Contacts of the helix formed by residues 778 - 786 (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 CYS 778 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D FMM 4.2 18.6 - - + +
776D HIS 4.2 0.3 - - - +
777D GLY* 1.3 74.4 - - - -
779D LEU* 1.3 66.4 + - - +
780D LEU* 3.1 10.0 + - - -
781D GLU* 3.3 38.3 + - - +
782D TYR* 3.2 17.8 + - - +
821D ALA 4.1 0.4 - - - +
822D ARG* 3.4 32.1 - - - +
824D VAL 3.4 7.4 - - - +
825D LEU* 3.7 11.2 - - + +
826D VAL* 4.2 0.4 - - - -
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Residues in contact with LEU 779 (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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777D GLY 3.8 1.4 + - - -
778D CYS* 1.3 71.9 - - - +
780D LEU* 1.3 56.1 + - - +
782D TYR* 3.8 3.4 - - + -
783D VAL* 3.0 37.3 + - + +
798D TRP* 3.7 46.9 - - + -
802D ILE* 4.4 3.4 - - + -
821D ALA* 3.9 6.5 - - - +
824D VAL* 2.7 43.2 + - + +
826D VAL* 3.6 23.8 - - + +
832D VAL* 3.8 14.4 - - + -
888D LEU* 3.7 28.7 - - + -
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Residues in contact with LEU 780 (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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778D CYS* 3.1 4.5 - - - -
779D LEU* 1.3 77.0 - - - +
781D GLU* 1.3 74.5 + - - +
783D VAL* 3.3 19.7 - - - +
784D HIS* 3.2 41.0 + - + +
821D ALA* 3.3 21.2 + - + +
822D ARG* 3.7 33.0 - - + +
861D TRP* 5.4 2.9 - - + -
887D GLU* 3.5 24.7 - - - +
892D GLY* 4.4 8.0 - - - +
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Residues in contact with GLU 781 (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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91D FMM 6.1 1.1 - - + -
776D HIS 5.9 0.9 - - - +
778D CYS* 3.3 27.0 + - - +
780D LEU* 1.3 88.8 - - - +
782D TYR* 1.3 59.6 + - - +
784D HIS* 3.2 15.2 + - - +
785D GLU* 3.0 32.8 + - - +
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Residues in contact with TYR 782 (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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776D HIS* 3.7 48.0 + + + +
778D CYS 3.2 16.2 + - - +
779D LEU* 3.8 7.0 - - + +
780D LEU 3.3 0.4 - - - -
781D GLU* 1.3 78.4 - - - +
783D VAL* 1.3 59.1 + - - +
785D GLU* 3.2 3.5 + - - -
786D HIS* 3.0 70.3 + + + +
790D ILE* 4.4 7.9 - - + -
794D LEU* 5.7 2.4 - - + +
798D TRP* 4.0 34.3 - + - -
826D VAL* 3.9 16.4 - - + -
829D PRO* 3.4 32.4 - - + +
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Residues in contact with VAL 783 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779D LEU* 3.0 26.9 + - + +
780D LEU* 3.3 14.8 - - - +
782D TYR* 1.3 70.6 - - - +
784D HIS* 1.3 64.5 + - - +
787D LYS* 3.4 24.6 + - - +
790D ILE* 3.8 11.2 - - + -
795D LEU* 5.3 1.6 - - + -
798D TRP* 3.4 35.7 - - + -
821D ALA* 6.1 0.2 - - + -
887D GLU 4.8 2.2 - - - +
888D LEU* 4.4 17.0 - - + +
891D PHE* 3.9 15.8 - - + +
892D GLY* 3.5 24.7 - - - +
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Residues in contact with HIS 784 (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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780D LEU* 3.2 37.3 + - + +
781D GLU* 3.2 23.6 + - - +
783D VAL* 1.3 80.5 - - - +
785D GLU* 1.3 58.6 + - - +
787D LYS* 3.2 36.2 - - - +
891D PHE 3.5 17.5 - - - -
892D GLY* 2.8 24.2 + - - -
894D LYS* 5.4 10.5 + - + -
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Residues in contact with GLU 785 (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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781D GLU* 3.0 18.4 + - - +
782D TYR* 3.2 4.6 + - - +
784D HIS* 1.3 79.3 - - - +
786D HIS* 1.3 82.1 + - + +
787D LYS* 3.4 3.8 + - - +
788D ASP* 6.2 0.2 - - - -
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Residues in contact with HIS 786 (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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776D HIS* 5.6 1.4 + - - -
782D TYR* 3.0 66.2 + + + +
785D GLU* 1.3 104.6 + - + +
787D LYS* 1.3 64.3 + - - +
788D ASP 3.2 3.4 - - - -
789D ASN* 2.9 30.9 + - + +
790D ILE* 3.2 27.5 - - + +
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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