Contacts of the helix formed by residues 149 - 163 (chain F) in PDB entry 3EXG
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 ASN 149 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 3.7 4.7 - - - -
148F TRP* 1.3 104.7 - - + +
150F SER* 1.3 64.7 + - - +
151F GLU* 3.0 33.0 + - - +
152F ASP* 2.9 24.9 + - - -
153F ALA* 3.0 20.8 + - - +
180F PHE* 3.7 36.1 - - + +
199F LYS* 5.7 0.2 - - - +
201F GLU* 3.5 9.3 + - - -
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Residues in contact with SER 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F VAL* 2.6 29.7 + - - -
4F THR 3.2 0.5 - - - -
5F VAL* 2.9 25.1 + - - +
8F ALA* 3.1 23.7 - - - +
149F ASN* 1.3 74.6 - - - +
151F GLU* 1.3 65.4 + - - +
153F ALA* 3.2 0.5 + - - -
154F LYS* 3.0 20.8 + - - +
180F PHE* 3.6 17.2 - - - -
182F PHE* 3.8 14.8 - - - -
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Residues in contact with GLU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F ASN* 3.0 14.2 + - - +
150F SER* 1.3 76.7 - - - +
152F ASP* 1.3 67.4 + - - +
154F LYS* 3.3 1.0 + - - +
155F GLY 2.9 20.4 + - - -
180F PHE* 5.5 1.0 - - + +
182F PHE* 3.6 17.7 - - + -
183F PRO* 3.3 32.0 - - + +
186F ALA* 5.1 2.9 - - + -
191F PHE* 3.6 32.2 - - + -
193F ILE* 4.1 3.1 - - + -
199F LYS* 3.7 24.4 + - - -
239F ARG* 4.0 9.5 + - - -
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Residues in contact with ASP 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F PRO* 3.8 8.7 - - + -
148F TRP* 3.3 15.6 - - - +
149F ASN* 2.9 41.8 + - - +
151F GLU* 1.3 74.0 - - - +
153F ALA* 1.3 58.7 + - - +
156F LEU* 2.8 41.0 + - + +
193F ILE* 3.5 10.8 - - + -
201F GLU* 4.2 2.1 - - - +
237F ASN* 3.0 22.7 - - - +
239F ARG* 3.2 28.1 + - - +
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Residues in contact with ALA 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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5F VAL* 3.6 30.5 - - + +
8F ALA* 4.4 0.2 - - + -
9F ILE* 3.7 24.3 - - + +
147F PRO* 3.5 22.1 - - + +
148F TRP 5.8 0.2 - - - -
149F ASN 3.0 11.2 + - - +
150F SER 3.6 7.6 - - - +
152F ASP* 1.3 70.7 - - - +
154F LYS* 1.3 61.3 + - - +
157F ILE* 3.1 27.9 + - - +
169F VAL* 6.0 0.7 - - - +
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Residues in contact with LYS 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ALA* 3.1 29.0 - - + +
11F GLN* 3.3 20.5 + - + +
12F GLY* 4.0 4.3 - - - -
15F GLU* 3.0 40.2 + - - -
150F SER 3.0 16.8 + - - +
151F GLU 4.0 2.5 - - - +
153F ALA* 1.3 73.6 - - - +
155F GLY* 1.3 62.6 + - - +
157F ILE* 3.3 4.5 - - - +
158F LYS* 3.2 35.4 + - + +
182F PHE* 3.7 19.5 - - + -
186F ALA 2.8 24.7 + - - +
187F GLN 3.2 13.1 + - - -
188F SER 3.2 4.9 + - - -
191F PHE* 4.8 5.2 - - + -
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Residues in contact with GLY 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 GLU 2.9 15.3 + - - -
154F LYS* 1.3 73.2 - - - +
156F LEU* 1.3 58.2 + - - +
158F LYS* 3.5 2.3 + - - +
159F SER* 2.9 28.8 + - - -
191F PHE* 3.8 18.7 - - - -
192F LEU* 4.3 0.5 - - - -
193F ILE* 3.6 32.7 + - - -
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Residues in contact with LEU 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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145F VAL* 4.3 26.6 - - + +
147F PRO* 3.9 30.7 - - + -
152F ASP* 2.8 22.5 + - + +
153F ALA* 4.6 0.9 - - - +
155F GLY* 1.3 70.5 - - - -
157F ILE* 1.3 61.3 + - - +
159F SER* 3.7 2.4 - - - -
160F ALA* 2.9 30.0 + - - +
169F VAL* 4.8 3.9 - - + +
193F ILE* 3.6 35.9 - - + +
194F PRO 4.7 5.8 - - - +
195F ILE* 4.7 9.0 - - + +
239F ARG* 4.0 38.4 - - + +
