Contacts of the helix formed by residues 148 - 155 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D TYR* 3.2 8.5 - - - -
115D GLN* 3.3 11.0 - - - +
117D VAL* 4.0 19.7 - - + -
143D PHE* 4.4 4.3 - - + -
144D THR 3.9 3.1 - - - +
145D LEU* 2.6 28.4 + - + +
147D ASP* 1.3 81.2 - - - +
149D LEU* 1.3 65.3 + - - +
150D LEU* 4.0 3.6 + - - +
151D GLY 3.4 8.3 + - - -
152D TYR* 2.9 22.9 + - - +
192D VAL* 5.4 0.3 - - - +
196D PHE* 3.8 30.5 - - + -
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Residues in contact with LEU 149 (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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67D CYS* 4.3 9.6 - - - +
70D TYR* 3.1 42.4 - - + -
71D THR* 5.1 2.5 - - + -
77D MET* 3.8 21.8 - - + -
80D VAL* 4.4 22.9 - - + -
85D VAL* 5.1 4.0 - - + -
113D GLY* 4.5 17.7 - - - +
115D GLN* 2.9 20.3 - - - +
148D THR* 1.3 70.1 - - - +
150D LEU* 1.3 65.6 + - + +
152D TYR* 3.4 1.9 - - - +
153D LEU* 3.0 55.7 + - + +
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Residues in contact with LEU 150 (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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85D VAL* 5.4 0.9 - - + -
109D LEU* 3.7 40.6 - - + +
110D MET* 4.1 33.4 - - + +
113D GLY* 4.0 33.2 - - - +
115D GLN* 4.7 1.2 - - - +
148D THR* 3.4 4.0 + - - +
149D LEU* 1.3 81.9 - - + +
151D GLY* 1.3 61.5 + - - +
153D LEU* 3.4 22.4 + - + +
154D ALA 3.5 8.5 + - - -
188D PHE* 3.5 20.7 - - + -
192D VAL* 4.4 16.4 - - + -
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Residues in contact with GLY 151 (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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145D LEU* 3.3 21.8 - - - +
146D GLU* 3.9 7.2 - - - -
148D THR* 3.2 8.5 + - - -
150D LEU* 1.3 78.7 - - - +
152D TYR* 1.3 57.3 + - - +
154D ALA 3.4 0.7 + - - -
155D ASP* 3.0 28.6 + - - +
188D PHE* 5.2 0.2 - - - -
189D TRP* 3.3 27.5 - - - -
192D VAL* 5.0 0.4 - - - +
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Residues in contact with TYR 152 (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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66D ARG* 3.3 62.5 + - + +
69D LYS* 4.3 15.1 - - + +
70D TYR* 3.6 35.7 - + + -
73D ILE* 5.1 7.8 - - + +
146D GLU 3.3 16.1 + - - +
147D ASP* 5.8 0.7 - - - -
148D THR 2.9 17.7 + - - +
149D LEU 3.4 4.0 - - - +
151D GLY* 1.3 74.2 - - - +
153D LEU* 1.3 66.7 + - + +
154D ALA 3.3 0.7 + - - -
155D ASP* 3.5 9.1 + - + +
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Residues in contact with LEU 153 (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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63D VAL* 3.7 21.9 - - + +
66D ARG* 3.1 26.3 + - + +
67D CYS* 3.3 43.5 - - + +
85D VAL* 3.6 29.4 - - + -
89D PHE* 4.4 15.5 - - + -
149D LEU* 3.0 37.7 + - + +
150D LEU* 3.7 23.6 - - + +
151D GLY 3.3 0.2 - - - -
152D TYR* 1.3 78.1 - - + +
154D ALA* 1.3 56.7 + - - +
157D LEU* 3.3 10.7 - - - +
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Residues in contact with ALA 154 (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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66D ARG* 3.9 0.7 - - - -
89D PHE* 4.2 7.4 - - + -
150D LEU 3.5 1.6 + - - +
151D GLY 3.4 1.8 + - - -
152D TYR 3.2 0.4 - - - -
153D LEU* 1.3 77.9 - - - +
155D ASP* 1.3 66.6 + - - +
156D ASP 3.3 0.5 + - - -
157D LEU* 3.1 24.9 + - - +
159D TRP* 3.6 21.3 - - + -
188D PHE* 3.5 35.2 - - + -
189D TRP* 3.6 13.2 + - + -
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Residues in contact with ASP 155 (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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66D ARG* 2.9 28.8 + - - +
129D LYS* 2.8 29.3 + - - +
133D HIS* 3.7 19.2 + - - -
146D GLU* 3.9 20.5 - - + +
151D GLY 3.0 17.3 + - - +
152D TYR* 3.5 14.2 + - + +
154D ALA* 1.3 75.9 - - - +
156D ASP* 1.3 74.7 + - - +
157D LEU 3.1 3.5 + - - -
189D TRP* 4.0 7.5 - - - -
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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