Contacts of the helix formed by residues 141 - 157 (chain B) in PDB entry 4IRX
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 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B ALA* 1.3 67.7 - - - +
142B ASN* 1.3 59.9 + - - +
143B VAL* 3.4 9.7 + - - +
144B ALA* 3.1 27.4 + - - +
145B GLY 3.1 20.1 + - - -
305B SER* 3.5 18.4 + - - +
306B LEU 2.8 17.6 + - - +
307B LYS* 4.8 1.7 - - + +
308B PRO* 3.4 16.4 - - + +
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Residues in contact with ASN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP 3.9 12.3 + - - -
137B HIS* 5.9 0.4 + - - -
140B ALA* 3.0 28.5 + - - +
141B ASP* 1.3 71.3 + - - +
143B VAL* 1.3 61.6 + - - +
145B GLY* 3.7 2.1 - - - +
146B GLY 3.0 24.1 + - - -
173B SER* 5.7 0.2 + - - -
174B SER* 3.4 31.7 - - - +
177B GLU* 3.7 27.8 + - + +
178B ARG* 2.9 45.3 + - + +
257B PHE* 3.6 9.0 - - - -
278B GLN* 5.1 0.6 + - - -
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP* 3.4 7.8 + - - +
142B ASN* 1.3 78.0 - - - +
144B ALA* 1.3 57.8 + - - +
146B GLY 3.3 0.2 + - - -
147B ARG* 2.9 30.4 + - + +
177B GLU* 3.4 38.6 - - + +
180B LYS* 4.2 20.0 - - + +
181B GLY* 3.4 10.0 - - - +
184B ASP* 3.9 21.3 - - - +
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Residues in contact with ALA 144 (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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141B ASP* 3.1 34.1 + - + +
143B VAL* 1.3 77.1 - - - +
145B GLY* 1.3 57.4 + - - +
147B ARG* 3.4 6.6 + - - +
148B ALA* 3.0 29.3 + - - +
307B LYS* 5.7 3.4 - - + -
308B PRO* 4.0 12.9 - - + +
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Residues in contact with GLY 145 (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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141B ASP 3.1 11.6 + - - -
142B ASN 3.3 3.5 + - - -
143B VAL 3.2 0.4 - - - -
144B ALA* 1.3 74.3 - - - +
146B GLY* 1.3 62.9 + - - +
148B ALA* 3.2 14.0 + - - +
149B MSE 3.3 16.1 + - - +
257B PHE* 3.8 22.4 - - - -
276B VAL* 4.4 4.3 - - - +
308B PRO* 3.5 18.3 - - - +
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Residues in contact with GLY 146 (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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142B ASN 3.0 11.3 + - - -
143B VAL 3.8 1.6 - - - -
145B GLY* 1.3 75.1 - - - +
147B ARG* 1.3 61.5 + - - +
149B MSE 3.2 13.0 + - - +
150B ALA 3.1 17.8 + - - -
178B ARG* 3.4 26.7 - - - +
181B GLY 3.5 7.0 - - - -
182B VAL* 3.5 14.6 + - - +
257B PHE* 4.2 1.8 - - - -
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Residues in contact with ARG 147 (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 VAL* 2.9 20.2 + - + +
144B ALA* 3.7 7.9 - - - +
146B GLY* 1.3 76.8 - - - +
148B ALA* 1.3 57.6 + - - +
150B ALA* 3.3 1.1 + - - +
151B ASP* 2.8 63.5 + - - +
181B GLY* 3.3 12.2 - - - +
184B ASP* 3.5 24.0 + - + +
185B GLY* 3.4 23.5 - - - +
188B ALA* 3.7 22.4 - - - +
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Residues in contact with ALA 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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144B ALA 3.0 15.1 + - - +
145B GLY* 3.2 11.4 + - - +
147B ARG* 1.3 76.6 - - - +
149B MSE 1.3 61.3 + - - +
151B ASP* 3.4 8.1 + - - +
152B TRP* 3.1 22.7 + - - +
276B VAL* 5.5 2.7 - - + -
308B PRO* 6.1 2.5 - - + +
309B VAL* 6.2 0.2 - - - -
310B LEU* 4.2 31.9 - - + +
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Residues in contact with MSE 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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145B GLY 3.5 10.3 - - - +
146B GLY* 3.2 16.7 + - - +
148B ALA* 1.3 76.0 - - - +
150B ALA* 1.3 63.7 + - - +
152B TRP* 3.3 13.1 + - - +
153B VAL* 3.3 17.5 + - - +
182B VAL* 4.3 4.5 - - + -
228B LEU* 4.1 20.9 - - + -
