Contacts of the helix formed by residues 778 - 786 (chain B) 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 CYS 778 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B FMM 4.2 18.8 - - + -
776B HIS 4.6 0.3 - - - +
777B GLY* 1.3 76.3 - - - -
779B LEU* 1.3 65.6 + - - +
780B LEU* 4.2 11.0 - - - -
781B GLU* 3.3 34.0 + - - +
782B TYR* 3.1 19.2 + - - +
822B ARG* 3.5 31.2 - - - +
824B VAL 3.5 6.7 - - - +
825B LEU* 3.8 11.0 - - + +
826B VAL* 4.1 0.9 - - - -
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Residues in contact with LEU 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B CYS* 1.3 72.3 - - - +
780B LEU* 1.3 62.3 + - - +
782B TYR* 3.3 3.5 + - + -
783B VAL* 3.0 39.7 + - + +
798B TRP* 4.0 26.7 - - + -
802B ILE* 4.2 7.2 - - + -
821B ALA* 3.6 7.0 - - - +
824B VAL* 2.7 42.2 + - + +
826B VAL* 3.8 22.9 - - + +
832B VAL* 3.9 17.3 - - + -
888B LEU* 3.7 36.3 - - + -
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Residues in contact with LEU 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B CYS* 3.2 5.1 - - - -
779B LEU* 1.3 77.2 - - - +
781B GLU* 1.3 61.3 + - - +
783B VAL* 3.3 18.7 - - + +
784B HIS* 3.6 9.0 + - - +
821B ALA* 3.2 27.7 + - + -
822B ARG* 3.9 22.4 - - + +
861B TRP* 6.3 0.7 - - + -
887B GLU* 3.6 24.7 - - + +
892B GLY* 4.1 28.0 - - - +
893B GLY 5.4 0.7 - - - +
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Residues in contact with GLU 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B HIS 5.9 1.8 - - - +
777B GLY* 6.1 0.4 - - - -
778B CYS* 3.3 24.6 + - - +
780B LEU* 1.3 77.5 - - - +
782B TYR* 1.3 65.1 + - - +
784B HIS* 3.3 7.8 + - - +
785B GLU* 3.1 31.9 + - + +
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Residues in contact with TYR 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776B HIS* 4.0 44.0 + + + +
778B CYS 3.1 13.4 + - - +
779B LEU* 3.3 11.0 + - + +
781B GLU* 1.3 77.5 - - - +
783B VAL* 1.3 56.9 - - - +
785B GLU* 3.2 4.0 + - - -
786B HIS* 3.0 71.2 + + + +
790B ILE* 4.3 7.0 - - + -
794B LEU* 5.8 1.6 - - + -
798B TRP* 4.2 32.8 - + - -
826B VAL* 4.0 22.9 - - + -
829B PRO* 3.4 29.9 - - + +
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Residues in contact with VAL 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B LEU* 3.0 29.0 + - + +
780B LEU* 3.3 20.4 - - + +
782B TYR* 1.3 74.8 - - - +
784B HIS* 1.3 60.2 + - - +
786B HIS 4.2 0.4 - - - -
787B LYS* 3.5 20.3 + - - -
790B ILE* 3.8 10.3 - - + -
795B LEU* 5.2 0.9 - - + -
798B TRP* 3.5 33.4 - - + -
821B ALA* 6.1 0.2 - - + -
887B GLU 4.5 4.3 - - - +
888B LEU* 4.5 14.8 - - + +
891B PHE* 3.6 21.3 - - + +
892B GLY* 3.6 24.9 - - - +
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Residues in contact with HIS 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B LEU 3.9 8.5 - - - +
781B GLU* 3.3 10.4 + - - +
782B TYR 3.2 0.4 - - - -
783B VAL* 1.3 81.6 - - - +
785B GLU* 1.3 64.7 + - - +
786B HIS 3.6 0.2 + - - -
787B LYS* 3.7 26.6 - - + +
891B PHE 3.6 17.4 + - - +
892B GLY* 4.7 9.6 + - - -
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Residues in contact with GLU 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B GLU* 3.1 24.9 + - + +
782B TYR* 3.9 3.8 - - - +
784B HIS* 1.3 79.8 - - - +
786B HIS* 1.3 82.2 + - + +
787B LYS 3.5 1.0 + - - -
788B ASP* 4.3 6.9 - - - +
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Residues in contact with HIS 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B TYR* 3.0 63.1 + + + +
785B GLU* 1.3 102.4 + - + +
787B LYS* 1.3 54.8 + - - +
788B ASP* 3.2 4.5 - - - -
789B ASN* 2.7 37.8 + - + +
790B ILE* 3.2 27.9 + - + +
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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
------------------------------------------------------------
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