Contacts of the helix formed by residues 143 - 155 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F GLY 2.9 7.2 + - - -
142F SER* 1.3 80.7 - - - +
144F LYS* 1.3 64.9 + - - +
145F THR 3.2 3.1 - - - -
146F GLN* 3.3 9.8 + - - +
147F LEU* 3.2 20.4 + - - +
315F LEU* 4.6 2.4 - - - +
323F ARG* 4.1 1.6 - - - -
340F PHE* 5.4 2.4 - - - -
342F ILE* 4.1 21.8 - - - +
347F ILE* 4.9 1.7 - - - +
355F SO4 3.0 9.2 + - - -
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Residues in contact with LYS 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F VAL* 3.5 41.7 - - + +
137F PHE* 4.1 0.9 - - - -
138F GLY 3.2 28.2 + - - +
139F GLU 3.5 8.5 + - - -
140F PHE* 4.4 0.6 - - - +
142F SER* 3.4 4.2 + - - +
143F GLY* 1.3 78.0 - - - +
145F THR* 1.3 60.1 + - - +
146F GLN 3.3 0.2 - - - -
147F LEU* 3.7 8.8 - - - +
148F ALA* 3.2 19.4 + - - +
239F SER* 6.5 0.4 - - - -
280F PHE* 4.0 2.3 - - - -
282F THR* 3.8 20.1 - - + +
283F ASN 3.5 31.2 - - - +
284F GLN* 3.6 11.7 - - - +
315F LEU* 4.2 7.0 - - + -
355F SO4 3.0 30.1 + - - +
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Residues in contact with THR 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F LYS* 1.3 75.1 - - - +
146F GLN* 1.3 65.8 + - - +
148F ALA* 3.3 4.7 - - - +
149F HIS* 2.8 49.3 + - + -
170F TRP* 4.8 1.1 - - + -
174F GLU* 5.4 2.1 + - - -
176F THR* 4.0 22.2 + - - +
238F ASP* 3.2 34.4 + - - +
355F SO4 2.8 28.3 + - - -
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Residues in contact with GLN 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F GLY* 3.3 15.4 + - - +
145F THR* 1.3 78.2 - - - +
147F LEU* 1.3 58.7 + - - +
149F HIS* 2.8 27.8 + - - +
150F THR* 2.8 17.5 + - - +
181F ARG* 3.0 47.6 + - - +
185F ILE* 4.8 0.8 - - - +
342F ILE* 3.6 36.9 - - + +
346F GLY 5.6 0.2 - - - -
347F ILE* 4.4 4.9 - - + -
355F SO4 4.3 2.0 + - - +
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Residues in contact with LEU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F THR* 4.3 12.6 - - + -
120F LEU* 4.2 15.7 - - + -
128F ILE* 5.8 0.4 - - + -
136F VAL* 4.1 5.8 - - + -
143F GLY 3.2 8.2 + - - +
144F LYS 3.7 9.4 - - - +
146F GLN* 1.3 78.5 - - - +
148F ALA* 1.3 62.2 + - - +
150F THR* 3.4 0.9 + - - -
151F LEU* 3.0 52.2 + - + +
280F PHE* 3.8 19.7 - - + -
313F VAL* 6.2 1.6 - - + -
315F LEU* 4.0 25.1 - - + -
340F PHE* 5.4 0.4 - - + -
347F ILE* 3.2 29.1 - - + +
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Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F LYS 3.2 12.6 + - - +
145F THR* 3.3 13.0 - - - +
146F GLN 3.0 0.4 - - - -
147F LEU* 1.3 82.0 - - - +
149F HIS* 1.3 62.0 + - - +
151F LEU* 3.3 1.9 + - - +
152F ALA* 3.0 17.5 + - - +
170F TRP* 3.6 20.4 - - + -
236F ILE* 3.4 26.2 - - + +
238F ASP* 4.8 2.5 - - - +
280F PHE* 3.9 18.4 - - + -
282F THR* 5.1 2.0 - - + -
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Residues in contact with HIS 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F THR* 2.8 33.3 + - + -
146F GLN* 2.8 21.1 + - - +
148F ALA* 1.3 72.3 - - - +
150F THR* 1.3 68.5 + - - +
152F ALA* 3.1 8.5 + - - +
153F VAL* 3.4 4.9 + - - +