229B CYS 3.3 34.5 - - - +
230B LEU* 4.2 15.7 - - + -
255B ILE* 3.6 27.1 - - + +
256B GLY 3.3 15.0 - - - +
257B PHE* 4.0 19.1 - - - -
276B VAL* 4.0 14.1 - - + -
310B LEU* 4.5 7.2 - - + -
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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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146B GLY 3.1 9.5 + - - +
147B ARG 3.8 3.8 - - - +
149B MSE 1.3 76.8 - - - +
151B ASP* 1.3 67.1 + - - +
153B VAL* 3.1 8.9 + - - +
154B VAL* 3.0 25.4 + - - +
182B VAL* 3.4 31.2 - - + +
185B GLY* 3.7 16.8 - - - -
186B LEU* 3.8 15.4 - - + +
228B LEU* 4.6 2.9 - - - +
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Residues in contact with ASP 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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147B ARG* 2.8 61.2 + - - +
148B ALA* 3.8 8.3 - - - +
149B MSE 3.3 0.2 - - - -
150B ALA* 1.3 77.8 - - - +
152B TRP* 1.3 61.9 + - - +
154B VAL* 3.3 7.0 + - - +
155B LYS* 3.0 26.2 + - - +
185B GLY* 4.1 5.4 - - - +
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Residues in contact with TRP 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 ALA 3.1 12.7 + - - +
149B MSE 3.5 9.0 - - - +
150B ALA 3.2 0.2 - - - -
151B ASP* 1.3 77.6 - - - +
153B VAL* 1.3 62.6 + - + +
155B LYS* 3.8 11.9 - - + +
156B THR* 2.7 67.6 + - + -
157B TYR* 4.0 21.5 - + - -
226B VAL* 4.3 12.3 - - + -
253B LYS* 4.4 12.6 - - + -
255B ILE* 3.6 26.9 - - + -
273B VAL* 3.4 40.1 - - + +
274B ALA* 5.3 0.7 - - + -
310B LEU* 3.9 25.1 - - + -
312B THR* 4.6 13.4 - - + +
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Residues in contact with VAL 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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149B MSE 3.5 13.5 - - - +
150B ALA* 3.1 10.2 + - - +
152B TRP* 1.3 93.6 - - + +
154B VAL* 1.3 57.4 + - - +
156B THR 3.2 0.3 + - - -
157B TYR* 2.9 36.4 + - + +
161B ALA* 4.0 26.0 - - + -
163B VAL* 4.1 14.8 - - + -
186B LEU* 4.3 6.1 - - + -
193B PHE* 4.1 10.3 - - + -
226B VAL* 4.0 23.1 - - + -
228B LEU* 4.1 12.3 - - + -
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Residues in contact with VAL 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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150B ALA 3.0 16.0 + - - +
151B ASP* 3.3 8.0 + - - +
153B VAL* 1.3 76.3 - - - +
155B LYS* 1.3 60.9 + - - +
158B PRO* 3.6 21.5 - - - +
185B GLY 3.7 22.0 - - - +
186B LEU* 4.3 4.7 - - + -
189B GLY* 4.1 15.0 - - - +
193B PHE* 3.6 37.2 - - + -
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Residues in contact with LYS 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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251A LYS* 4.0 27.7 - - - +
151B ASP 3.0 18.2 + - - +
152B TRP* 3.8 11.3 - - + +
154B VAL* 1.3 80.0 - - - +
156B THR* 1.3 65.5 + - - +
158B PRO* 3.7 11.4 - - - +
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Residues in contact with THR 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 TRP* 2.7 57.4 + - + -
155B LYS* 1.3 80.9 - - - +
157B TYR* 1.3 83.3 - - + +
158B PRO* 3.3 9.0 - - - +
253B LYS* 6.5 0.2 - - - -
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Residues in contact with TYR 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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152B TRP* 4.0 7.9 - + - -
153B VAL* 2.9 21.0 + - + +
154B VAL 3.8 2.5 - - - -
156B THR* 1.3 98.8 - - + +
158B PRO* 1.3 67.9 - - - +
159B ALA 3.1 3.1 - - - -
160B GLY 2.9 30.4 + - - +
161B ALA* 3.9 11.7 - - + -
193B PHE* 3.1 11.8 - - + -
225B ASP* 3.6 29.0 + - + +
226B VAL* 3.6 26.0 - - + -
251B LYS 5.2 2.1 + - - -
253B LYS* 3.5 27.2 + - - +
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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