Contacts of the helix formed by residues 145 - 160 (chain F) in PDB entry 4PHZ
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 SER 145 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B ILE* 3.4 24.1 + - - +
140F LEU* 3.4 4.0 - - - +
143F SER* 3.2 8.5 + - - -
144F GLY* 1.3 78.3 - - - +
146F TYR* 1.3 57.5 + - - +
147F VAL* 3.0 19.1 + - - +
148F ILE* 3.1 31.1 + - - +
149F THR* 3.0 27.9 + - - -
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Residues in contact with TYR 146 (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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249B ILE* 5.9 1.2 - - - +
251B THR 4.6 4.5 + - - -
252B ILE* 3.2 38.4 - - - +
140F LEU* 3.9 6.4 - - - +
144F GLY 4.3 0.6 + - - -
145F SER* 1.3 71.8 + - - +
147F VAL* 1.3 78.3 + - + +
149F THR* 3.8 3.4 - - - -
150F ALA* 2.8 31.4 + - - +
233F TYR* 3.6 5.5 - + + +
234F PHE* 4.1 10.5 - + - -
237F TRP* 3.4 65.3 - + + -
238F PHE* 3.2 40.2 - + - -
241F ARG* 6.3 0.2 - - - -
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Residues in contact with VAL 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ILE* 3.9 24.7 + - + +
184C LEU* 6.4 1.1 - - + -
188C ILE* 4.3 30.7 - - + -
145F SER* 3.0 7.5 + - - +
146F TYR* 1.3 102.2 - - + +
148F ILE* 1.3 71.9 + - + +
150F ALA* 3.3 9.0 - - - +
151F VAL* 3.1 25.3 + - + +
234F PHE* 3.8 15.0 - - + -
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Residues in contact with ILE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ILE* 4.9 8.5 - - + -
139F ILE* 4.0 11.2 - - + -
143F SER* 3.6 31.2 - - - +
145F SER* 3.1 26.2 + - - +
147F VAL* 1.3 80.7 - - + +
149F THR* 1.3 59.6 + - - +
151F VAL* 2.9 5.3 + - - -
152F VAL* 2.8 45.5 + - + -
153F GLY 3.5 1.0 + - - -
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Residues in contact with THR 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F GLN* 3.8 5.8 - - - +
136F LEU* 3.6 34.8 - - + +
139F ILE* 3.6 9.8 - - + -
140F LEU* 3.3 25.1 + - + +
145F SER 3.0 18.7 + - - -
146F TYR* 3.8 2.5 - - - -
147F VAL 3.4 0.2 - - - -
148F ILE* 1.3 72.7 - - - +
150F ALA* 1.3 62.3 + - - +
153F GLY* 2.6 31.1 + - - -
154F SER 2.9 4.0 + - - -
233F TYR* 3.5 27.1 - - + +
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Residues in contact with ALA 150 (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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146F TYR 2.8 23.6 + - - +
147F VAL 3.3 6.5 - - - +
149F THR* 1.3 71.8 - - - +
151F VAL* 1.3 57.6 + - + +
154F SER* 2.5 23.9 + - - -
230F MET* 3.3 14.6 - - + +
233F TYR* 3.4 29.3 - - + -
234F PHE* 3.5 30.3 - - + -
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Residues in contact with VAL 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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188C ILE* 5.5 6.5 - - + -
191C PHE* 4.5 30.7 - - + +
192C MET* 5.4 7.4 - - - -
147F VAL* 3.1 18.2 + - + +
148F ILE* 2.9 9.6 + - - +
149F THR 2.9 3.6 + - - -
150F ALA* 1.3 78.6 - - + +
152F VAL* 1.3 73.0 + - + +
155F LEU* 3.1 29.9 + - + +
230F MET* 3.8 24.9 - - + +
234F PHE* 5.9 2.7 - - + -
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Residues in contact with VAL 152 (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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135F TRP* 2.9 24.9 + - + -
139F ILE* 3.6 35.2 - - + -
148F ILE* 2.8 24.9 + - + +
151F VAL* 1.3 83.0 - - + +
153F GLY* 1.3 66.2 + - - +
155F LEU* 3.9 9.5 - - + +
156F GLY 3.0 12.5 + - - -
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Residues in contact with GLY 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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135F TRP* 3.0 30.2 - - - -
136F LEU* 3.2 18.2 - - - +
