Contacts of the helix formed by residues 147 - 161 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ATP 4.4 6.4 + - - -
145B LEU* 3.4 1.8 - - - +
146B ASP* 1.3 84.9 - - - +
148B ILE* 1.3 59.9 + - - +
149B ILE* 4.4 9.7 - - - +
150B ALA* 2.9 32.6 + - - +
151B ARG* 2.6 32.0 + - - +
174I ARG* 4.6 2.5 - - - -
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B SER* 1.3 72.9 - - - +
149B ILE* 1.3 74.2 + - + +
150B ALA 3.2 1.1 - - - -
151B ARG* 2.7 21.2 + - + +
152B ARG* 2.7 35.1 + - + +
200B ILE* 5.8 0.4 - - + -
204B LEU* 4.6 7.0 - - + -
207B TYR* 3.9 44.6 - - + -
208B PRO 6.0 0.2 - - - +
174I ARG* 3.8 37.0 - - + -
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLN* 5.8 2.0 - - - +
147B SER* 4.5 7.4 - - - +
148B ILE* 1.3 76.9 - - + +
150B ALA* 1.3 55.0 + - - +
152B ARG* 2.7 16.2 + - - +
153B TRP* 2.6 35.3 + - + +
377B LYS* 4.7 24.2 - - + +
907B PRO 4.6 2.9 - - - +
908B GLN* 3.7 35.7 - - + +
909B THR* 4.3 6.7 - - - +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ATP 3.4 25.6 - - + +
127B ILE* 3.9 8.5 - - + +
128B GLN* 4.6 4.2 + - - -
145B LEU* 3.5 23.8 - - + -
147B SER* 2.9 21.7 + - - +
149B ILE* 1.3 79.2 - - - +
151B ARG* 1.3 63.9 + - - +
153B TRP* 3.0 5.8 + - - +
154B ILE* 2.8 25.6 + - - +
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B CYS* 5.3 1.3 - - + -
145B LEU* 2.8 39.5 + - + +
147B SER 2.6 33.4 + - - +
148B ILE* 2.7 16.6 + - + +
150B ALA* 1.3 75.0 - - - +
152B ARG* 1.3 64.4 + - + +
154B ILE* 3.2 8.2 + - - +
155B ASN* 2.8 23.6 + - - +
179B ASP* 2.6 35.6 + - - +
180B GLY 2.9 21.4 + - - -
181B GLY* 3.8 0.4 - - - -
200B ILE* 4.4 19.7 - - + +
207B TYR* 3.5 20.3 + - - -
173I LEU 3.7 12.0 + - - -
174I ARG* 3.0 25.4 + - - +
175I GLY 3.3 6.3 + - - -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ILE* 2.7 41.2 + - + +
149B ILE* 2.7 13.1 + - - +
151B ARG* 1.3 71.3 - - - +
153B TRP* 1.3 64.1 + - - +
155B ASN* 2.9 26.1 + - - +
156B GLY* 3.0 6.9 + - - -
200B ILE* 4.2 11.4 - - + +
201B GLU* 2.8 42.9 + - - +
204B LEU* 4.1 12.9 - - + +
374B LEU* 3.1 27.9 + - - +
375B GLN* 3.9 19.4 + - - +
376B MET* 4.5 9.1 - - - +
909B THR* 3.3 33.0 + - - +
910B VAL* 4.7 2.6 - - - +
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Residues in contact with TRP 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ILE* 3.5 31.6 - - + -
128B GLN* 3.5 37.3 - - + +
130B PHE 3.7 16.8 - - - -
135B TYR* 3.6 24.2 - + - -
149B ILE 2.6 12.9 + - - +
150B ALA* 3.3 11.7 - - - +
152B ARG* 1.3 72.4 - - - +
154B ILE* 1.3 81.9 + - - +
156B GLY* 2.8 18.7 + - - -
157B MET* 3.1 31.4 + - + -
908B GLN* 3.2 33.9 - - + +
909B THR 3.2 7.1 + - - -
910B VAL* 4.0 2.7 - - - +
911B LEU* 3.6 33.2 + - + +
131D ASN* 5.2 2.0 - - - -
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 3.3 31.0 - - + -
127B ILE* 4.3 4.3 - - + -
135B TYR* 4.5 9.0 - - + -
141B ILE* 4.4 12.1 - - + -
143B CYS* 4.0 20.6 - - - -
145B LEU* 5.0 0.2 - - + -
150B ALA 2.8 15.0 + - - +
