Contacts of the helix formed by residues 734 - 747 (chain A) in PDB entry 3BWT
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 THR 734 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699A PRO* 3.8 20.0 - - - +
700A GLU* 5.2 1.6 + - - -
732A HIS 3.5 2.6 + - - -
733A GLY* 1.3 72.9 - - - +
735A THR* 1.3 59.3 + - - +
736A GLU* 3.0 26.5 - - + +
737A GLN* 2.7 32.6 + - + +
738A CYS* 2.7 33.3 + - - -
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Residues in contact with THR 735 (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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733A GLY 3.8 1.4 + - - -
734A THR* 1.3 74.2 - - - +
736A GLU* 1.3 58.0 + - - +
738A CYS* 3.8 5.1 - - - +
739A ASP* 2.8 46.9 + - - +
772A LYS* 5.7 3.1 + - - -
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Residues in contact with GLU 736 (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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734A THR* 3.0 13.8 - - + +
735A THR* 1.3 78.2 - - - +
737A GLN* 1.3 65.4 + - + +
739A ASP* 3.5 5.3 + - - +
740A ASN* 3.0 40.6 + - - +
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Residues in contact with GLN 737 (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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699A PRO* 3.1 34.7 + - - +
702A PHE* 4.1 2.0 - - - -
703A GLN* 3.2 36.0 + - - +
706A PHE* 3.6 37.1 - - + -
733A GLY* 3.6 4.5 - - - -
734A THR* 2.7 46.4 + - + +
736A GLU* 1.3 80.9 - - + +
738A CYS* 1.3 63.2 + - - +
740A ASN* 3.4 5.8 + - - +
741A LEU* 3.0 23.2 + - - +
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Residues in contact with CYS 738 (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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706A PHE* 4.4 1.6 - - - -
729A CYS 3.7 12.3 - - - -
730A LEU* 3.9 27.8 - - + -
733A GLY* 3.3 37.7 - - - -
734A THR 2.7 13.6 + - - +
735A THR* 4.0 5.8 - - - +
737A GLN* 1.3 74.1 - - - +
739A ASP* 1.3 59.3 + - - +
741A LEU* 3.6 5.9 - - - +
742A CYS* 2.8 38.2 + - - -
772A LYS* 5.9 4.7 - - - +
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Residues in contact with ASP 739 (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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735A THR* 2.8 37.6 + - - +
736A GLU* 3.7 6.0 - - - +
738A CYS* 1.3 78.1 - - - +
740A ASN* 1.3 70.2 + - - +
742A CYS 3.1 1.0 + - - -
743A ASP* 2.8 26.3 + - - +
776A ASP* 4.7 6.8 - - - +
777A TYR* 2.9 36.2 + - - +
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Residues in contact with ASN 740 (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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710A SER* 5.8 3.8 - - - +
736A GLU* 3.0 36.9 + - - +
737A GLN* 3.9 5.4 - - - +
739A ASP* 1.3 78.2 - - - +
741A LEU* 1.3 60.2 + - - +
743A ASP* 3.6 14.4 - - - +
744A LYS* 3.2 29.8 + - - +
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Residues in contact with LEU 741 (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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706A PHE* 3.6 28.7 - - + +
709A ILE* 3.9 27.6 - - + -
710A SER* 5.6 6.7 - - - +
713A CYS* 4.6 4.9 - - - -
726A LEU* 4.6 8.7 - - + +
729A CYS* 3.7 20.9 - - + -
730A LEU* 4.3 14.6 - - + -
737A GLN 3.0 17.7 + - - +
738A CYS 3.6 4.5 - - - +
740A ASN* 1.3 75.6 - - - +
742A CYS* 1.3 60.1 + - - +
744A LYS* 3.2 8.1 + - + +
745A LEU* 3.0 52.8 + - + +
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Residues in contact with CYS 742 (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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730A LEU* 3.8 22.7 - - - -
738A CYS* 2.8 31.0 + - - +
741A LEU* 1.3 70.2 - - - +
743A ASP* 1.3 57.7 + - - +
745A LEU* 3.6 9.4 - - - +
746A LEU* 2.7 37.4 + - - +
765A ILE* 4.2 25.3 - - + +
777A TYR* 3.5 38.6 - - + -
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Residues in contact with ASP 743 (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 ASP* 2.8 21.8 + - - +
740A ASN* 3.6 16.7 - - - +
742A CYS* 1.3 76.2 - - - +
744A LYS* 1.3 63.7 + - + +
746A LEU* 3.2 7.4 + - - +
747A ALA* 3.1 21.8 + - - +
777A TYR* 2.7 30.0 + - - -
780A LYS* 5.1 4.2 + - - -
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Residues in contact with LYS 744 (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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710A SER* 3.2 55.4 + - - +
711A ASP* 4.4 5.1 + - - -
713A CYS* 4.2 15.5 - - + -
740A ASN* 3.2 19.3 - - - +
741A LEU* 3.2 9.5 + - + +
743A ASP* 1.3 76.1 - - + +
745A LEU* 1.3 62.9 + - - +
747A ALA* 3.2 20.2 + - - +
748A LEU* 3.5 16.2 + - + +
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Residues in contact with LEU 745 (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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713A CYS* 3.6 23.3 - - - -
717A ALA* 4.2 14.6 - - + -
726A LEU* 4.4 7.4 - - + -
730A LEU* 5.1 5.2 - - + -
741A LEU* 3.0 39.4 + - + +
742A CYS* 3.6 15.7 - - - +
744A LYS* 1.3 76.7 - - - +
746A LEU* 1.3 58.0 + - - +
748A LEU* 2.8 21.4 + - + +
749A VAL* 3.1 11.0 + - - +
752A LEU* 3.6 18.3 - - + +
761A VAL* 3.9 29.2 - - + -
765A ILE* 4.2 19.1 - - + -
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Residues in contact with LEU 746 (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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742A CYS 2.7 21.7 + - - +
743A ASP* 3.5 8.5 - - - +
745A LEU* 1.3 68.3 - - - +
747A ALA* 1.3 61.3 + - - +
748A LEU 3.0 6.3 + - - -
749A VAL* 3.4 22.3 + - + +
765A ILE* 5.8 1.5 - - + +
777A TYR* 4.4 13.9 - - + +
780A LYS* 3.8 34.1 - - + +
781A ILE* 3.9 40.2 - - + +
784A LEU* 4.0 21.6 - - + +
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Residues in contact with ALA 747 (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 ASP 3.1 11.9 + - - +
744A LYS* 3.2 14.1 + - - +
746A LEU* 1.3 75.3 - - - +
748A LEU* 1.3 66.0 + - + +
749A VAL 3.6 0.2 - - - -
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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