Contacts of the helix formed by residues 148 - 155 (chain C) in PDB entry 1ZVM
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 THR 148 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C TYR* 3.4 5.6 - - - -
115C GLN* 3.6 12.6 - - + +
117C VAL* 4.0 18.4 - - + -
143C PHE* 5.5 2.0 - - + -
144C THR 4.1 2.0 - - - +
145C LEU* 2.6 28.0 + - + +
147C ASP* 1.3 81.2 - - + +
149C LEU* 1.3 66.4 + - - +
150C LEU* 3.8 6.0 + - - +
151C GLY* 3.1 12.0 + - - -
152C TYR* 2.9 23.0 + - - +
192C VAL* 5.2 0.2 - - - +
196C PHE* 3.8 31.9 - - + -
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C CYS* 4.2 12.1 - - - +
70C TYR* 3.3 43.0 - - + -
71C THR* 4.9 4.3 - - + -
77C MET* 3.8 22.2 - - + -
80C VAL* 4.3 22.7 - - + -
85C VAL* 5.2 3.1 - - + -
113C GLY* 4.4 15.7 - - - +
115C GLN* 2.7 22.2 - - - +
148C THR* 1.3 70.6 - - - +
150C LEU* 1.3 61.1 + - + +
152C TYR* 3.5 1.4 - - - +
153C LEU* 2.9 58.6 + - + +
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C VAL* 5.5 0.4 - - + -
109C LEU* 3.8 38.8 - - + -
110C MET* 4.2 27.1 - - + +
113C GLY* 3.5 39.3 - - - +
114C THR* 5.3 0.4 - - - -
115C GLN* 4.6 0.6 - - - +
148C THR* 3.3 4.6 + - - +
149C LEU* 1.3 80.9 - - + +
151C GLY* 1.3 61.5 + - - +
153C LEU* 3.5 14.6 + - + +
154C ALA* 3.5 15.2 + - - +
188C PHE* 3.5 21.8 - - + -
192C VAL* 4.3 18.8 - - + -
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Residues in contact with GLY 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LEU* 3.3 23.5 - - - +
146C GLU* 3.7 10.4 - - - -
148C THR* 3.1 10.7 + - - -
150C LEU* 1.3 74.8 - - - +
152C TYR* 1.3 59.9 + - - +
154C ALA 3.4 1.0 + - - -
155C ASP* 3.0 32.7 + - - +
189C TRP* 3.6 18.6 - - - -
192C VAL* 5.5 0.4 - - - -
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Residues in contact with TYR 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ARG* 3.3 70.3 + - + +
69C LYS* 4.5 15.0 - - + +
70C TYR* 3.6 34.8 - + + -
73C ILE* 5.9 3.0 - - + +
146C GLU 3.5 16.6 + - - +
148C THR 2.9 17.2 + - - +
149C LEU 3.5 3.8 - - - +
151C GLY* 1.3 77.1 - - - +
153C LEU* 1.3 63.6 + - + +
154C ALA 3.3 0.3 + - - -
155C ASP* 3.7 7.7 + - + +
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C VAL* 3.4 30.9 - - + +
66C ARG* 3.0 27.3 + - + +
67C CYS* 3.3 40.6 - - + +
85C VAL* 3.7 28.3 - - + -
89C PHE* 4.7 10.8 - - + -
149C LEU* 2.9 36.0 + - + +
150C LEU* 3.7 21.8 - - + +
151C GLY 3.3 0.4 - - - -
152C TYR* 1.3 77.6 - - + +
154C ALA* 1.3 57.4 + - - +
157C LEU* 3.1 11.1 - - - +
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Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C VAL* 5.9 0.2 - - - -
66C ARG* 3.9 0.2 - - - -
89C PHE* 4.5 7.4 - - + -
150C LEU 3.5 1.9 + - - +
151C GLY 3.4 1.8 + - - -
152C TYR 3.3 0.4 - - - -
153C LEU* 1.3 76.6 - - - +
155C ASP* 1.3 69.2 + - - +
156C ASP 3.3 0.7 + - - -
157C LEU* 3.0 25.3 + - - +
159C TRP* 3.8 19.0 - - + -
188C PHE* 3.4 36.3 - - + -
189C TRP* 3.6 12.8 + - + -
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Residues in contact with ASP 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ARG* 2.9 27.4 + - - +
129C LYS* 2.8 32.9 + - - +
133C HIS* 3.7 20.3 + - - -
146C GLU* 3.8 18.5 - - + +
151C GLY 3.0 18.6 + - - +
152C TYR* 4.0 10.3 - - + +
153C LEU 3.7 1.8 - - - -
154C ALA* 1.3 74.2 - - - +
156C ASP* 1.3 72.7 + - - +
157C LEU* 3.1 3.5 + - - +
189C TRP* 3.7 8.9 - - - -
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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