151B ARG* 3.3 13.2 - - - +
153B TRP* 1.3 94.5 - - + +
155B ASN* 1.3 67.0 + - - +
157B MET* 3.9 3.1 - - + -
158B LEU* 3.0 43.1 + - + +
177B LEU* 4.2 10.3 - - + -
200B ILE* 6.0 0.2 - - + -
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Residues in contact with ASN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ARG 2.8 14.3 + - - +
152B ARG 2.9 14.5 + - - +
154B ILE* 1.3 81.8 - - - +
156B GLY* 1.3 64.5 + - - +
158B LEU* 3.6 3.3 + - - +
159B ILE* 3.3 21.9 + - - +
177B LEU* 4.3 12.1 - - - +
192B ILE* 4.6 3.5 - - - +
194B PRO* 5.4 1.0 - - - +
199B CYS* 3.4 14.6 - - - +
200B ILE* 3.3 35.6 + - + +
201B GLU* 3.7 31.9 + - - +
345B ALA* 4.2 9.3 - - - +
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Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ARG 3.0 7.5 + - - -
153B TRP 2.8 8.3 + - - -
155B ASN* 1.3 76.7 - - - +
157B MET* 1.3 54.6 + - - -
158B LEU 2.9 1.1 - - - -
159B ILE* 2.4 38.1 + - - +
160B SER* 3.1 10.6 + - - -
345B ALA* 6.0 2.2 - - - -
910B VAL* 4.8 8.1 - - - -
911B LEU* 4.6 10.1 - - - -
912B PHE* 4.9 10.0 - - - +
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Residues in contact with MET 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ASN* 4.1 3.6 - - - -
132B ASP* 3.4 46.4 - - + +
135B TYR* 3.5 39.5 - - + -
153B TRP* 3.1 32.0 + - + +
154B ILE* 3.8 9.4 - - + +
156B GLY* 1.3 72.6 - - - +
158B LEU* 1.3 60.9 + - - +
160B SER* 2.7 47.0 + - - +
161B LEU* 3.3 10.5 - - + +
911B LEU* 3.7 16.5 - - + +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TYR* 4.9 4.3 - - + +
141B ILE* 3.7 23.8 - - + -
154B ILE* 3.0 30.9 + - + +
155B ASN* 3.9 5.4 - - - +
156B GLY 2.7 4.9 + - - -
157B MET* 1.3 75.4 - - + +
159B ILE* 1.3 58.6 + - - +
161B LEU* 3.8 24.3 - - + +
162B LEU* 4.4 3.6 - - - +
175B VAL* 3.4 43.3 + - + +
177B LEU* 3.4 38.1 - - + -
194B PRO* 3.8 19.5 - - + +
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ASN* 3.3 33.0 - - - +
156B GLY* 2.4 28.1 + - - +
158B LEU* 1.3 65.6 - - - +
160B SER* 1.3 52.6 + - - +
161B LEU 2.7 5.7 + - - -
162B LEU* 2.5 55.1 + - + +
194B PRO* 3.6 20.0 - - + -
199B CYS* 4.5 4.7 - - + -
345B ALA* 4.2 15.7 - - + +
346B CYS* 4.1 33.9 - - + +
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ASP* 5.8 1.8 - - - -
136B ARG* 4.4 6.9 + - - -
156B GLY 3.1 5.8 + - - -
157B MET* 2.7 46.3 + - - +
159B ILE* 1.3 75.8 - - - +
161B LEU* 1.3 59.5 + - - +
162B LEU 3.2 7.9 + - - +
911B LEU* 5.5 0.8 - - - +
912B PHE* 5.2 15.1 - - - +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ASP* 3.6 34.1 - - + -
135B TYR* 4.2 4.5 - - + -
136B ARG* 3.8 55.2 + - + +
157B MET* 3.3 21.5 - - + +
158B LEU* 3.8 31.4 - - + +
159B ILE 2.7 0.6 + - - -
160B SER* 1.3 75.7 - - - +
162B LEU* 1.3 66.4 + - - +
163B ASN* 3.3 5.4 + - - +
173B SER* 3.6 18.6 - - - +
175B VAL* 3.9 15.9 - - + -
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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