Contacts of the helix formed by residues 143 - 155 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141E GLY 2.9 9.7 + - - -
142E SER* 1.3 79.9 - - - +
144E LYS* 1.3 63.8 + - - +
145E THR 3.2 2.7 - - - -
146E GLN* 3.3 10.1 + - - +
147E LEU* 3.2 20.1 + - - +
315E LEU* 4.6 2.4 - - - +
323E ARG* 4.5 1.1 - - - -
340E PHE* 5.4 2.1 - - - -
342E ILE* 4.1 21.8 - - - +
347E ILE* 4.9 1.9 - - - +
354E SO4 2.9 9.4 + - - -
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Residues in contact with LYS 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E VAL* 3.6 40.8 - - + +
137E PHE* 4.1 1.1 - - - -
138E GLY 3.0 27.9 + - - +
139E GLU 3.4 5.7 + - - -
140E PHE* 4.5 0.6 - - - +
142E SER* 3.4 3.5 + - - +
143E GLY* 1.3 78.6 - - - +
145E THR* 1.3 56.9 + - - +
147E LEU* 3.6 8.9 + - - +
148E ALA* 3.2 22.0 + - - +
238E ASP* 5.7 0.9 - - - -
239E SER* 6.4 0.4 - - - -
280E PHE* 4.0 1.7 - - - -
282E THR* 3.8 20.3 - - + +
283E ASN 3.3 34.1 - - - +
284E GLN* 3.6 13.1 - - - +
315E LEU* 4.2 6.5 - - + -
354E SO4 3.0 32.2 + - - +
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Residues in contact with THR 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E GLY 3.2 0.4 - - - -
144E LYS* 1.3 76.0 - - - +
146E GLN* 1.3 61.8 + - - +
148E ALA* 3.4 4.4 + - - +
149E HIS* 2.7 53.5 + - + -
170E TRP* 4.9 1.6 - - + -
174E GLU* 5.5 1.6 + - - -
176E THR* 3.9 22.5 + - - +
238E ASP* 3.0 35.0 + - - +
354E SO4 2.6 25.6 + - - -
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Residues in contact with GLN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E GLY* 3.5 13.9 - - - +
145E THR* 1.3 78.7 - - - +
147E LEU* 1.3 65.9 + - - +
149E HIS* 2.9 10.9 + - - +
150E THR* 2.8 28.1 + - - +
181E ARG* 3.1 41.0 + - - +
185E ILE* 4.9 0.2 - - - +
342E ILE* 3.6 42.1 - - + +
347E ILE* 4.4 3.8 - - + -
354E SO4 5.2 2.0 - - - +
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E THR* 4.3 12.1 - - + -
120E LEU* 4.3 15.0 - - + -
124E LEU* 6.4 0.2 - - + -
128E ILE* 5.7 0.7 - - + -
136E VAL* 4.1 5.8 - - + -
143E GLY 3.2 8.1 + - - +
144E LYS 3.6 9.0 - - - +
146E GLN* 1.3 79.6 - - - +
148E ALA* 1.3 63.0 + - - +
150E THR* 3.5 1.0 + - - -
151E LEU* 3.0 52.7 + - + +
280E PHE* 3.7 19.3 - - + -
313E VAL* 6.2 1.6 - - + -
315E LEU* 4.0 25.6 - - + -
340E PHE* 5.5 0.2 - - + -
347E ILE* 3.2 29.3 - - + +
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Residues in contact with ALA 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E LYS 3.2 11.5 + - - +
145E THR* 3.4 13.0 - - - +
146E GLN 3.0 0.4 - - - -
147E LEU* 1.3 81.4 - - - +
149E HIS* 1.3 62.0 + - - +
151E LEU* 3.3 2.3 + - - +
152E ALA* 3.0 18.0 + - - +
170E TRP* 3.7 20.0 - - + -
236E ILE* 3.4 26.2 - - + +
238E ASP* 4.7 3.1 - - - +
280E PHE* 3.9 18.4 - - + -
282E THR* 5.1 1.8 - - + -
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Residues in contact with HIS 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E THR* 2.7 34.0 + - + -
146E GLN* 2.9 14.4 + - - +
148E ALA* 1.3 75.8 - - - +
150E THR* 1.3 66.9 + - - +
152E ALA* 3.0 15.6 + - - +
