Contacts of the helix formed by residues 858 - 865 (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 ALA 858 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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856D TRP 3.9 0.4 + - - -
857D MET* 1.3 76.3 - - - +
859D LEU* 1.3 61.6 + - - +
860D GLU* 3.3 24.9 - - - +
861D SER* 2.9 25.6 + - - -
862D ILE* 3.0 6.4 + - - +
871D SER* 4.0 17.4 + - - -
874D TRP* 3.4 40.3 - - + +
934D ARG* 4.0 0.7 - - - +
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Residues in contact with LEU 859 (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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857D MET 3.8 1.0 + - - -
858D ALA* 1.3 72.3 - - - +
860D GLU* 1.3 57.0 + - - +
862D ILE* 3.1 10.8 + - + +
863D LEU* 2.7 60.9 + - + +
874D TRP* 4.2 15.2 - - + -
900D SER* 3.8 31.6 - - - +
903D LEU* 4.1 17.0 - - + -
904D GLU* 4.3 19.7 - - + +
929D ILE* 3.1 42.0 - - + +
934D ARG* 5.4 0.9 - - - +
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Residues in contact with GLU 860 (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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858D ALA* 3.7 9.9 - - - +
859D LEU* 1.3 77.0 + - - +
861D SER* 1.3 59.8 + - - +
863D LEU* 4.3 5.2 - - - +
864D HIS* 2.7 36.3 + - + +
865D ARG 3.1 4.2 + - - -
866D ILE* 3.4 40.6 + - + +
868D THR* 5.0 1.9 + - - -
871D SER* 4.0 7.6 + - - -
929D ILE 4.5 3.7 - - - +
931D ALA* 3.9 10.9 - - + +
934D ARG* 2.8 45.2 + - - -
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Residues in contact with SER 861 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857D MET* 3.5 11.7 - - - +
858D ALA* 2.9 29.6 + - - -
860D GLU* 1.3 82.9 - - - +
862D ILE* 1.3 49.8 + - - +
865D ARG* 2.7 42.3 + - - -
866D ILE 3.3 13.7 + - - +
867D TYR* 2.8 38.8 - - - -
871D SER* 4.5 3.9 - - - -
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Residues in contact with ILE 862 (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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854D ILE* 3.8 40.4 - - + +
857D MET* 3.7 36.6 - - + +
858D ALA 3.0 11.0 + - - +
859D LEU* 3.4 16.6 - - + +
861D SER* 1.3 77.6 - - - +
863D LEU* 1.3 63.5 + - + +
865D ARG* 3.1 19.6 + - - +
899D ILE* 3.8 16.4 - - + -
900D SER* 4.4 19.1 - - - +
903D LEU* 4.5 5.2 - - + -
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Residues in contact with LEU 863 (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 LEU* 2.7 37.4 + - + +
860D GLU* 4.5 0.2 - - - -
862D ILE* 1.3 80.3 - - + +
864D HIS* 1.3 89.0 + - + +
865D ARG 3.8 0.2 - - - -
900D SER* 4.0 23.8 - - - +
904D GLU* 3.4 23.8 - - - +
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Residues in contact with HIS 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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860D GLU* 2.7 22.4 + - + +
863D LEU* 1.3 99.7 + - + +
865D ARG* 1.3 72.1 + - - +
866D ILE* 3.0 27.4 + - + +
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Residues in contact with ARG 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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812D ARG* 5.1 1.7 + - - -
852D VAL* 4.4 19.6 - - - +
854D ILE* 4.3 12.3 - - - +
857D MET* 3.8 11.0 - - - +
861D SER 2.7 35.1 + - - -
862D ILE* 3.1 27.3 + - - +
864D HIS* 1.3 74.9 - - - +
866D ILE* 1.3 60.0 + - - +
867D TYR* 3.4 37.3 + - + -
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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