Contacts of the helix formed by residues 795 - 809 (chain A) in PDB entry 4BWM
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 ARG 795 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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774A GLU 5.1 1.6 + - - -
775A MET* 3.7 55.9 + - + +
791A ALA* 4.4 0.2 - - - -
792A PRO* 2.8 25.1 + - + +
794A GLU* 1.3 101.8 - - + +
796A ALA* 1.3 59.0 + - - +
797A GLU 3.3 2.9 - - - -
798A ALA* 3.1 11.6 + - - +
799A VAL* 2.8 37.2 + - + +
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Residues in contact with ALA 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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605A LEU* 3.9 28.5 - - + -
607A VAL* 4.0 5.8 - - + +
791A ALA* 3.9 15.9 - - + -
792A PRO 3.1 8.5 + - - +
793A LYS 3.5 14.0 + - - +
794A GLU 3.6 0.2 - - - -
795A ARG* 1.3 75.9 - - - +
797A GLU* 1.3 60.7 + - + +
799A VAL* 3.7 1.6 - - - +
800A ALA* 2.8 30.5 + - - +
823A ILE* 3.7 16.8 - - + +
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Residues in contact with GLU 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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793A LYS 4.9 3.1 + - - +
794A GLU 5.4 0.6 + - - -
795A ARG 3.3 0.4 - - - -
796A ALA* 1.3 77.9 - - + +
798A ALA* 1.3 62.1 + - - +
800A ALA* 3.4 2.8 + - - +
801A ARG* 3.1 43.9 + - - +
823A ILE* 3.9 20.6 - - + +
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Residues in contact with ALA 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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775A MET* 3.7 19.6 - - + +
794A GLU 5.7 0.4 + - - +
795A ARG* 3.1 15.3 + - - +
797A GLU* 1.3 74.8 - - - +
799A VAL* 1.3 66.0 + - - +
801A ARG* 3.3 27.1 + - - +
802A LEU* 3.0 24.4 + - - +
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Residues in contact with VAL 799 (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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607A VAL* 4.3 8.3 - - + -
772A LEU* 3.8 21.5 - - + -
775A MET* 3.6 28.3 - - + -
777A ALA* 3.8 22.4 - - + -
789A LEU* 3.9 16.2 - - + -
791A ALA* 3.9 19.5 - - + -
795A ARG* 2.8 22.1 + - + +
796A ALA 3.7 3.8 - - - +
798A ALA* 1.3 76.8 - - - +
800A ALA* 1.3 57.8 + - - +
802A LEU* 3.3 3.3 + - - +
803A ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 800 (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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607A VAL* 3.8 17.3 - - + -
796A ALA 2.8 17.6 + - - +
797A GLU 3.7 4.5 - - - +
799A VAL* 1.3 76.6 - - - +
801A ARG* 1.3 63.1 + - + +
803A ALA* 4.1 1.9 - - - +
804A LYS* 3.1 26.7 + - - +
821A VAL* 3.7 27.9 - - + +
823A ILE* 3.9 15.3 - - + -
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Residues in contact with ARG 801 (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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797A GLU* 3.1 34.9 + - - +
798A ALA* 3.5 30.4 - - - +
800A ALA* 1.3 78.6 - - + +
802A LEU* 1.3 62.1 + - - +
804A LYS* 3.8 6.0 - - - +
805A GLU* 3.2 24.6 + - - +
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Residues in contact with LEU 802 (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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768A LEU* 4.0 16.2 - - + -
771A ARG* 3.9 44.4 - - + +
772A LEU* 4.4 6.1 - - + +
775A MET* 3.6 28.3 - - - -
798A ALA 3.0 16.8 + - - +
799A VAL* 3.3 3.1 + - - +
801A ARG* 1.3 76.1 - - - +
803A ALA* 1.3 57.7 + - - +
805A GLU* 3.4 13.7 + - - +
806A VAL* 3.0 43.6 + - + +
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Residues in contact with ALA 803 (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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609A LEU* 3.6 32.1 - - + -
768A LEU* 3.8 28.3 - - + -
789A LEU* 3.8 7.4 - - + -
799A VAL* 2.9 18.1 + - + +
800A ALA* 4.1 0.7 - - - +
802A LEU* 1.3 75.4 - - - +
804A LYS* 1.3 66.6 + - - +
806A VAL* 4.0 0.2 - - - +
807A MET* 3.0 31.4 + - - +
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Residues in contact with LYS 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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609A LEU* 3.6 13.8 - - + +
800A ALA 3.1 17.7 + - - +
801A ARG* 3.8 6.3 - - - +
802A LEU 3.3 0.2 - - - -
803A ALA* 1.3 75.8 - - - +
805A GLU* 1.3 58.4 + - - +
807A MET* 3.9 0.2 - - - +
808A GLU* 2.7 73.7 + - - +
819A VAL* 2.8 29.3 + - + +
821A VAL* 4.0 19.6 - - + +
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Residues in contact with GLU 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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771A ARG* 5.1 6.6 + - - -
801A ARG 3.2 16.5 + - - +
802A LEU* 3.6 13.9 - - - +
803A ALA 3.2 0.2 - - - -
804A LYS* 1.3 80.5 - - - +
806A VAL* 1.3 67.1 + - + +
808A GLU* 3.9 5.0 - - - +
809A GLY* 3.0 21.3 + - - -
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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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764A ALA* 4.0 5.8 - - - +
767A LYS* 3.9 28.9 - - + +
768A LEU* 4.0 27.4 - - + +
771A ARG* 3.5 33.9 - - - +
802A LEU* 3.0 28.9 + - + +
803A ALA 4.0 2.7 - - - +
805A GLU* 1.3 79.3 - - + +
807A MET* 1.3 65.1 + - + +
809A GLY* 3.6 1.8 - - - -
810A VAL* 3.1 24.1 + - - +
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Residues in contact with MET 807 (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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609A LEU* 3.6 42.4 - - + +
611A TYR* 2.7 62.4 + - + +
761A MET* 4.3 14.6 - - + -
764A ALA* 4.2 13.5 - - + -
768A LEU* 4.9 8.5 - - + -
787A LEU* 4.2 18.4 - - + -
803A ALA* 3.0 21.6 + - - +
804A LYS 3.9 0.4 - - - +
806A VAL* 1.3 77.3 - - + +
808A GLU* 1.3 62.3 + - - +
809A GLY 3.4 0.5 + - - -
810A VAL* 3.4 10.6 - - - +
817A LEU* 4.1 0.5 - - - +
819A VAL* 3.8 15.5 - - + -
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Residues in contact with GLU 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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804A LYS* 2.7 60.4 + - - +
805A GLU* 4.1 4.1 - - - +
807A MET* 1.3 75.4 - - - +
809A GLY* 1.3 59.2 + - - +
810A VAL 3.7 0.3 + - - -
811A TYR 4.9 2.6 - - - +
817A LEU* 3.5 43.9 + - - +
818A GLU* 3.6 5.9 - - - +
819A VAL* 2.9 30.4 + - + -
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Residues in contact with GLY 809 (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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767A LYS* 4.7 2.8 + - - -
805A GLU 3.0 15.9 + - - -
806A VAL 3.6 3.4 - - - -
808A GLU* 1.3 77.8 - - - +
810A VAL* 1.3 63.7 + - - +
811A TYR* 3.2 7.3 + - - -
812A PRO* 5.4 0.9 - - - +
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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