Contacts of the helix formed by residues 141 - 157 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ALA* 1.3 68.1 - - - +
142A ASN* 1.3 59.1 + - - +
143A VAL* 3.5 9.7 + - - +
144A ALA* 3.1 28.4 + - - +
145A GLY 3.0 20.4 + - - -
257A PHE* 5.6 0.2 - - - -
305A SER* 3.4 20.1 + - - +
306A LEU 2.9 17.9 + - - +
307A LYS* 4.8 1.6 - - - -
308A PRO* 3.5 15.4 - - + +
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP 3.8 12.1 + - - -
137A HIS* 5.9 0.4 + - - -
140A ALA* 3.0 29.0 + - - +
141A ASP* 1.3 72.4 + - - +
143A VAL* 1.3 61.5 + - - +
145A GLY* 3.6 2.0 - - - +
146A GLY 2.9 24.9 + - - -
173A SER* 5.5 0.8 + - - -
174A SER* 3.5 30.8 - - - +
177A GLU* 3.7 28.3 + - + +
178A ARG* 2.9 44.3 + - + +
257A PHE* 3.6 9.2 - - - -
278A GLN* 5.1 0.6 + - - -
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 3.4 7.7 + - - +
142A ASN* 1.3 78.4 - - - +
144A ALA* 1.3 57.9 + - - +
146A GLY 3.3 0.3 + - - -
147A ARG* 2.9 30.5 + - + +
177A GLU* 3.4 38.6 + - + +
180A LYS* 4.4 18.6 - - + +
181A GLY* 3.4 8.1 - - - +
184A ASP* 4.0 20.4 - - - +
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Residues in contact with ALA 144 (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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141A ASP* 3.1 35.0 + - + +
143A VAL* 1.3 76.5 - - - +
145A GLY* 1.3 57.4 + - - +
147A ARG* 3.4 6.4 + - - +
148A ALA* 2.9 29.8 + - - +
307A LYS* 5.8 2.9 - - + -
308A PRO* 4.0 12.9 - - + +
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Residues in contact with GLY 145 (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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141A ASP 3.0 12.0 + - - -
142A ASN 3.2 3.5 + - - -
143A VAL 3.2 0.4 - - - -
144A ALA* 1.3 76.6 - - - +
146A GLY* 1.3 60.6 + - - +
148A ALA* 3.3 7.9 + - - +
149A MSE 3.3 24.1 + - - +
257A PHE* 3.8 23.2 - - - -
276A VAL* 4.4 2.3 - - - +
308A PRO* 3.5 18.3 - - - +
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Residues in contact with GLY 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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142A ASN 2.9 15.0 + - - -
143A VAL 3.8 1.1 - - - -
145A GLY* 1.3 72.1 - - - +
147A ARG* 1.3 61.5 + - - +
149A MSE 3.2 12.8 + - - +
150A ALA 3.1 17.7 + - - -
178A ARG* 3.4 26.7 - - - +
181A GLY 3.5 7.0 - - - -
182A VAL* 3.5 13.9 + - - +
257A PHE* 4.3 1.8 - - - -
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Residues in contact with ARG 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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143A VAL* 2.9 19.6 + - + +
144A ALA* 3.7 7.6 - - - +
146A GLY* 1.3 77.2 - - - +
148A ALA* 1.3 57.9 + - - +
150A ALA* 3.3 1.1 + - - +
151A ASP* 2.8 63.1 + - - +
181A GLY* 3.3 12.4 - - - +
184A ASP* 3.5 24.6 + - + +
185A GLY* 3.3 23.5 - - - +
188A ALA* 3.6 22.8 - - - +
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Residues in contact with ALA 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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144A ALA 2.9 14.6 + - - +
145A GLY* 3.5 11.7 - - - +
146A GLY 3.3 0.2 - - - -
147A ARG* 1.3 77.1 - - - +
149A MSE 1.3 61.4 + - + +
151A ASP* 3.9 7.3 - - - +
152A TRP* 3.0 24.3 + - - +
276A VAL* 5.3 3.6 - - + -
308A PRO* 5.8 3.8 - - + +
309A VAL 5.9 0.2 - - - -
310A LEU* 4.5 28.5 - - + +
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Residues in contact with MSE 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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145A GLY 3.4 13.0 - - - +
146A GLY* 3.4 8.3 - - - +
148A ALA* 1.3 78.0 - - - +
150A ALA* 1.3 61.7 + - - +
152A TRP* 3.3 9.7 + - - +
153A VAL* 3.2 24.1 + - - +
178A ARG* 5.5 0.2 - - - -
182A VAL* 4.4 9.4 - - + -
228A LEU* 4.2 19.9 - - + +
229A CYS 3.3 34.1 - - - +
230A LEU* 4.2 16.2 - - - -
255A ILE* 3.7 24.9 - - + +
256A GLY 3.4 16.6 - - - +
