.3 77.0 - - - +
793A MET* 1.3 65.0 + - - +
795A GLN* 3.1 16.5 + - - +
796A CYS* 3.0 21.9 + - - -
805A PRO* 4.2 13.0 - - + -
809A THR* 5.1 4.5 - - + -
810A ILE* 4.2 35.9 - - + +
813A GLU* 4.1 27.8 - - + -
814A LEU* 4.0 34.3 - - + -
817A ILE* 5.3 0.9 - - + -
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Residues in contact with MET 793 (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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747A GLY* 3.4 9.6 - - - +
750A LEU* 3.8 30.2 - - + +
751A TRP* 3.8 25.4 - - - +
754A PHE* 5.3 0.2 - - + -
782A PRO* 4.8 1.6 - - + -
785A CYS* 3.7 30.1 - - - -
789A VAL* 2.9 16.6 + - + +
790A PHE* 3.2 23.3 + - + +
792A LEU* 1.3 72.2 - - - +
794A GLU* 1.3 63.1 + - - +
796A CYS* 3.0 20.3 + - - +
797A TRP* 3.1 60.7 + - + -
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Residues in contact with GLU 794 (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* 6.4 1.1 - - + -
790A PHE* 2.9 55.2 + - + +
791A ARG* 3.5 17.2 - - - +
792A LEU 3.3 0.2 - - - -
793A MET* 1.3 75.2 - - - +
795A GLN* 1.3 62.2 + - + +
797A TRP* 3.3 22.5 + - + +
798A ALA* 3.4 9.7 + - - +
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Residues in contact with GLN 795 (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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791A ARG* 3.1 24.5 + - - +
792A LEU* 3.1 20.4 + - - +
794A GLU* 1.3 72.8 - - + +
796A CYS* 1.3 64.5 + - - +
797A TRP 3.1 0.2 - - - -
798A ALA* 3.2 22.1 + - - +
803A GLN 4.2 4.2 - - - +
804A ARG* 3.6 3.8 - - - -
805A PRO* 3.5 26.9 - - + +
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Residues in contact with CYS 796 (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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743A VAL* 3.4 39.9 - - - +
744A TRP* 3.4 11.6 - - - -
746A PHE* 4.7 0.7 - - - -
747A GLY* 3.7 20.4 - - - -
750A LEU* 4.6 7.6 - - - -
792A LEU* 3.0 21.8 + - - -
793A MET* 3.0 9.6 + - - +
795A GLN* 1.3 74.8 - - - +
797A TRP* 1.3 59.0 + - - +
798A ALA 3.4 0.7 - - - -
804A ARG* 3.1 22.9 + - - -
805A PRO* 3.8 5.6 - - - +
810A ILE* 4.0 18.6 - - - -
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Residues in contact with TRP 797 (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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744A TRP* 3.2 50.3 + + + -
747A GLY* 3.2 26.0 - - - -
748A ILE* 3.3 27.5 - - + +
751A TRP* 4.2 1.8 - + + -
761A TYR* 5.8 0.9 - - - -
778A ARG* 2.8 53.2 + - + +
779A LEU* 3.8 40.8 - - + -
790A PHE* 4.4 8.1 - + - -
793A MET* 3.1 44.0 + - + -
794A GLU* 3.5 14.6 - - + +
795A GLN 3.1 0.8 - - - -
796A CYS* 1.3 81.3 - - - +
798A ALA* 1.3 64.5 + - - +
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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