Contacts of the helix formed by residues 143 - 155 (chain D) in PDB entry 1PZN
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 GLY 143 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D GLY 2.9 7.9 + - - -
142D SER* 1.3 80.6 - - - +
144D LYS* 1.3 62.5 + - - +
145D THR 3.2 0.9 - - - -
146D GLN* 3.2 10.5 + - - +
147D LEU* 3.1 21.0 + - - +
315D LEU* 4.6 2.9 - - - +
323D ARG* 4.6 0.9 - - - -
340D PHE* 5.5 2.1 - - - -
342D ILE* 4.1 21.5 - - - +
347D ILE* 4.9 1.9 - - - +
353D SO4 2.9 11.6 + - - -
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Residues in contact with LYS 144 (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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136D VAL* 3.5 42.6 - - + +
137D PHE* 4.1 0.9 - - - -
138D GLY 3.1 27.2 + - - +
139D GLU 3.5 6.3 + - - -
140D PHE* 4.4 1.2 - - - +
142D SER* 3.4 4.5 + - - +
143D GLY* 1.3 76.4 - - - +
145D THR* 1.3 57.3 + - - +
146D GLN 3.3 0.2 - - - -
147D LEU* 3.6 9.5 - - - +
148D ALA* 3.2 22.0 + - - +
238D ASP* 5.7 0.2 - - - -
280D PHE* 4.0 2.3 - - - -
282D THR* 3.8 20.4 - - + +
283D ASN 3.4 33.0 - - - +
284D GLN* 3.6 12.3 - - - +
315D LEU* 4.2 6.3 - - + -
353D SO4 2.6 33.1 + - - +
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Residues in contact with THR 145 (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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144D LYS* 1.3 72.0 - - - +
146D GLN* 1.3 62.9 + - - +
148D ALA* 3.3 6.2 + - - +
149D HIS* 2.7 53.6 + - + -
170D TRP* 4.8 2.0 - - + -
174D GLU* 5.4 1.9 + - - -
176D THR* 4.0 21.8 + - - +
238D ASP* 3.1 33.5 + - - +
353D SO4 2.8 34.4 + - - -
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Residues in contact with GLN 146 (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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143D GLY* 3.2 14.3 + - - +
145D THR* 1.3 75.5 - - - +
147D LEU* 1.3 58.2 + - - +
148D ALA 3.0 1.3 - - - -
149D HIS* 2.7 29.6 + - - +
150D THR* 2.8 17.7 + - - +
181D ARG* 3.2 46.5 + - - +
185D ILE* 5.3 1.0 - - - +
342D ILE* 3.6 35.4 - - + +
346D GLY* 5.4 1.1 - - - -
347D ILE* 4.5 4.7 - - + -
353D SO4 5.2 0.9 - - - +
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Residues in contact with LEU 147 (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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115D THR* 4.3 13.5 - - + -
120D LEU* 5.1 13.5 - - + -
128D ILE* 5.7 0.4 - - + -
136D VAL* 4.2 5.8 - - + -
143D GLY 3.1 8.4 + - - +
144D LYS 3.6 9.2 - - - +
146D GLN* 1.3 77.5 - - - +
148D ALA* 1.3 62.2 + - - +
150D THR* 3.7 0.7 - - - -
151D LEU* 3.0 51.3 + - + +
280D PHE* 3.7 19.1 - - + -
313D VAL* 6.3 1.6 - - + -
315D LEU* 4.0 25.6 - - + -
340D PHE* 5.5 2.5 - - + -
347D ILE* 3.2 30.6 - - + +
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Residues in contact with ALA 148 (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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144D LYS 3.2 12.0 + - - +
145D THR* 3.3 13.2 - - - +
146D GLN 3.0 0.8 - - - -
147D LEU* 1.3 80.0 - - - +
149D HIS* 1.3 62.1 + - - +
151D LEU* 3.3 3.4 + - - +
152D ALA* 3.0 17.7 + - - +
170D TRP* 3.7 20.0 - - + -
236D ILE* 3.4 25.8 - - + +
238D ASP* 4.8 2.9 - - - +
280D PHE* 3.8 17.9 - - + -
282D THR* 5.1 2.0 - - + -
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Residues in contact with HIS 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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145D THR* 2.7 38.2 + - + -
146D GLN* 2.7 20.7 + - - +
148D ALA* 1.3 68.9 - - - +
150D THR* 1.3 66.0 + - - +
