Contacts of the helix formed by residues 773 - 781 (chain D) in PDB entry 3LZB
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 773 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ITI 3.9 19.4 + - + +
771D PHE 4.1 0.9 - - - +
772D GLY* 1.3 74.6 - - - +
774D LEU* 1.3 66.0 + - - +
775D LEU* 3.2 11.1 + - - -
776D ASP* 3.6 39.3 + - - +
777D TYR* 3.3 19.8 + - - +
816D ALA 4.0 2.5 - - - +
817D ARG* 3.5 28.9 - - - +
819D VAL 3.4 8.5 - - - +
820D LEU* 4.3 2.9 - - + +
821D VAL* 4.0 0.4 - - - -
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Residues in contact with LEU 774 (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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773D CYS* 1.3 73.1 - - - +
775D LEU* 1.3 57.1 + - - +
777D TYR* 3.2 5.0 + - + +
778D VAL* 2.8 47.8 + - + +
793D TRP* 3.9 40.8 - - + -
797D ILE* 4.1 12.6 - - + -
816D ALA* 3.8 7.0 - - + +
819D VAL* 2.6 40.1 + - + +
821D VAL* 3.8 20.8 - - + +
827D VAL* 4.3 5.6 - - + -
883D LEU* 3.7 29.2 - - + -
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Residues in contact with LEU 775 (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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773D CYS* 3.2 8.3 - - - -
774D LEU* 1.3 78.7 - - - +
776D ASP* 1.3 60.5 + - - +
778D VAL* 3.2 6.6 - - + +
779D ARG* 2.8 65.5 + - - +
816D ALA* 3.4 25.0 + - + +
817D ARG* 4.0 20.0 - - + +
856D TRP* 6.1 1.3 - - + -
882D GLU* 4.0 24.7 - - + +
887D GLY* 3.5 32.1 - - - -
888D SER 5.4 0.2 - - - +
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Residues in contact with ASP 776 (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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1D ITI 3.7 27.7 - - - +
771D PHE 6.0 1.1 - - - +
773D CYS* 3.6 25.6 + - - +
774D LEU 3.4 0.2 - - - -
775D LEU* 1.3 80.6 - - - +
777D TYR* 1.3 68.4 + - - +
779D ARG* 3.0 19.8 + - - +
780D GLU* 2.8 40.5 + - - +
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Residues in contact with TYR 777 (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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771D PHE* 3.9 38.8 + + + +
773D CYS 3.3 11.5 + - - +
774D LEU* 3.2 12.9 + - + +
776D ASP* 1.3 79.7 - - - +
778D VAL* 1.3 66.0 + - - +
780D GLU* 3.2 8.9 + - - -
781D HIS* 2.8 66.4 + + - -
785D ILE* 4.5 4.5 - - + -
789D TYR* 5.6 1.2 - + - -
793D TRP* 3.8 35.7 - + - -
821D VAL* 4.1 13.9 - - + -
824D PRO* 3.4 30.0 - - + +
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Residues in contact with VAL 778 (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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774D LEU* 2.8 33.4 + - + +
775D LEU* 3.2 15.9 - - + +
777D TYR* 1.3 69.1 - - - +
779D ARG* 1.3 68.0 + - - +
781D HIS 3.3 2.8 - - - +
782D LYS* 3.1 21.8 + - - -
785D ILE* 3.6 13.0 - - + +
790D LEU* 5.3 0.2 - - + -
793D TRP* 3.7 29.4 - - + -
882D GLU 4.6 3.4 - - - +
883D LEU* 4.2 15.0 - - + +
886D PHE* 3.6 13.6 - - + +
887D GLY* 3.5 27.6 - - - +
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Residues in contact with ARG 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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775D LEU* 2.8 55.9 + - - +
776D ASP* 3.0 16.2 + - - +
778D VAL* 1.3 74.6 - - - +
780D GLU* 1.3 64.4 + - - +
782D LYS* 2.8 47.3 + - - +
886D PHE 3.9 7.0 - - - -
887D GLY* 2.5 47.6 + - - -
888D SER 4.7 4.4 + - - -
889D LYS* 4.9 13.9 - - - +
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Residues in contact with GLU 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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1D ITI 4.9 11.2 - - - +
776D ASP* 2.8 34.9 + - - +
777D TYR* 3.5 13.1 - - - +
779D ARG* 1.3 73.6 - - + +
781D HIS* 1.3 73.0 + - + +
782D LYS* 3.3 2.3 + - - +
784D ASN* 4.8 1.7 - - - +
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Residues in contact with HIS 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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771D PHE* 5.6 1.0 - + - -
777D TYR* 2.8 69.6 + + - -
778D VAL 3.3 3.8 - - - -
780D GLU* 1.3 91.4 + - + +
782D LYS* 1.3 65.3 + - - +
783D ASP 3.2 3.0 + - - -
784D ASN* 3.3 26.9 + - - +
785D ILE* 3.0 34.9 - - + +
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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
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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