Contacts of the helix formed by residues 147 - 161 (chain F) in PDB entry 1R4N
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 147 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F ATP 4.8 3.7 + - - -
145F LEU* 3.5 1.6 - - - +
146F ASP* 1.3 85.3 - - - +
148F ILE* 1.3 60.7 + - - +
149F ILE* 4.4 11.2 - - - +
150F ALA* 2.9 32.7 + - - +
151F ARG* 2.7 31.0 + - - +
174K ARG* 4.6 2.2 - - - -
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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
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147F SER* 1.3 75.7 - - - +
149F ILE* 1.3 73.1 + - + +
151F ARG* 2.7 21.3 + - + +
152F ARG* 2.7 35.4 + - + +
200F ILE* 5.8 0.4 - - + -
204F LEU* 4.6 7.4 - - + -
207F TYR* 3.9 48.5 - - + -
208F PRO 6.1 0.4 - - - +
174K ARG* 3.9 30.3 - - + -
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Residues in contact with ILE 149 (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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128F GLN* 5.8 1.6 - - - +
147F SER* 4.5 8.5 - - - +
148F ILE* 1.3 77.6 - - + +
150F ALA* 1.3 54.6 + - - +
152F ARG* 2.8 15.4 + - - +
153F TRP* 2.5 35.7 + - + +
377F LYS* 4.7 24.5 - - + +
907F PRO 4.5 2.9 - - - +
908F GLN* 3.7 35.7 - - + +
909F THR* 4.3 6.3 - - - +
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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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7F ATP 3.9 21.8 - - - +
127F ILE* 3.8 6.5 - - + +
128F GLN* 4.6 6.0 + - - +
145F LEU* 3.5 27.6 - - + -
147F SER* 2.9 21.1 + - - +
148F ILE 3.2 0.4 - - - -
149F ILE* 1.3 78.3 - - - +
151F ARG* 1.3 63.6 + - - +
153F TRP* 3.3 5.4 - - - +
154F ILE* 2.8 26.5 + - - +
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Residues in contact with ARG 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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143F CYS* 5.3 1.3 - - + -
145F LEU* 2.8 37.4 + - + +
147F SER 2.7 33.1 + - - +
148F ILE* 2.7 16.6 + - + +
150F ALA* 1.3 75.0 - - - +
152F ARG* 1.3 63.4 + - - +
154F ILE* 3.3 11.4 - - - +
155F ASN* 2.9 24.0 + - - +
179F ASP* 2.6 34.8 + - - +
180F GLY 2.9 20.8 + - - -
181F GLY* 3.8 0.2 - - - -
200F ILE* 4.4 18.4 - - + +
207F TYR* 3.5 20.1 + - - -
173K LEU 3.7 14.2 + - - -
174K ARG* 3.1 24.0 + - - +
175K GLY 3.3 6.5 + - - -
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Residues in contact with ARG 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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148F ILE* 2.7 42.1 + - + +
149F ILE* 2.8 13.8 + - - +
151F ARG* 1.3 71.7 - - - +
153F TRP* 1.3 62.8 + - - +
155F ASN* 2.9 25.5 + - - +
156F GLY* 3.0 6.6 + - - -
200F ILE* 4.2 11.9 - - + +
201F GLU* 2.8 41.9 + - - +
204F LEU* 4.2 11.9 - - + +
374F LEU* 3.1 28.1 + - - +
375F GLN* 3.9 19.4 + - - +
376F MET* 4.7 8.5 - - - +
909F THR* 3.3 33.3 + - - +
910F VAL* 4.6 3.0 - - - +
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Residues in contact with TRP 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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127F ILE* 3.5 30.5 - - + -
128F GLN* 3.5 37.7 - - + +
130F PHE 3.7 16.4 - - - -
135F TYR* 3.6 21.5 - + - -
149F ILE 2.5 13.7 + - - +
150F ALA* 3.3 12.3 - - - +
152F ARG* 1.3 71.4 - - - +
154F ILE* 1.3 83.4 + - + +
156F GLY* 2.7 19.9 + - - -
157F MET* 3.1 34.2 + - + -
908F GLN* 3.2 35.2 - - + +
909F THR 3.2 6.7 + - - -
910F VAL* 4.1 2.7 + - - +
911F LEU* 3.6 31.9 + - + +
131H ASN* 5.3 1.8 - - - -
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Residues in contact with ILE 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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54F ILE* 3.2 31.9 - - + -
127F ILE* 4.2 3.6 - - + -
