Contacts of the helix formed by residues 863 - 869 (chain D) in PDB entry 3BBT
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 ALA 863 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861D TRP 4.0 0.4 + - - -
862D MET* 1.3 77.4 - - - +
864D LEU* 1.3 66.5 + - - +
865D GLU* 3.3 21.3 - - - +
866D CYS* 3.1 17.5 + - - +
867D ILE* 3.4 12.1 + - - +
876D SER* 4.0 15.6 + - - +
879D TRP* 3.5 31.0 - - + +
939D ARG* 3.8 11.9 - - - +
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Residues in contact with LEU 864 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862D MET 4.0 0.6 + - - -
863D ALA* 1.3 73.0 - - - +
865D GLU* 1.3 64.4 + - - +
867D ILE* 3.3 16.2 + - + +
868D HIS* 3.2 44.2 - - + +
879D TRP* 4.2 19.0 - - + -
905D PRO* 3.6 27.4 - - + +
908D LEU* 3.9 23.1 - - + -
909D GLU* 4.0 26.5 - - + +
913D ARG* 6.4 0.2 - - - +
934D ILE* 4.3 29.2 - - + +
939D ARG* 5.3 0.9 - - - +
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Residues in contact with GLU 865 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863D ALA* 3.5 5.0 - - - +
864D LEU* 1.3 73.8 + - - +
866D CYS* 1.3 58.6 + - - +
867D ILE 3.5 0.2 - - - -
868D HIS* 5.2 0.2 - - - -
869D TYR* 3.2 29.4 + - + +
870D ARG 3.1 17.3 + - - -
871D LYS* 3.3 32.5 + - + +
873D THR* 4.4 3.8 + - - -
876D SER* 3.4 12.6 + - - -
934D ILE 4.5 4.9 - - - +
936D ALA* 3.5 16.9 - - - +
939D ARG* 2.9 42.9 + - - -
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Residues in contact with CYS 866 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862D MET* 3.6 14.8 - - + +
863D ALA* 3.1 20.5 + - - +
865D GLU* 1.3 76.9 - - - +
867D ILE* 1.3 65.2 + - - +
868D HIS 3.3 0.4 - - - -
870D ARG* 3.2 33.2 + - - +
871D LYS 3.4 11.4 - - - -
872D PHE* 3.6 31.6 - - + -
876D SER* 3.1 37.2 - - - -
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Residues in contact with ILE 867 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859D ILE* 4.1 31.2 - - + +
862D MET* 3.9 33.2 - - + +
863D ALA 3.4 18.8 - - - +
864D LEU* 3.3 13.9 + - + +
866D CYS* 1.3 79.4 - - - +
868D HIS* 1.3 65.5 + - + +
870D ARG* 5.3 2.3 - - - +
904D ILE* 5.7 0.9 - - + -
905D PRO* 4.6 24.7 - - + -
908D LEU* 4.4 14.6 - - + -
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Residues in contact with HIS 868 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864D LEU* 3.2 48.3 + - + +
867D ILE* 1.3 84.6 - - + +
869D TYR* 1.3 93.7 + + + +
870D ARG* 3.7 1.4 - - - +
905D PRO* 4.2 18.5 - - + +
909D GLU* 4.3 15.4 + - - -
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Residues in contact with TYR 869 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865D GLU* 3.2 24.0 + - + +
868D HIS* 1.3 100.1 - + + +
870D ARG* 1.3 72.6 + - - +
871D LYS* 3.2 7.8 + - + +
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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