240F THR* 5.3 1.1 - - - +
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Residues in contact with ILE 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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9F ILE* 4.6 12.3 - - + +
12F GLY* 4.2 20.9 - - - -
13F MET* 4.6 9.0 - - + +
77F ILE* 5.5 1.1 - - + -
113F VAL* 4.5 7.2 - - + -
115F ARG* 3.5 33.7 - - + -
153F ALA 3.1 19.5 + - - +
154F LYS* 3.3 15.5 - - - +
156F LEU* 1.3 78.3 - - - +
158F LYS* 1.3 64.5 + - + +
160F ALA* 3.5 2.1 + - - +
161F ILE* 3.1 41.4 + - + +
169F VAL* 3.9 30.8 - - + +
171F GLU* 4.6 2.2 - - - +
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Residues in contact with LYS 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F GLY* 3.9 13.3 + - - -
15F GLU* 2.7 41.3 + - - +
16F GLU* 3.0 35.4 + - + +
154F LYS* 3.2 35.3 + - + +
155F GLY 3.9 1.1 - - - +
157F ILE* 1.3 77.5 - - - +
159F SER* 1.3 67.9 + - - +
160F ALA 3.0 1.3 - - - -
161F ILE* 2.8 14.6 + - - +
162F ARG* 2.9 21.8 + - - +
189F LYS 3.6 16.3 + - - -
191F PHE 3.2 24.7 - - - +
192F LEU* 3.7 11.2 - - + -
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Residues in contact with SER 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 GLY 2.9 12.2 + - - -
156F LEU* 3.9 4.9 - - - -
158F LYS* 1.3 76.4 - - - +
160F ALA* 1.3 55.1 + - - +
162F ARG* 3.6 4.9 + - - +
163F ASP* 3.1 27.5 + - - +
192F LEU* 3.6 23.1 - - - +
193F ILE 2.8 29.5 + - - -
194F PRO* 4.2 2.9 - - - +
195F ILE* 4.0 17.7 - - - +
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Residues in contact with ALA 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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113F VAL* 3.3 19.0 - - + +
145F VAL* 5.6 0.4 - - + -
156F LEU 2.9 18.5 + - - +
157F ILE* 3.5 6.5 - - - +
158F LYS 2.9 0.2 + - - -
159F SER* 1.3 73.6 - - - +
161F ILE* 1.3 64.8 + - - +
162F ARG 3.4 0.2 + - - -
163F ASP* 3.4 8.7 - - - +
167F VAL* 3.8 20.9 - - + +
169F VAL* 3.9 21.8 - - + -
195F ILE* 4.3 3.3 - - + +
1008F K 2.7 19.8 - - - -
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Residues in contact with ILE 161 (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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13F MET* 4.5 7.9 - - - -
16F GLU* 3.8 43.7 - - + +
19F ARG* 5.8 0.4 - - - +
23F VAL* 4.3 23.1 - - + -
75F ARG* 3.1 20.9 + - + +
77F ILE* 3.5 32.5 - - + -
113F VAL* 3.9 11.7 - - + -
157F ILE* 3.1 27.4 - - + +
158F LYS 2.8 6.3 + - - +
160F ALA* 1.3 80.3 - - - +
162F ARG* 1.3 59.3 + - + +
1008F K 2.7 20.2 - - - -
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Residues in contact with ARG 162 (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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16F GLU* 2.4 48.5 + - - +
19F ARG* 3.3 48.0 - - - +
75F ARG* 3.0 14.6 + - - +
158F LYS* 2.9 23.6 + - - +
159F SER* 4.2 4.0 - - - +
161F ILE* 1.3 75.5 - - + +
163F ASP* 1.3 64.9 + - - +
164F ASN* 3.7 5.2 + - - +
189F LYS 4.4 5.7 + - - -
190F ASP* 5.0 11.3 + - - +
192F LEU* 4.0 35.4 - - + +
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Residues in contact with ASP 163 (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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343E ASP* 4.9 2.5 - - - +
75F ARG* 2.9 12.0 + - - -
111F PRO* 4.3 0.3 - - - +
143F LYS* 3.0 36.8 + - - +
159F SER 3.1 18.5 + - - +
160F ALA* 3.4 11.2 - - - +
162F ARG* 1.3 76.7 - - - +
164F ASN* 1.3 62.1 + - - +
165F ASN* 2.7 41.3 + - - +
167F VAL* 4.0 10.5 - - + -
195F ILE* 3.8 8.5 - - + +
1008F K 2.9 17.7 - - - -
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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