Contacts of the helix formed by residues 139 - 153 (chain C) in PDB entry 4I02
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 ASP 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C PHE 4.3 0.4 + - - -
138C LEU* 1.3 74.7 - - - +
140C ALA* 1.3 66.9 + - - +
141C THR* 3.3 11.2 + - - -
142C GLY* 3.0 22.3 + - - -
143C ARG* 2.8 25.9 + - - +
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Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ASP* 1.3 76.6 - - - +
141C THR* 1.3 57.0 + - - +
143C ARG* 3.7 17.0 - - - +
144C ILE* 2.9 34.1 + - - +
179C CYS* 3.7 22.0 - - - -
183C THR* 4.2 6.3 - - + -
186C ARG* 5.6 1.6 - - - +
187C ILE* 3.7 19.1 - - + -
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Residues in contact with THR 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ASP* 3.1 11.7 + - - -
140C ALA* 1.3 79.2 - - - +
142C GLY* 1.3 59.6 + - - +
144C ILE* 3.4 2.3 + - - +
145C ALA* 2.9 30.3 + - + +
186C ARG* 5.5 1.4 + - - -
187C ILE* 3.7 23.6 - - + +
190C MET* 3.4 35.7 - - + +
191C LEU* 4.6 10.5 - - + +
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 3.7 22.2 - - - +
139C ASP* 3.0 16.6 + - - -
141C THR* 1.3 78.3 - - - +
143C ARG* 1.3 60.6 + - - +
145C ALA* 3.5 7.2 + - - +
146C GLN* 3.0 23.9 + - - +
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Residues in contact with ARG 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ASN* 3.4 31.4 - - + +
135C LEU* 3.7 27.0 + - - +
138C LEU* 3.1 30.6 + - + +
139C ASP* 2.8 31.0 + - - +
140C ALA* 3.7 8.6 - - - +
142C GLY* 1.3 74.6 - - - +
144C ILE* 1.3 58.8 + - - +
146C GLN* 3.4 4.3 + - - +
147C THR* 2.9 32.7 + - - -
177C VAL* 2.9 41.9 + - + +
178C GLY 3.5 15.6 + - - -
179C CYS* 3.5 13.9 - - - -
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Residues in contact with ILE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ALA 2.9 14.2 + - - +
141C THR 3.9 2.7 - - - +
143C ARG* 1.3 74.8 - - - +
145C ALA* 1.3 64.9 + - - +
147C THR* 3.1 2.4 + - - -
148C LEU* 2.9 42.3 + - + +
173C ILE* 4.4 11.4 - - + -
177C VAL* 4.0 26.5 - - + -
179C CYS* 4.7 4.7 - - - -
184C VAL* 4.0 25.6 - - + +
187C ILE* 3.5 46.2 - - + -
188C LEU* 4.1 16.2 - - + -
191C LEU* 4.4 0.9 - - + -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C THR* 2.9 19.6 + - + +
142C GLY* 3.6 8.3 - - - +
144C ILE* 1.3 77.2 - - - +
146C GLN* 1.3 63.6 + - - +
148C LEU* 3.4 10.5 + - - +
149C LEU* 3.2 27.4 + - + +
191C LEU* 4.8 13.1 - - + +
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Residues in contact with GLN 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLU* 4.7 10.8 - - - +
134C ASN* 3.7 29.5 + - - +
138C LEU* 4.7 7.7 - - + +
142C GLY 3.0 17.9 + - - +
143C ARG* 3.8 4.9 - - - +
144C ILE 3.3 0.2 - - - -
145C ALA* 1.3 76.3 - - - +
147C THR* 1.3 58.5 + - - +
149C LEU* 3.2 24.1 + - - +
150C ASN* 2.8 59.2 + - - +
153C LYS* 4.7 2.9 + - - -
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Residues in contact with THR 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ARG 2.9 18.3 + - - -
144C ILE* 3.6 4.3 - - - -
146C GLN* 1.3 77.8 - - - +
148C LEU* 1.3 58.4 + - + +
150C ASN* 3.2 10.9 + - + +
151C LEU* 2.8 49.5 + - + +
173C ILE* 4.8 8.5 - - + -
176C ILE* 3.8 31.0 - - + +
177C VAL* 3.1 20.7 - - + +
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Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ILE* 2.9 24.1 + - + +
145C ALA* 3.7 5.6 - - - +
147C THR* 1.3 77.3 - - + +
149C LEU* 1.3 61.3 + - - +
151C LEU* 3.4 7.1 + - + +
152C ALA* 3.0 24.1 + - - +
166C ILE* 4.0 20.9 - - + -
173C ILE* 4.2 24.0 - - + -
188C LEU* 4.0 11.9 - - + -
191C LEU* 3.8 28.0 - - + -
197C ILE* 4.2 16.6 - - + -
204C ILE* 4.4 12.8 - - + -
206C VAL* 4.0 20.7 - - + +
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ALA* 3.2 16.3 + - + +
146C GLN* 3.2 33.0 + - - +
148C LEU* 1.3 75.0 - - - +
150C ASN* 1.3 64.9 + - - +
152C ALA* 3.2 15.3 + - - +
153C LYS* 3.3 22.9 + - - +
206C VAL* 4.6 5.6 - - + -
207C TYR 5.7 0.4 - - - +
209C THR* 3.5 27.3 - - + +
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Residues in contact with ASN 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLU* 4.7 9.3 + - - +
134C ASN* 4.8 5.5 - - - +
146C GLN* 2.8 45.6 + - - +
147C THR* 3.6 10.2 + - + +
149C LEU* 1.3 77.8 - - - +
151C LEU* 1.3 63.4 + - + +
153C LYS* 3.0 42.8 + - - +
154C GLN* 3.5 12.9 + - - +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C TYR* 3.7 33.9 - - + -
147C THR* 2.8 41.6 + - + +
148C LEU* 3.9 5.4 - - + +
150C ASN* 1.3 74.8 - - + +
152C ALA* 1.3 62.3 + - - +
154C GLN* 3.1 24.6 + - + +
156C ASP* 5.0 0.5 - - - +
157C ALA* 3.8 3.8 + - - +
166C ILE* 3.6 39.4 - - + +
168C ILE* 3.5 31.6 - - + -
173C ILE* 4.7 1.8 - - + -
176C ILE* 4.2 6.5 - - + -
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU 3.0 13.9 + - - +
149C LEU 3.4 10.8 - - - +
150C ASN 3.2 0.2 - - - -
151C LEU* 1.3 76.4 - - - +
153C LYS* 1.3 58.6 + - + +
154C GLN 3.3 0.4 - - - +
157C ALA* 3.5 16.0 - - - +
164C MET* 3.8 30.2 - - + +
166C ILE* 3.9 10.3 - - - +
206C VAL* 4.4 7.9 - - + -
209C THR* 4.0 22.9 - - + +
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Residues in contact with LYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLU* 5.7 1.8 + - - -
146C GLN* 4.7 3.6 + - - -
149C LEU* 3.3 23.5 + - - +
150C ASN* 3.0 35.5 + - - +
152C ALA* 1.3 79.1 - - + +
154C GLN* 1.3 64.6 + - - +
155C PRO* 3.8 2.3 - - - +
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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