152D ALA* 2.9 17.1 + - - +
153D VAL* 3.3 10.0 + - - +
170D TRP* 3.7 18.6 - + - -
176D THR 3.5 21.3 - - - -
177D PHE* 3.6 10.8 - + - -
178D ARG* 3.2 38.9 + - + +
181D ARG* 4.2 21.5 - - + -
182D ILE* 4.2 11.0 - - + +
185D ILE* 4.5 9.6 - - + -
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Residues in contact with THR 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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115D THR 2.9 28.7 - - - +
116D GLY* 4.5 2.2 - - - -
146D GLN 2.8 15.6 + - - -
147D LEU* 3.7 7.6 - - - -
149D HIS* 1.3 72.4 - - - +
151D LEU* 1.3 54.4 + - - +
153D VAL* 2.6 30.7 + - - +
154D MSE 3.1 26.7 + - + -
185D ILE* 4.4 8.7 - - + +
345D LYS 3.9 15.0 - - - +
346D GLY* 3.3 8.7 - - - -
347D ILE* 3.0 28.1 + - - +
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Residues in contact with LEU 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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113D ILE* 4.3 6.1 - - + +
114D SER 3.3 23.6 - - - +
115D THR* 3.5 21.1 - - + +
128D ILE* 4.0 21.8 - - + -
147D LEU* 3.0 35.8 + - + +
148D ALA* 3.5 4.9 - - - +
150D THR* 1.3 79.5 - - - +
152D ALA* 1.3 61.6 + - - +
153D VAL 3.0 0.9 + - - -
154D MSE 4.1 4.3 - - - -
155D VAL* 3.2 18.7 + - - +
234D LEU* 3.1 23.2 - - + +
236D ILE* 5.1 0.2 - - + -
280D PHE* 3.8 35.9 - - + -
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Residues in contact with ALA 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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148D ALA 3.0 11.8 + - - +
149D HIS* 2.9 13.9 + - - +
151D LEU* 1.3 76.9 - - - +
153D VAL* 1.3 59.7 + - + +
155D VAL* 3.8 3.2 - - - +
156D GLN* 3.4 26.2 + - - +
168D VAL* 3.9 9.9 - - + +
170D TRP* 3.7 23.1 - - + -
182D ILE* 5.1 2.0 - - + -
200D ILE* 3.7 24.0 - - + +
234D LEU* 3.9 9.0 - - - -
236D ILE* 4.5 0.2 - - + -
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Residues in contact with VAL 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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149D HIS 3.7 12.6 - - - +
150D THR 2.6 14.1 + - - +
152D ALA* 1.3 73.1 - - - +
154D MSE 1.3 60.5 + - + +
155D VAL 3.2 1.3 - - - -
156D GLN* 2.6 38.9 + - - +
157D LEU* 3.7 2.6 + - + +
182D ILE* 4.1 28.5 - - + +
185D ILE* 3.9 27.1 - - + -
186D ALA* 4.4 10.3 - - - +
189D ARG* 4.6 10.8 - - - -
191D LEU* 4.2 24.0 - - + +
196D VAL* 4.4 9.0 - - + -
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Residues in contact with MSE 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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113D ILE* 3.8 6.5 - - + -
114D SER* 3.1 52.0 - - - +
116D GLY* 3.9 5.8 - - - -
150D THR* 3.5 24.9 - - + +
151D LEU 4.3 0.9 - - - +
153D VAL* 1.3 74.9 - - - +
155D VAL* 1.3 55.7 + - - +
156D GLN 2.7 12.3 + - - -
157D LEU* 2.8 42.7 + - + +
161D GLU 4.1 16.6 - - - +
162D GLY 4.3 3.4 - - - +
163D GLY* 3.4 4.7 - - - -
189D ARG* 2.9 38.8 - - - +
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Residues in contact with VAL 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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113D ILE* 3.5 36.4 - - + +
151D LEU 3.2 19.9 + - - +
152D ALA 3.8 5.4 - - - +
153D VAL 3.0 0.2 + - - -
154D MSE 1.3 77.1 - - - +
156D GLN* 1.3 62.3 + - + +
157D LEU 3.5 0.2 - - - -
163D GLY* 4.2 4.7 - - - -
164D LEU* 3.2 3.0 + - + -
165D ASN 3.1 11.3 + - - -
166D GLY 3.0 24.2 + - - +
168D VAL* 3.4 30.1 - - + -
233D LYS* 3.6 25.8 - - + -
234D LEU* 4.1 11.4 - - + +
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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