Contacts of the helix formed by residues 153 - 170 (chain B) in PDB entry 2IHM
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 ASN 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B HIS* 2.9 12.2 + - - +
152B HIS* 1.3 82.3 - - - +
154B THR* 1.3 58.1 + - - +
155B LEU 3.5 2.0 - - - -
156B LEU* 3.5 16.4 + - + +
157B SER* 2.9 28.9 + - - -
186B LEU* 3.7 30.2 + - + +
189B LEU* 4.0 7.1 - - - +
191B CYS 3.1 24.5 + - - -
192B PRO* 4.4 0.3 - - - +
193B VAL* 2.7 41.3 + - - +
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Residues in contact with THR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS* 3.4 25.7 + - + +
152B HIS 3.8 0.9 - - - -
153B ASN* 1.3 74.7 + - - +
155B LEU* 1.3 63.4 + - + +
157B SER* 3.7 1.1 - - - -
158B GLU* 2.9 58.3 + - + +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASN 3.5 0.2 - - - -
154B THR* 1.3 81.8 - - + +
156B LEU* 1.3 67.0 + - + +
158B GLU* 3.4 17.7 + - + +
159B ALA* 3.2 21.3 + - - +
216B LEU* 4.7 6.8 - - + +
220B GLY 5.8 3.8 - - - +
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASN* 3.5 19.6 + - + +
154B THR 3.4 0.2 - - - -
155B LEU* 1.3 79.1 - - + +
157B SER* 1.3 64.8 + - - +
159B ALA* 3.1 18.7 + - - +
160B LEU* 3.4 10.0 + - - +
186B LEU* 3.9 17.0 - - + -
193B VAL* 3.6 43.1 - - + +
213B ILE* 3.9 23.6 - - + +
216B LEU* 3.6 34.8 - - + -
217B LEU* 4.3 14.6 - - + -
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS* 3.8 15.3 - - - -
153B ASN 2.9 19.7 + - - -
154B THR 3.7 2.9 - - - -
156B LEU* 1.3 77.9 - - - +
158B GLU* 1.3 62.5 + - - +
160B LEU* 3.4 3.9 + - - +
161B GLU* 3.1 29.2 + - - +
183B ALA* 3.3 24.9 + - - +
186B LEU* 3.9 12.9 - - - +
187B LYS* 3.5 19.5 - - - +
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Residues in contact with GLU 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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154B THR* 2.9 50.2 + - + +
155B LEU* 3.8 17.2 - - - +
157B SER* 1.3 72.8 - - - +
159B ALA* 1.3 65.6 + - - +
161B GLU* 3.2 13.1 + - - +
162B THR* 2.9 27.6 + - - +
229B ARG* 4.2 12.6 + - - +
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU 3.2 8.5 + - - +
156B LEU 3.1 11.3 + - - +
158B GLU* 1.3 77.6 - - - +
160B LEU* 1.3 64.5 + - + +
162B THR* 3.3 4.0 + - - -
163B LEU* 3.2 24.3 + - - +
212B VAL* 4.4 4.7 - - + -
216B LEU* 3.4 31.4 - - + -
225B VAL* 3.9 20.5 - - + +
229B ARG* 4.4 8.0 - - - +
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Residues in contact with LEU 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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156B LEU 3.4 7.5 + - - +
157B SER 3.9 5.8 - - - +
158B GLU 3.3 0.4 - - - -
159B ALA* 1.3 75.7 - - + +
161B GLU* 1.3 57.3 + - - +
163B LEU* 3.1 8.3 + - + +
164B ALA* 2.8 28.6 + - - +
179B PHE* 3.6 30.1 - - + +
182B ALA* 4.0 23.3 - - + -
183B ALA* 4.0 13.7 - - + +
186B LEU* 3.8 27.8 - - + -
205B PHE* 4.2 10.8 - - + -
209B SER* 4.3 17.0 - - - +
212B VAL* 4.4 20.2 - - + -
213B ILE* 4.3 7.4 - - + -
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Residues in contact with GLU 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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157B SER* 3.1 19.0 + - - +
158B GLU* 3.2 15.4 + - - +
160B LEU* 1.3 72.1 - - - +
162B THR* 1.3 60.4 + - - +
164B ALA* 3.2 10.2 + - + +
165B GLU* 2.9 30.1 + - - +
180B SER* 6.0 0.9 - - - -
183B ALA* 3.8 14.8 - - + +
187B LYS* 3.0 35.9 + - - -
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Residues in contact with THR 162 (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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158B GLU 2.9 9.1 + - - -
159B ALA 3.5 9.0 - - - -
161B GLU* 1.3 74.5 - - - +
163B LEU* 1.3 62.7 + - + +