153E VAL* 3.4 6.2 + - - +
170E TRP* 3.7 18.6 - + - -
176E THR 3.5 22.0 - - - -
177E PHE* 3.7 6.7 - + - -
178E ARG* 3.1 40.4 + - + +
181E ARG* 4.1 12.3 - - + -
182E ILE* 3.6 22.7 - - + +
185E ILE* 4.0 16.6 - - + -
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Residues in contact with THR 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E THR 2.9 32.3 - - - +
116E GLY* 4.2 3.4 - - - -
146E GLN 2.8 21.1 + - - -
147E LEU 3.7 4.0 - - - -
149E HIS* 1.3 70.8 - - - +
151E LEU* 1.3 54.5 + - - +
153E VAL* 2.7 27.2 + - - +
154E MSE 3.0 23.4 + - + +
185E ILE* 3.9 10.9 - - + +
345E LYS 3.9 15.3 - - - +
346E GLY* 3.2 9.2 - - - -
347E ILE* 3.0 26.7 + - - +
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ILE* 4.2 6.1 - - + +
114E SER 3.4 23.8 - - - +
115E THR* 3.5 20.9 - - + -
128E ILE* 3.9 20.9 - - + -
147E LEU* 3.0 40.8 + - + +
148E ALA* 3.5 4.5 - - - +
150E THR* 1.3 76.1 - - - +
152E ALA* 1.3 61.0 + - - +
153E VAL 3.1 1.0 + - - -
154E MSE 4.4 4.9 - - - -
155E VAL* 3.2 19.8 + - - +
234E LEU* 3.2 21.2 - - + +
236E ILE* 5.1 0.2 - - + -
280E PHE* 3.7 34.3 - - + -
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E ALA 3.0 13.6 + - - +
149E HIS 3.0 10.9 + - - +
150E THR 3.0 0.4 + - - -
151E LEU* 1.3 75.6 - - - +
153E VAL* 1.3 58.3 + - - +
155E VAL* 3.8 3.3 - - - +
156E GLN* 3.3 26.9 + - - +
168E VAL* 3.8 11.3 - - + +
170E TRP* 3.8 16.8 - - + -
182E ILE* 3.6 17.5 - - + -
200E ILE* 3.8 12.2 - - + +
234E LEU* 3.7 8.9 - - - +
236E ILE* 4.5 0.7 - - + -
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Residues in contact with VAL 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E HIS 3.7 13.0 - - - +
150E THR 2.7 14.5 + - - +
152E ALA* 1.3 73.5 - - - +
154E MSE 1.3 60.7 + - + +
155E VAL 3.2 1.1 - - - -
156E GLN* 2.6 39.8 + - - +
157E LEU* 3.7 2.1 + - + -
182E ILE* 4.0 27.1 - - + +
185E ILE* 3.8 28.9 - - + +
186E ALA* 4.0 15.9 - - + +
189E ARG* 4.9 5.8 - - + -
191E LEU* 3.4 27.8 - - + +
196E VAL* 4.6 0.9 - - + -
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Residues in contact with MSE 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ILE* 3.8 6.5 - - + -
114E SER* 3.2 53.2 - - - +
116E GLY* 4.0 4.0 - - - +
150E THR* 3.5 26.2 - - + +
151E LEU 4.2 0.7 - - - +
153E VAL* 1.3 77.2 - - - +
155E VAL* 1.3 63.0 + - - +
156E GLN 2.8 1.6 + - - -
157E LEU* 2.9 29.9 + - + +
161E GLU 4.0 17.5 - - - +
162E GLY 4.7 0.9 - - - +
163E GLY* 3.0 14.0 - - - -
185E ILE* 6.1 0.2 - - - -
189E ARG* 3.1 45.1 - - - +
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Residues in contact with VAL 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ILE* 3.6 28.5 - - + +
151E LEU 3.2 19.8 + - - +
152E ALA 3.8 5.2 - - - +
154E MSE 1.3 77.7 - - - +
156E GLN* 1.3 63.5 + - + +
157E LEU 3.4 0.2 - - - -
163E GLY* 4.0 4.0 - - - -
164E LEU* 3.0 13.7 + - + -
165E ASN 3.1 0.2 + - - -
166E GLY 3.0 19.8 + - - +
168E VAL* 3.4 29.2 - - + -
233E LYS* 3.6 31.2 - - + -
234E LEU* 4.1 12.3 - - + +
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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