170F TRP* 3.7 14.1 - + - -
176F THR 3.5 21.8 - - - -
177F PHE* 3.5 7.9 - + - -
178F ARG* 3.1 35.9 + - + -
181F ARG* 4.1 12.3 - - + +
182F ILE* 3.3 36.8 - - + +
185F ILE* 3.8 17.5 - - + -
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Residues in contact with THR 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F THR 3.0 28.9 - - - +
116F GLY* 4.4 1.3 - - - -
146F GLN 2.8 17.9 + - - -
147F LEU 3.7 7.2 - - - -
149F HIS* 1.3 71.8 - - - +
151F LEU* 1.3 52.6 - - - +
153F VAL* 2.6 29.5 + - - +
154F MSE 3.0 23.4 + - + -
185F ILE* 3.7 10.3 - - - +
189F ARG* 4.3 4.7 - - - +
345F LYS 3.9 15.9 - - - +
346F GLY* 3.3 9.0 - - - -
347F ILE* 3.1 27.1 + - - +
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Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ILE* 4.2 7.3 - - + +
114F SER 3.5 8.5 - - - +
115F THR* 3.4 35.9 - - + -
128F ILE* 3.8 22.0 - - + -
147F LEU* 3.0 40.5 + - + +
148F ALA* 3.5 4.7 - - - +
150F THR* 1.3 75.3 - - - +
152F ALA* 1.3 61.3 + - - +
153F VAL 3.0 1.4 + - - -
154F MSE 4.1 4.9 - - - -
155F VAL* 3.2 25.6 + - - +
234F LEU* 3.3 15.5 - - + +
280F PHE* 3.8 33.9 - - + -
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Residues in contact with ALA 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F ALA 3.0 13.9 + - - +
149F HIS 3.4 10.8 - - - +
150F THR 2.9 0.8 + - - -
151F LEU* 1.3 75.3 - - - +
153F VAL* 1.3 56.8 + - - +
155F VAL* 3.7 3.7 - - - +
156F GLN* 3.3 26.7 + - - +
168F VAL* 3.8 12.9 - - + +
170F TRP* 3.8 20.6 - - + -
182F ILE* 3.9 3.1 - - + -
200F ILE* 3.7 22.6 - - + +
234F LEU* 3.8 9.4 - - - +
236F ILE* 4.5 0.7 - - + -
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Residues in contact with VAL 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F HIS 3.7 13.0 - - - +
150F THR 2.6 14.9 + - - +
152F ALA* 1.3 72.6 - - - +
154F MSE 1.3 58.8 + - + +
155F VAL 3.2 0.9 - - - -
156F GLN* 2.6 39.9 + - + +
157F LEU* 3.7 4.5 + - + +
182F ILE* 4.1 24.0 - - + +
185F ILE* 3.8 32.3 - - + +
186F ALA* 4.5 9.0 - - + +
189F ARG* 4.8 10.1 - - + +
191F LEU* 3.9 27.0 - - + +
196F VAL* 4.5 5.4 - - + -
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Residues in contact with MSE 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ILE* 3.8 7.2 - - + -
114F SER* 3.1 54.5 - - - +
116F GLY* 3.9 10.5 - - - +
150F THR* 3.6 24.5 - - + +
151F LEU 4.1 0.4 - - - +
153F VAL* 1.3 75.9 - - - +
155F VAL* 1.3 65.2 + - - +
156F GLN 2.8 1.6 + - - -
157F LEU* 2.9 31.6 + - + +
161F GLU 3.9 18.2 - - - +
162F GLY 4.6 0.7 - - - +
163F GLY* 2.9 14.1 - - - -
189F ARG* 3.3 31.9 - - - +
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Residues in contact with VAL 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ILE* 3.6 28.8 - - + +
151F LEU 3.2 19.6 + - - +
152F ALA 3.7 5.8 - - - +
154F MSE 1.3 78.3 - - - +
156F GLN* 1.3 61.9 + - + +
163F GLY* 3.8 4.0 - - - -
164F LEU* 2.8 23.4 + - + +
165F ASN 3.1 7.3 + - - -
166F GLY 3.2 8.5 + - - +
168F VAL* 3.5 29.4 - - + -
233F LYS* 3.6 31.2 - - + -
234F LEU* 4.2 13.7 - - + +
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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