165B GLU* 3.2 10.3 + - - +
166B ALA* 2.8 28.1 + - - +
225B VAL* 4.2 10.3 - - + -
228B VAL* 3.8 25.8 - - + -
229B ARG* 2.9 40.9 + - + +
234B TYR* 4.3 12.7 + - - +
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Residues in contact with LEU 163 (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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159B ALA 3.2 10.2 + - - +
160B LEU* 3.1 11.3 + - + +
162B THR* 1.3 80.1 - - + +
164B ALA* 1.3 62.1 + - - +
166B ALA* 3.5 5.4 - - + +
167B ALA* 2.9 25.3 + - - +
179B PHE* 3.8 35.0 - - + -
212B VAL* 4.0 29.4 - - + -
224B GLU* 4.0 34.5 - - + +
225B VAL* 4.1 17.7 - - + -
228B VAL* 4.1 19.7 - - + -
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Residues in contact with ALA 164 (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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160B LEU 2.8 13.6 + - - +
161B GLU* 3.2 15.0 - - + +
162B THR 3.1 0.2 - - - -
163B LEU* 1.3 78.7 - - - +
165B GLU* 1.3 56.9 + - - +
167B ALA* 3.2 0.5 + - - +
168B GLY 3.0 23.4 + - - -
176B LEU* 3.3 29.0 - - + +
179B PHE* 3.6 23.1 - - + -
180B SER* 3.9 12.8 - - - +
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU 2.9 15.7 + - - +
162B THR* 3.6 6.2 + - - +
164B ALA* 1.3 73.5 - - - +
166B ALA* 1.3 65.0 + - - +
168B GLY* 3.3 1.9 + - - +
169B PHE* 3.0 47.5 + - + -
176B LEU* 4.9 5.6 - - - -
234B TYR* 2.7 25.1 + - + -
238B LYS* 3.0 30.6 + - - +
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Residues in contact with ALA 166 (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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162B THR 2.8 20.3 + - - +
163B LEU* 3.5 10.3 - - + +
165B GLU* 1.3 71.5 - - - +
167B ALA* 1.3 65.2 + - - +
169B PHE* 3.1 13.6 + - - +
170B GLU* 3.2 20.1 + - - +
228B VAL* 3.9 30.3 - - + -
234B TYR* 4.2 14.3 - - + -
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Residues in contact with ALA 167 (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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163B LEU 2.9 13.8 + - - +
164B ALA 3.4 9.4 - - - +
166B ALA* 1.3 72.7 - - - +
168B GLY* 1.3 67.8 + - - +
170B GLU* 2.9 17.3 + - - +
172B ASN* 3.0 28.2 + - + +
175B ARG* 3.7 16.4 - - + -
176B LEU* 3.7 21.1 - - - +
179B PHE* 4.6 4.5 - - + -
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Residues in contact with GLY 168 (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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164B ALA 3.0 10.9 + - - -
165B GLU 3.3 2.9 + - - -
166B ALA 3.3 0.4 - - - -
167B ALA* 1.3 76.8 - - - +
169B PHE* 1.3 57.8 + - - +
171B ALA* 2.9 21.2 + - - -
172B ASN 4.5 1.3 - - - -
173B GLU* 3.9 12.3 - - - +
176B LEU* 3.5 28.4 - - - +
248B VAL* 3.8 15.6 - - - +
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Residues in contact with PHE 169 (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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165B GLU* 3.0 44.1 + - + -
166B ALA* 3.1 8.9 + - - +
168B GLY* 1.3 75.2 - - - +
170B GLU* 1.3 66.0 + - - +
171B ALA 3.3 1.9 + - - -
233B ARG* 3.0 19.8 + - - -
234B TYR* 3.8 24.5 - + - -
237B MET* 3.3 32.5 - - + +
238B LYS* 3.4 41.3 - - + -
241B THR* 3.2 24.7 - - + -
248B VAL* 4.0 20.7 - - + +
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Residues in contact with GLU 170 (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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166B ALA* 3.3 15.2 - - + +
167B ALA* 2.9 9.6 + - - +
169B PHE* 1.3 86.4 - - - +
171B ALA* 1.3 69.4 + - - +
172B ASN* 3.2 23.6 + - - +
233B ARG* 2.7 49.4 + - - +
234B TYR* 5.9 0.3 - - - -
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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