Contacts of the helix formed by residues 761 - 772 (chain A) in PDB entry 4BI2
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 GLU 761 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A PRO* 3.4 23.6 - - + +
624A ARG* 3.1 28.1 + - - +
625A LYS* 3.9 14.7 + - - -
759A ILE* 3.2 14.4 - - + +
760A PRO* 1.4 78.4 - - + +
762A LYS* 1.3 63.7 + - - +
763A ASP* 3.2 4.3 - - + +
764A LEU* 3.3 28.2 + - + +
765A GLN 3.3 15.2 + - - -
790A TYR* 3.9 16.5 - - + -
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Residues in contact with LYS 762 (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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759A ILE 4.4 6.7 - - - +
760A PRO 3.0 12.4 + - - +
761A GLU* 1.3 67.5 - - - +
763A ASP* 1.3 64.8 + - - +
765A GLN* 3.3 12.4 + - - +
766A ASP* 3.2 20.4 + - - +
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Residues in contact with ASP 763 (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 LYS* 5.6 2.0 + - - +
761A GLU* 4.9 2.0 - - + -
762A LYS* 1.3 78.4 - - - +
764A LEU* 1.3 57.7 + - - +
766A ASP* 3.0 23.5 + - - +
767A VAL* 3.0 15.8 + - - +
788A HIS* 3.6 8.9 - - + -
789A PRO* 3.6 34.5 - - - +
790A TYR* 3.8 19.9 + - + +
793A ILE* 4.7 9.0 - - - +
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Residues in contact with LEU 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A ARG* 3.6 17.7 - - - +
724A LEU* 3.7 22.2 - - + -
728A THR* 3.4 28.3 - - + +
759A ILE* 4.0 13.0 - - + -
761A GLU* 3.3 44.5 + - + +
763A ASP* 1.3 77.2 - - - +
765A GLN* 1.3 61.6 + - - +
767A VAL* 3.5 2.9 + - - +
768A LEU* 3.2 28.2 + - + +
790A TYR* 3.5 35.8 - - + +
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Residues in contact with GLN 765 (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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729A TYR* 3.7 17.5 - - - +
756A PHE* 3.7 26.6 + - + +
757A PRO 3.8 0.2 - - - +
758A ASP* 3.3 28.3 - - - +
759A ILE* 3.6 14.7 + - + +
761A GLU 3.3 10.6 + - - +
762A LYS* 3.4 13.6 - - - +
763A ASP 3.2 0.4 - - - -
764A LEU* 1.3 76.1 - - - +
766A ASP* 1.4 55.8 + - - +
768A LEU* 3.2 8.5 + - - +
769A LYS* 2.9 38.5 + - + +
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Residues in contact with ASP 766 (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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762A LYS 3.2 8.7 + - - +
763A ASP* 3.0 10.6 + - - +
765A GLN* 1.4 75.8 - - - +
767A VAL* 1.4 53.4 + - - +
769A LYS* 3.2 9.9 + - - +
770A CYS* 2.8 54.4 + - - -
788A HIS* 2.8 26.7 + - + +
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Residues in contact with VAL 767 (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 TRP* 3.9 11.9 - - + +
724A LEU* 3.7 24.0 - - + -
763A ASP 3.0 10.7 + - - +
764A LEU* 3.6 8.5 - - - +
765A GLN 3.4 0.2 - - - -
766A ASP* 1.4 73.0 - - - +
768A LEU* 1.4 53.5 + - - +
770A CYS* 3.1 8.3 + - - +
771A CYS* 2.8 35.6 + - - -
785A LEU* 3.7 21.1 - - + -
788A HIS* 3.5 39.9 - - + +
790A TYR* 3.6 20.0 - - + -
791A VAL* 5.9 0.2 - - + -
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Residues in contact with LEU 768 (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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721A GLY* 3.6 12.8 - - - +
724A LEU* 3.7 20.6 - - + -
725A TYR* 3.5 31.6 - - + +
728A THR* 3.7 20.0 - - + +
729A TYR* 3.7 32.3 - - + -
756A PHE* 3.4 18.2 - - + -
764A LEU 3.2 15.5 - - - +
765A GLN* 3.2 9.5 + - - +
767A VAL* 1.4 70.9 - - - +
769A LYS* 1.3 60.4 + - - +
770A CYS 3.3 0.2 + - - -
771A CYS* 3.3 3.9 + - - +
772A LEU* 2.9 37.7 + - + +
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Residues in contact with LYS 769 (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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756A PHE* 3.7 39.1 - - + -
765A GLN* 2.9 29.5 + - + +
766A ASP* 3.5 11.2 - - - +
768A LEU* 1.3 76.5 - - - +
770A CYS* 1.4 58.4 + - - +
772A LEU 4.1 1.6 - - - -
773A LYS* 3.4 24.0 + - - +
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Residues in contact with CYS 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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766A ASP* 2.8 44.9 + - - +
767A VAL* 3.3 10.1 - - - +
769A LYS* 1.4 72.4 - - - +
771A CYS* 1.3 64.3 + - - +
773A LYS* 3.7 14.4 + - - +
778A GLN 4.6 0.2 - - - +
779A ARG* 3.6 5.5 - - - +
780A ILE* 3.5 50.0 + - + +
788A HIS* 5.0 1.6 - - - -
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Residues in contact with CYS 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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628A TRP* 4.2 11.9 - - - -
717A VAL* 3.7 35.4 - - - +
718A TRP* 3.8 9.2 - - - -
721A GLY* 3.7 15.3 - - - -
767A VAL* 2.8 29.4 + - - +
768A LEU 4.0 2.2 - - - +
770A CYS* 1.3 72.4 - - - +
772A LEU* 1.3 59.4 + - - +
773A LYS 3.3 4.8 + - - -
779A ARG* 3.3 22.3 + - - -
780A ILE* 3.8 0.7 - - - -
785A LEU* 3.7 29.6 - - - -
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Residues in contact with LEU 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A TRP* 3.2 38.8 - - + +
721A GLY* 3.6 31.4 - - - +
722A CYS* 3.7 7.0 - - - +
725A TYR* 3.6 33.0 - - + -
733A PRO* 3.6 20.2 - - + -
734A PHE* 6.3 0.2 - - + -
754A ILE* 5.2 8.2 - - + +
756A PHE* 3.7 24.1 - - + -
768A LEU* 2.9 16.6 + - + +
769A LYS 4.1 4.3 - - - -
771A CYS* 1.3 79.6 - - - +
773A LYS* 1.4 56.5 + - - +
774A ARG* 3.5 3.6 + - - +
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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