Contacts of the helix formed by residues 721 - 733 (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 HIS 721 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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681A SER 3.5 16.8 - - - +
682A LYS 3.5 19.1 - - - +
684A LEU* 3.4 46.6 - - + +
687A ASN* 3.9 24.0 + - + +
719A HIS* 3.0 15.4 + + + +
720A ARG* 1.3 100.4 + - + +
722A GLY* 1.3 69.7 + - - +
723A CYS 2.9 2.2 - - - -
724A CYS* 2.8 21.4 + - - +
725A VAL* 3.2 10.2 + - - +
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Residues in contact with GLY 722 (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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681A SER 3.4 15.8 + - - -
682A LYS* 5.1 0.2 - - - -
716A ILE* 3.0 28.3 - - - -
719A HIS* 3.4 12.6 + - - -
721A HIS* 1.3 77.1 - - - +
723A CYS* 1.3 54.4 + - - +
725A VAL* 3.3 4.9 + - - +
726A LEU* 2.7 38.1 + - - +
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Residues in contact with CYS 723 (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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716A ILE 3.3 3.7 + - - -
717A ALA 3.5 17.3 - - - +
719A HIS 3.0 13.9 + - - +
720A ARG 3.5 18.4 - - - -
721A HIS 2.9 0.8 - - - -
722A GLY* 1.3 79.8 - - - +
724A CYS* 1.3 69.9 + - - +
726A LEU* 3.6 3.3 - - - +
727A GLN* 3.2 36.6 + - - +
757A PHE* 3.9 29.6 - - + +
760A TYR* 5.1 5.6 - - - -
761A VAL* 4.0 10.1 - - + +
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Residues in contact with CYS 724 (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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687A ASN* 4.6 2.7 - - - +
691A GLN* 3.8 23.4 - - - +
720A ARG 4.1 14.4 - - - -
721A HIS* 2.8 11.5 + - - +
723A CYS* 1.3 84.7 - - - +
725A VAL* 1.3 58.3 - - - +
727A GLN* 3.3 13.6 + - - +
728A ARG* 3.1 29.7 + - - +
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Residues in contact with VAL 725 (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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681A SER* 3.9 16.4 - - - +
687A ASN* 3.6 42.0 - - + +
690A ILE* 3.8 26.0 - - + -
691A GLN* 3.8 11.9 - - + +
694A LEU* 4.0 3.3 - - + +
705A ILE* 4.4 5.2 - - + -
709A ILE* 4.1 18.2 - - + -
721A HIS 3.2 4.9 + - - +
722A GLY* 3.7 8.7 - - - +
724A CYS* 1.3 75.0 - - - +
726A LEU* 1.3 64.6 + - + +
728A ARG* 3.2 3.8 + - - +
729A CYS* 3.1 21.7 + - - -
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Residues in contact with LEU 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A ILE* 3.8 21.8 - - + -
713A CYS 4.7 0.7 - - - +
716A ILE* 2.6 34.3 - - + +
717A ALA* 2.9 44.0 - - + +
722A GLY* 2.7 24.4 + - - +
723A CYS 3.6 5.8 - - - +
725A VAL* 1.3 77.1 - - + +
727A GLN* 1.3 61.5 + - - +
729A CYS* 3.2 23.2 + - - +
730A LEU* 3.3 13.8 + - - +
741A LEU* 4.6 7.2 - - + +
745A LEU* 4.4 12.3 - - + -
761A VAL* 4.0 18.8 - - + -
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Residues in contact with GLN 727 (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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723A CYS* 3.2 21.2 + - - +
724A CYS* 3.7 14.6 - - - +
725A VAL 3.2 0.6 - - - -
726A LEU* 1.3 74.2 - - - +
728A ARG* 1.3 65.6 + - - +
730A LEU* 3.4 2.9 + - + +
731A ASP* 3.2 20.0 + - - +
760A TYR* 3.4 41.4 + - - +
761A VAL* 4.0 7.9 - - + +
764A TYR* 3.3 55.3 - - + +
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Residues in contact with ARG 728 (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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691A GLN* 2.9 51.7 + - + +
694A LEU* 3.7 11.9 - - + +
695A GLN* 3.2 31.5 + - - +
724A CYS* 3.1 14.8 + - - +
725A VAL 3.2 9.2 + - - +
727A GLN* 1.3 75.5 - - - +
729A CYS* 1.3 65.0 + - - +
731A ASP* 3.1 28.2 + - - +
732A HIS* 3.2 39.2 + - + +
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Residues in contact with CYS 729 (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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694A LEU* 4.0 17.5 - - - -
705A ILE* 4.1 9.4 - - - -
706A PHE* 3.4 31.4 - - + -
709A ILE* 3.6 28.5 - - - -
725A VAL 3.1 19.5 + - - -
726A LEU* 3.2 9.6 + - - +
728A ARG* 1.3 76.6 - - - +
730A LEU* 1.3 55.1 + - - +
733A GLY* 2.7 35.9 + - - -
738A CYS* 3.7 0.7 - - - -
741A LEU* 3.7 12.1 - - + -
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Residues in contact with LEU 730 (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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726A LEU* 3.3 13.1 + - + +
727A GLN* 3.8 7.9 - - - +
728A ARG 3.3 0.4 - - - -
729A CYS* 1.3 75.4 - - - +
731A ASP* 1.3 63.1 + - - +
732A HIS 3.4 0.2 - - - -
733A GLY 4.6 0.7 + - - +
738A CYS* 3.9 27.5 - - + -
741A LEU* 4.3 16.6 - - + -
742A CYS* 3.8 24.7 - - - -
745A LEU* 5.1 6.3 - - + -
761A VAL* 4.9 5.6 - - + +
764A TYR* 4.2 24.9 - - + +
765A ILE* 3.9 31.2 - - + +
768A LYS* 3.5 21.0 - - + +
772A LYS* 5.2 4.3 + - - -
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Residues in contact with ASP 731 (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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727A GLN* 3.2 12.6 + - - +
728A ARG* 3.1 29.1 + - - +
730A LEU* 1.3 80.6 - - - +
732A HIS* 1.3 77.3 + - + +
733A GLY 5.2 0.4 - - - +
764A TYR* 2.6 31.3 + - - -
768A LYS* 2.9 29.0 + - - +
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Residues in contact with HIS 732 (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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694A LEU* 3.5 30.0 + - + +
695A GLN* 3.7 31.9 + - + +
699A PRO* 4.8 3.6 - - - +
702A PHE* 3.6 18.3 - - + -
728A ARG* 3.2 39.8 + - + +
731A ASP* 1.3 90.3 + - + +
733A GLY* 1.3 69.2 + - - +
734A THR 3.5 1.4 + - - -
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Residues in contact with GLY 733 (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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702A PHE* 4.3 1.9 - - - -
706A PHE* 3.7 12.1 - - - -
729A CYS 2.7 26.7 + - - -
730A LEU 5.1 0.7 - - - +
731A ASP 3.7 0.7 - - - +
732A HIS* 1.3 76.2 - - - +
734A THR* 1.3 67.5 + - - -
735A THR 3.8 0.3 + - - -
737A GLN* 3.6 8.5 - - - -
738A CYS* 3.3 15.8 - - - -
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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