139F ILE* 4.0 10.1 - - - -
148F ILE 3.5 1.0 + - - -
149F THR* 2.6 26.6 + - - -
152F VAL* 1.3 77.8 - - - +
154F SER* 1.3 55.4 + - - -
157F TRP 3.1 10.9 + - - -
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Residues in contact with SER 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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74F VAL* 4.5 4.9 - - - -
136F LEU* 3.6 12.3 - - - +
149F THR 2.9 7.3 + - - -
150F ALA 2.5 26.3 + - - -
151F VAL 3.8 0.2 + - - -
153F GLY* 1.3 72.4 - - - +
155F LEU* 1.3 59.8 + - - +
157F TRP* 3.3 6.9 - - - +
158F GLY 3.0 23.0 + - - -
226F GLY* 3.8 9.1 - - - +
229F SER* 3.7 22.1 - - - -
230F MET* 3.1 17.5 + - - +
233F TYR* 4.3 10.3 - - - -
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Residues in contact with LEU 155 (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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151F VAL* 3.1 22.3 + - + +
152F VAL* 4.0 8.7 - - + +
154F SER* 1.3 74.6 + - - +
156F GLY* 1.3 64.3 + - - +
158F GLY* 3.5 1.2 + - - -
159F LEU* 3.0 37.5 + - + +
223F PHE* 4.5 19.5 - - + +
226F GLY* 4.1 20.6 + - - -
227F PHE* 4.0 27.6 - - + +
230F MET* 3.9 12.6 - - + -
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Residues in contact with GLY 156 (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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135F TRP* 3.4 26.4 - - - -
152F VAL 3.0 12.7 + - - -
155F LEU* 1.3 75.3 - - - +
157F TRP* 1.3 64.1 + - - +
159F LEU* 3.2 7.4 + - - -
160F LEU* 2.9 39.5 + - - +
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Residues in contact with TRP 157 (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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42F TYR* 4.5 2.0 - - - -
70F PRO* 2.9 29.5 + - + +
73F GLY* 3.4 8.7 - - - -
74F VAL* 3.1 36.3 - - + +
77F CYS* 3.8 26.5 - - - -
98F ALA* 5.2 0.4 - - + -
129F LEU* 4.2 27.6 - - + -
132F PRO* 3.3 58.7 - - + +
133F ALA* 3.7 22.9 - - + -
135F TRP* 3.8 1.8 - - - -
136F LEU* 4.1 12.6 - - + -
153F GLY 3.1 14.8 + - - +
154F SER* 3.3 12.6 - - - +
156F GLY* 1.3 77.5 - - - +
158F GLY* 1.3 68.2 + - - +
161F PHE* 3.6 10.7 + - - +
229F SER* 3.8 18.2 - - - -
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Residues in contact with GLY 158 (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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70F PRO* 4.3 3.8 - - - +
154F SER 3.0 11.1 + - - -
155F LEU 3.9 2.0 - - - -
157F TRP* 1.3 82.7 - - - +
159F LEU* 1.3 63.3 + - - +
161F PHE* 3.1 19.9 + - - +
162F TYR 4.7 0.3 + - - -
222F ALA* 3.7 11.8 - - - +
225F SER* 3.4 21.5 + - - -
226F GLY* 3.9 11.7 - - - -
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Residues in contact with LEU 159 (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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155F LEU* 3.0 35.1 + - + +
156F GLY* 3.9 5.6 - - - +
158F GLY* 1.3 73.9 - - - +
160F LEU* 1.3 61.0 + - + +
161F PHE 3.2 3.7 + - - -
162F TYR 4.3 0.7 + - - -
163F PRO* 3.4 18.0 - - - +
222F ALA* 3.8 26.6 + - + +
223F PHE* 3.6 55.4 - - + -
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Residues in contact with LEU 160 (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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240E ILE* 5.2 13.2 - - + -
243E THR* 4.2 25.4 - - + -
131F VAL* 4.3 17.5 - - + -
132F PRO* 4.4 10.8 - - + -
135F TRP* 4.0 33.4 - - + -
156F GLY* 2.9 32.2 + - - +
157F TRP 4.2 3.4 - - - +
158F GLY 3.2 0.2 + - - -
159F LEU* 1.3 73.4 - - + +
161F PHE* 1.3 63.8 + - - +
162F TYR 3.5 0.4 - - - -
163F PRO* 3.8 7.9 - - + -
164F ASN* 3.0 27.3 + - - +
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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