135F TYR* 4.5 9.9 - - + -
141F ILE* 4.4 11.7 - - + -
143F CYS* 4.0 21.5 - - - -
150F ALA 2.8 15.6 + - - +
151F ARG* 3.3 13.5 - - - +
153F TRP* 1.3 93.5 - - + +
155F ASN* 1.3 65.8 + - - +
157F MET* 4.3 2.9 - - + -
158F LEU* 3.1 44.2 + - + +
177F LEU* 4.3 9.9 - - + -
200F ILE* 6.0 0.2 - - + -
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Residues in contact with ASN 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 ARG 2.9 15.0 + - - +
152F ARG 2.9 13.8 + - - +
153F TRP 2.9 0.2 + - - -
154F ILE* 1.3 82.3 - - - +
156F GLY* 1.3 63.4 + - - +
158F LEU* 3.6 3.3 + - - +
159F ILE* 3.2 26.7 + - - +
177F LEU* 4.3 11.7 - - - +
192F ILE* 4.6 3.5 - - - +
194F PRO* 5.4 1.2 - - - +
199F CYS* 3.4 18.8 - - - +
200F ILE* 3.3 33.9 + - + +
201F GLU* 3.6 28.9 + - - +
345F ALA* 4.3 4.6 - - - +
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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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152F ARG 3.0 7.7 + - - -
153F TRP 2.7 8.2 + - - -
155F ASN* 1.3 76.2 - - - +
157F MET* 1.3 55.5 + - - -
158F LEU 2.9 1.3 - - - -
159F ILE* 2.4 38.3 + - - +
160F SER* 3.1 10.4 + - - -
345F ALA* 6.0 2.2 - - - -
910F VAL* 4.8 7.9 - - - -
911F LEU* 4.6 10.3 - - - -
912F PHE* 4.9 9.6 - - - +
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Residues in contact with MET 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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130F PHE 4.7 0.2 - - - +
131F ASN* 4.0 4.0 - - - -
132F ASP* 3.4 48.0 - - + +
135F TYR* 3.5 39.3 - - + -
153F TRP* 3.1 31.7 + - + +
154F ILE* 3.8 9.4 - - + +
156F GLY* 1.3 72.7 - - - +
158F LEU* 1.3 61.0 + - - +
160F SER* 2.6 47.3 + - - +
161F LEU* 3.3 9.9 - - + +
911F LEU* 3.8 15.5 - - + +
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Residues in contact with LEU 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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135F TYR* 4.9 4.0 - - + +
141F ILE* 3.6 24.2 - - + -
154F ILE* 3.1 31.9 + - + +
155F ASN* 4.0 5.4 - - - +
156F GLY 2.6 4.8 + - - -
157F MET* 1.3 74.3 - - - +
159F ILE* 1.3 59.3 + - - +
161F LEU* 3.9 25.8 - - + +
162F LEU* 4.4 3.5 - - - +
175F VAL* 3.4 44.8 + - + +
177F LEU* 3.4 37.7 - - + -
194F PRO* 3.8 19.8 - - + +
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Residues in contact with ILE 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 ASN* 3.2 34.5 - - - +
156F GLY* 2.4 27.0 + - - +
158F LEU 1.3 67.0 - - - +
160F SER* 1.3 53.3 + - - +
161F LEU 2.7 5.5 + - - -
162F LEU* 2.5 55.3 + - + +
194F PRO* 3.6 20.2 - - + -
199F CYS* 4.5 3.6 - - + -
345F ALA* 4.2 15.9 - - + +
346F CYS* 4.1 33.9 - - + +
912F PHE* 6.3 1.1 - - + -
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Residues in contact with SER 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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132F ASP* 5.7 2.0 - - - -
136F ARG* 4.4 6.9 + - - -
156F GLY 3.1 5.6 + - - -
157F MET* 2.6 46.9 + - - +
159F ILE* 1.3 75.5 - - - +
161F LEU* 1.3 60.5 + - - +
162F LEU 3.1 7.6 + - - +
911F LEU* 5.6 1.2 - - - +
912F PHE* 5.2 15.1 - - - +
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Residues in contact with LEU 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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132F ASP* 3.6 33.2 - - + -
135F TYR* 4.2 4.9 - - + -
136F ARG* 3.8 54.5 + - + +
157F MET* 3.3 22.9 - - + +
158F LEU* 3.9 32.8 - - + +
159F ILE 2.7 1.0 + - - -
160F SER* 1.3 76.6 - - - +
162F LEU* 1.3 67.6 + - - +
163F ASN* 3.3 5.4 + - - +
173F SER* 3.6 18.6 - - - +
175F VAL* 4.0 14.8 - - + -
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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