Contacts of the helix formed by residues 773 - 781 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ITI 3.6 19.5 - - + +
771A PHE 3.7 1.9 + - - +
772A GLY* 1.3 74.7 - - - -
774A LEU* 1.3 66.4 + - - +
775A LEU* 3.2 10.3 + - - -
776A ASP* 3.6 39.0 + - - +
777A TYR* 3.2 19.8 + - - +
816A ALA 4.0 0.4 - - - +
817A ARG* 3.5 31.0 - - - +
819A VAL 3.3 9.2 - - - +
820A LEU* 4.3 2.7 - - + +
821A VAL* 3.9 0.7 - - - -
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Residues in contact with LEU 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A CYS* 1.3 70.3 - - - +
775A LEU* 1.3 60.3 + - - +
777A TYR* 3.2 3.5 + - + -
778A VAL* 2.8 47.8 + - + +
793A TRP* 3.9 41.1 - - + -
797A ILE* 4.1 12.3 - - + -
816A ALA* 3.7 7.4 + - + +
819A VAL* 2.6 39.6 + - + +
821A VAL* 3.7 20.8 - - + +
827A VAL* 4.3 5.2 - - + -
883A LEU* 3.8 28.7 - - + -
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Residues in contact with LEU 775 (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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773A CYS* 3.2 8.9 - - - -
774A LEU* 1.3 79.2 - - - +
776A ASP* 1.3 59.8 + - - +
778A VAL* 3.2 6.7 - - + +
779A ARG* 2.8 65.3 + - - +
816A ALA* 3.7 19.9 + - + +
817A ARG* 4.0 24.9 - - + +
856A TRP* 6.1 1.3 - - + -
882A GLU* 4.0 24.2 - - + +
887A GLY* 3.5 32.1 - - - +
888A SER 5.5 0.4 - - - +
938B ARG* 5.6 2.2 - - - +
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Residues in contact with ASP 776 (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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1A ITI 4.7 19.2 - - - +
771A PHE 6.1 0.4 - - - +
773A CYS* 3.6 25.1 + - - +
775A LEU* 1.3 80.3 - - - +
777A TYR* 1.3 61.5 + - - +
779A ARG* 3.0 16.8 + - - +
780A GLU* 2.7 47.7 + - - +
938B ARG* 3.9 35.8 + - - +
942B ILE* 4.6 8.4 - - + +
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Residues in contact with TYR 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A PHE* 3.9 36.9 + + + +
773A CYS 3.2 12.0 + - - +
774A LEU* 3.2 15.1 + - + +
776A ASP* 1.3 78.7 - - - +
778A VAL* 1.3 59.4 + - - +
780A GLU* 3.2 10.9 + - - +
781A HIS* 3.0 71.6 + + - -
785A ILE* 4.4 5.4 - - + -
789A TYR* 5.7 1.5 - + - -
793A TRP* 3.8 36.1 - + - -
821A VAL* 4.2 12.6 - - + -
824A PRO* 3.4 29.6 - - + +
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Residues in contact with VAL 778 (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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774A LEU* 2.8 32.1 + - + +
775A LEU* 3.2 15.9 - - + +
777A TYR* 1.3 69.8 - - - +
779A ARG* 1.3 67.8 + - - +
781A HIS 3.3 1.9 - - - +
782A LYS* 3.0 22.3 + - - -
785A ILE* 3.6 13.0 - - + +
793A TRP* 3.7 30.7 - - + -
882A GLU 4.6 3.6 - - - +
883A LEU* 4.2 15.7 - - + +
886A PHE* 3.6 12.6 - - + +
887A GLY* 3.5 28.0 - - - +
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Residues in contact with ARG 779 (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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775A LEU* 2.8 54.5 + - - +
776A ASP* 3.0 11.1 + - - +
778A VAL* 1.3 76.0 - - - +
780A GLU* 1.3 59.0 + - - +
782A LYS* 2.9 37.2 - - - +
886A PHE 3.9 10.3 - - - +
887A GLY* 2.4 44.6 + - - -
888A SER 4.7 4.8 + - - -
889A LYS* 5.0 12.7 - - - +
938B ARG* 3.7 23.0 - - - +
939B GLU* 4.7 18.8 + - - +
942B ILE* 4.3 20.0 - - + +
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Residues in contact with GLU 780 (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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1A ITI 4.9 12.9 - - - +
776A ASP* 2.7 32.2 + - - +
777A TYR* 3.5 14.1 - - - +
779A ARG* 1.3 72.0 - - - +
781A HIS* 1.3 76.9 + - + +
782A LYS* 3.3 5.5 + - - +
784A ASN* 4.7 2.4 + - - +
942B ILE* 4.0 32.0 - - + +
949B ARG* 4.9 14.0 + - - +
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Residues in contact with HIS 781 (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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771A PHE* 5.6 0.6 - - - -
777A TYR* 3.0 67.7 + + - -
778A VAL 3.3 4.7 - - - -
779A ARG 3.1 0.2 - - - -
780A GLU* 1.3 92.3 + - + +
782A LYS* 1.3 63.1 + - - +
783A ASP 3.1 3.1 + - - -
784A ASN* 3.2 26.8 + - - +
785A ILE* 3.1 34.0 - - + +
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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