257A PHE* 3.9 17.7 - - - -
276A VAL* 4.0 13.9 - - + -
310A LEU* 4.8 4.2 - - + +
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Residues in contact with ALA 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 GLY 3.1 2.8 + - - -
147A ARG 3.8 3.8 - - - +
149A MSE 1.3 77.0 - - - +
151A ASP* 1.3 62.4 + - - +
153A VAL* 3.0 7.6 + - - +
154A VAL* 3.0 31.8 + - - +
181A GLY 4.2 0.2 - - - +
182A VAL* 3.3 37.0 - - + +
185A GLY* 3.6 17.9 - - - -
186A LEU* 3.8 14.8 - - + +
228A LEU* 4.6 3.1 - - - +
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Residues in contact with ASP 151 (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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147A ARG* 2.8 62.7 + - - +
148A ALA* 3.9 7.7 + - - +
150A ALA* 1.3 71.8 - - - +
152A TRP* 1.3 58.2 + - - +
154A VAL* 3.3 7.6 + - - +
155A LYS* 2.9 31.3 + - - +
185A GLY* 4.1 5.4 - - - +
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Residues in contact with TRP 152 (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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148A ALA 3.0 14.0 + - - +
149A MSE 3.4 8.5 - - - +
150A ALA 3.2 0.2 - - - -
151A ASP* 1.3 77.8 - - - +
153A VAL* 1.3 67.9 + - + +
155A LYS* 3.8 8.3 - - + +
156A THR* 2.7 65.0 + - + -
157A TYR* 4.3 2.7 - + - -
226A VAL* 4.1 22.4 - - + -
253A LYS* 3.8 27.8 - - + -
255A ILE* 3.2 31.9 - - + -
273A VAL* 3.9 25.0 - - + +
274A ALA* 5.1 1.9 - - + +
310A LEU* 3.8 27.8 - - + -
312A THR* 4.9 11.3 - - + +
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Residues in contact with VAL 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 MSE 3.5 13.5 - - - +
150A ALA* 3.0 8.8 + - - +
152A TRP* 1.3 93.2 - - + +
154A VAL* 1.3 59.8 + - - +
156A THR 3.2 0.3 + - - -
157A TYR* 2.8 36.3 + - + +
161A ALA* 4.2 10.5 - - + -
163A VAL* 4.0 23.3 - - + -
186A LEU* 4.2 6.5 - - + -
193A PHE* 4.2 16.6 - - + -
226A VAL* 4.0 11.2 - - + -
228A LEU* 4.0 25.4 - - + -
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Residues in contact with VAL 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 ALA 3.0 15.9 + - - +
151A ASP* 3.3 8.9 + - - +
153A VAL* 1.3 76.1 - - - +
155A LYS* 1.3 64.2 + - - +
157A TYR 3.7 13.2 - - - -
158A PRO* 3.7 8.6 - - + +
185A GLY 3.7 21.8 - - - +
186A LEU* 4.2 5.4 - - + -
189A GLY* 4.2 11.9 - - - -
193A PHE* 3.7 35.2 - - + -
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Residues in contact with LYS 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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151A ASP 2.9 17.6 + - - +
152A TRP* 3.9 7.9 - - + +
154A VAL* 1.3 78.1 - - - +
156A THR* 1.3 62.0 + - - +
158A PRO* 3.5 11.0 - - - +
317B THR* 3.2 24.0 - - + +
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Residues in contact with THR 156 (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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152A TRP* 2.7 56.2 + - + -
155A LYS* 1.3 80.4 - - - +
157A TYR* 1.3 87.8 + - + +
158A PRO* 3.4 7.4 - - - +
253A LYS* 5.0 6.7 - - - -
313B SER 5.1 0.3 - - - +
314B GLY 4.9 3.8 - - - +
315B ASN* 5.0 2.0 - - - -
316B LEU 4.6 8.8 + - - -
317B THR* 3.8 25.7 + - - +
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Residues in contact with TYR 157 (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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152A TRP* 4.3 4.9 - + - -
153A VAL* 2.8 19.3 + - + +
154A VAL 3.7 2.7 - - - -
156A THR* 1.3 99.6 - - + +
158A PRO* 1.3 65.9 - - - +
159A ALA 3.1 3.1 - - - -
160A GLY 2.9 30.5 + - - +
161A ALA* 3.7 15.3 - - + -
193A PHE* 3.0 13.0 - - + -
225A ASP* 3.6 36.2 + - + +
226A VAL* 3.5 22.7 - - + -
251A LYS* 4.6 3.3 + - - -
253A LYS* 3.3 26.9 - - - +
313B SER 4.3 11.4 - - - -
314B GLY* 3.5 28.1 + - - -
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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