Contacts of the helix formed by residues 712 - 718 (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 SER 712 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678A VAL* 3.4 31.8 - - - +
708A ALA 3.4 5.8 + - - -
709A ILE 3.1 5.5 + - - -
711A ASP* 1.3 81.2 + - - +
713A CYS* 1.3 60.7 + - - +
714A ILE* 3.4 0.9 - - - -
715A ASP* 2.8 35.4 - - - +
716A ILE* 3.0 19.2 + - - +
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Residues in contact with CYS 713 (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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709A ILE* 3.0 28.0 + - - +
710A SER 4.2 9.2 - - - +
711A ASP 3.6 2.2 - - - -
712A SER* 1.3 77.0 - - - +
714A ILE* 1.3 58.8 + - - +
716A ILE* 3.3 1.0 + - - +
717A ALA* 2.8 35.8 + - - +
726A LEU* 5.5 0.4 - - - -
741A LEU* 4.6 2.9 - - - -
744A LYS* 4.2 19.7 - - + -
745A LEU* 3.6 30.7 - - - -
748A LEU* 4.2 17.0 - - + -
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Residues in contact with ILE 714 (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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712A SER* 5.7 0.4 - - - -
713A CYS* 1.3 79.6 - - - +
715A ASP* 1.3 69.7 + - + +
717A ALA* 3.8 1.9 - - - +
718A THR* 2.7 56.6 + - + +
748A LEU* 4.1 26.4 - - + +
751A LYS* 4.2 34.8 - - + +
752A LEU* 4.3 8.5 - - + -
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Residues in contact with ASP 715 (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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678A VAL* 4.9 0.9 - - - +
682A LYS* 3.1 32.5 + - - +
712A SER* 2.8 36.5 - - - +
714A ILE* 1.3 86.4 - - + +
716A ILE* 1.3 57.3 + - - +
718A THR* 3.5 7.9 + - - -
719A HIS* 3.2 27.9 + - - +
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Residues in contact with ILE 716 (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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677A THR* 5.5 0.7 - - + -
678A VAL* 3.6 36.3 - - + -
681A SER* 4.2 17.7 - - - +
682A LYS* 4.4 17.9 - - + -
708A ALA* 5.9 0.2 - - + -
709A ILE* 4.0 28.9 - - + +
712A SER* 3.0 20.9 + - - +
713A CYS 4.3 0.4 - - - +
715A ASP* 1.3 77.1 - - - +
717A ALA* 1.3 63.7 + - - +
719A HIS* 3.4 5.5 + - - -
722A GLY* 3.0 32.9 - - - +
723A CYS 3.3 0.5 + - - -
726A LEU* 2.6 42.6 - - + -
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Residues in contact with ALA 717 (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* 2.8 23.0 + - - +
714A ILE* 3.8 1.1 - - - +
716A ILE* 1.3 76.6 - - - +
718A THR* 1.3 57.5 + - - +
719A HIS 3.3 3.2 + - - -
723A CYS* 3.5 17.5 - - - +
726A LEU* 2.9 24.9 - - + -
745A LEU* 4.2 12.1 - - + -
748A LEU* 6.0 0.2 - - + -
752A LEU* 3.7 23.6 - - + -
758A GLY* 3.6 14.0 + - - -
761A VAL* 3.9 4.6 - - + +
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Residues in contact with THR 718 (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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714A ILE* 2.7 34.7 + - + +
715A ASP* 3.5 10.2 + - - -
716A ILE 3.3 0.2 - - - -
717A ALA* 1.3 76.5 - - - +
719A HIS* 1.3 58.4 + - - +
751A LYS* 5.3 1.6 - - + +
752A LEU* 3.8 22.7 - - + -
755A ASP* 3.4 41.6 - - + +
757A PHE* 3.7 15.0 - - - -
758A GLY* 4.2 0.4 - - - +
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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