Contacts of the helix formed by residues 145 - 155 (chain A) in PDB entry 1FUU
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 THR 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.0 2.2 - - - -
96A ALA 3.6 14.8 - - - +
97A PRO 4.3 2.7 - - - +
98A THR* 3.6 31.2 - - - +
99A ARG* 3.8 11.3 - - + +
123A CYS 3.4 5.0 + - - -
124A ILE* 4.5 5.5 - - + +
125A GLY 4.9 1.0 + - - -
144A GLY* 1.3 74.8 - - - -
146A PRO* 1.3 74.7 - - + +
147A GLY 3.4 1.5 + - - -
148A ARG* 3.4 28.4 + - - +
149A VAL* 3.0 23.6 + - - +
179A PHE* 4.9 6.7 - - + -
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Residues in contact with PRO 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.1 19.5 - - + -
96A ALA 3.7 12.3 - - - +
144A GLY 4.5 0.7 - - - +
145A THR* 1.3 85.6 - - - +
147A GLY* 1.3 58.0 + - - +
149A VAL 3.4 0.5 + - - -
150A PHE* 2.8 31.5 + - - +
174A MSE 3.9 18.4 - - - -
179A PHE* 3.4 47.6 - - + -
182A GLN* 4.1 12.3 - - + +
183A ILE* 4.3 7.4 - - + +
186A ILE* 3.7 5.9 - - + +
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Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A THR* 3.4 1.4 + - - -
146A PRO* 1.3 75.9 - - - +
148A ARG* 1.3 66.6 + - - +
150A PHE* 3.1 4.2 + - - +
151A ASP* 2.8 33.8 + - - +
179A PHE* 4.1 10.5 - - - -
182A GLN* 4.4 19.1 - - - -
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 5.6 5.7 - - - +
123A CYS* 3.6 20.2 - - - +
124A ILE* 3.7 21.3 - - - +
125A GLY* 3.7 22.8 - - - +
127A THR* 5.5 2.5 - - + -
132A ASP* 5.7 0.4 - - - +
145A THR* 3.4 17.0 + - - +
147A GLY* 1.3 78.3 - - - +
149A VAL* 1.3 57.4 + - - +
151A ASP* 3.7 6.7 - - - +
152A ASN* 2.8 41.2 + - - +
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 4.0 17.5 - - + -
95A LEU* 3.6 17.7 - - + -
123A CYS* 4.1 24.7 - - + -
144A GLY* 4.2 7.4 - - - +
145A THR 3.0 22.6 + - - +
146A PRO 3.7 3.1 - - - +
148A ARG* 1.3 73.9 - - - +
150A PHE* 1.3 67.6 + - - +
152A ASN* 3.1 3.6 + - - +
153A ILE* 2.9 33.9 + - + +
158A PHE* 3.8 23.6 - - + -
186A ILE* 3.8 16.4 - - + -
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Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PRO 2.8 21.4 + - - +
147A GLY* 3.6 5.2 - - - +
149A VAL* 1.3 72.0 - - - +
151A ASP* 1.3 68.0 + - + +
153A ILE* 3.0 15.3 + - - +
154A GLN* 3.0 24.9 + - + +
182A GLN* 4.5 18.2 - - + -
185A GLN* 3.6 40.6 - - + -
186A ILE* 4.2 15.5 - - + -
189A LEU* 3.3 33.0 - - + -
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLY 2.8 20.1 + - - +
148A ARG* 3.7 9.5 - - - +
150A PHE* 1.3 79.8 - - + +
152A ASN* 1.3 63.0 + - - +
154A GLN* 3.3 5.1 + - - +
155A ARG* 3.0 62.4 + - - +
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Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A CYS* 3.3 16.5 - - - -
132A ASP* 2.7 34.3 + - - +
136A LEU* 3.5 11.2 - - + +
148A ARG* 2.8 30.5 + - - +
149A VAL* 3.1 4.0 + - - +
151A ASP* 1.3 78.5 - - - +
153A ILE* 1.3 60.1 + - - +
155A ARG* 3.1 27.4 + - - +
156A ARG 3.3 1.4 + - - -
157A ARG* 3.0 35.8 + - - +
158A PHE* 3.2 16.1 + - + -
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL* 2.9 33.4 + - + +
150A PHE 3.0 6.5 + - - +
152A ASN* 1.3 75.8 - - - +
154A GLN* 1.3 67.8 + - - +
156A ARG* 3.2 20.3 + - - +
158A PHE* 3.5 28.6 - - + +
160A THR* 3.7 29.4 - - + +
186A ILE* 4.5 10.1 - - + -
189A LEU* 3.9 33.4 - - + +
190A LEU* 4.2 16.6 - - + -
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Residues in contact with GLN 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 3.0 30.9 + - + +
151A ASP* 3.8 7.0 - - - +
153A ILE* 1.3 73.7 - - - +
155A ARG* 1.3 59.0 + - + +
156A ARG* 2.9 22.8 + - - +
189A LEU* 5.2 4.4 - - + +
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Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE* 4.0 33.9 + - - +
132A ASP* 4.3 3.0 + - - -
151A ASP* 3.0 45.4 + - - +
152A ASN* 3.1 33.9 + - - +
154A GLN* 1.3 74.0 - - + +
156A ARG* 1.3 70.3 + - - +
157A ARG* 3.4 10.2 + - + +
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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