Contacts of the helix formed by residues 171 - 189 (chain B) in PDB entry 1M6X
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 PHE 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B SER* 3.8 3.5 - - - +
170B ARG* 1.3 113.6 - - + +
172B THR* 1.3 65.0 + - - +
173B LYS* 4.1 9.2 - - + +
174B THR* 3.0 29.1 + - + +
175B LYS* 3.2 14.0 + - - +
3F A 6.1 0.2 - - - -
4F G 4.4 19.1 - - - -
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Residues in contact with THR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE* 1.3 72.6 - - - +
173B LYS* 1.3 69.0 + - - +
175B LYS* 3.1 12.5 + - - +
176B THR* 2.7 36.4 + - - +
247B GLU* 5.7 2.0 - - - +
251B ASN* 3.6 25.1 - - - +
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE* 4.1 6.0 - - + +
172B THR* 1.3 80.3 - - - +
174B THR* 1.3 54.5 + - + +
176B THR* 3.0 2.8 + - - -
177B LEU* 2.7 54.1 + - + +
251B ASN* 3.3 37.6 + - + +
252B SER* 3.4 25.2 + - - +
253B GLU* 4.9 12.5 + - - +
276B LYS* 3.0 33.3 - - - +
5F T 5.9 2.5 - - - +
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER* 3.8 0.5 - - - -
171B PHE* 3.0 29.1 + - + -
173B LYS* 1.3 78.7 - - + +
175B LYS* 1.3 62.0 + - - -
177B LEU* 4.2 11.0 - - + -
178B TYR* 2.8 49.9 + - + +
4F G 3.1 55.6 + - - +
5F T 4.6 7.2 - - - +
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE 3.6 20.9 - - - +
166B GLU* 3.1 49.8 + - - +
169B SER* 3.3 14.8 - - - +
171B PHE 3.2 14.1 + - - +
172B THR* 3.1 12.3 + - - +
174B THR* 1.3 81.1 + - - +
176B THR* 1.3 70.2 + - - +
178B TYR* 4.0 2.0 - - - +
179B GLN* 3.0 49.4 + - - +
247B GLU* 5.9 1.6 + - - +
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Residues in contact with THR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 2.7 22.3 + - - +
173B LYS* 3.2 11.7 - - - +
175B LYS* 1.3 85.1 - - - +
177B LEU* 1.3 59.1 + - + +
179B GLN* 3.9 3.8 - - - +
180B PHE* 2.8 32.4 + - - +
244B TYR* 4.9 1.0 - - - +
247B GLU* 2.9 39.0 + - + +
248B PHE* 3.2 23.6 - - + +
251B ASN* 3.5 18.2 + - + +
252B SER* 6.1 0.2 - - - -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LYS* 2.7 46.8 + - + +
174B THR* 3.6 11.2 - - + +
176B THR* 1.3 73.5 - - + +
178B TYR* 1.3 59.8 + - - +
180B PHE* 3.3 3.5 + - + +
181B LEU* 2.8 35.3 + - - +
248B PHE* 3.7 23.8 - - + -
252B SER* 3.6 23.3 - - - +
275B LEU* 4.4 4.3 - - + -
276B LYS* 6.1 3.1 - - + +
279B LEU* 3.9 38.4 - - + +
5F T 5.6 5.4 - - - +
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Residues in contact with TYR 178 (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 PHE* 3.5 39.3 - + + -
169B SER* 3.7 11.0 - - - -
174B THR* 2.8 36.1 + - + +
175B LYS 4.0 1.8 - - - +
177B LEU* 1.3 74.0 - - - +
179B GLN* 1.3 58.2 + - - +
182B PHE* 2.8 32.3 + - - +
279B LEU* 3.9 16.8 - - + -
282B SER* 3.3 27.5 + - - -
283B TYR* 3.5 41.7 - + + -
286B ALA* 3.9 8.7 - - + -
4F G 3.2 42.0 + - - -
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Residues in contact with GLN 179 (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 LEU* 3.0 52.6 + - + +
163B ASN* 4.4 2.6 - - - +
165B PHE* 4.0 9.2 - - + -
166B GLU* 3.7 29.7 + - - +
175B LYS* 3.0 43.6 + - - +
176B THR* 4.0 3.0 - - - +
178B TYR* 1.3 75.1 - - - +
180B PHE* 1.3 63.6 + - - +
182B PHE* 4.6 0.9 - - - -
183B LEU* 3.1 22.7 + - - +
244B TYR* 3.7 30.1 + - + -
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Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B THR 2.8 23.0 + - - +
177B LEU 3.6 3.1 - - - +
179B GLN* 1.3 71.1 - - - +
181B LEU* 1.3 60.0 + - - +
183B LEU* 3.7 1.2 - - - +
184B ALA* 2.7 38.7 + - + +
195B ILE* 4.4 8.5 - - + -
232B PHE* 3.3 43.3 - + - -
241B PRO 5.7 0.2 - - - -
244B TYR* 3.8 22.3 - - + +
245B LEU* 3.7 20.4 - - + -
248B PHE* 3.6 57.2 - + + -
274B LEU* 3.9 15.7 - - + -
275B LEU* 4.2 10.5 - - + -
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Residues in contact with LEU 181 (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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177B LEU 2.8 21.5 + - - +
178B TYR 3.7 2.7 - - - +
180B PHE* 1.3 76.7 - - + +
182B PHE* 1.3 67.4 + - - +
184B ALA* 3.0 5.4 + - - +
185B THR* 2.8 46.8 + - + +
192B PHE* 3.8 32.8 - - + -
195B ILE* 4.1 9.9 - - + -
275B LEU* 3.8 20.6 - - + -
279B LEU* 4.1 15.9 - - + -
283B TYR* 3.8 37.0 - - + -
304B SER* 5.1 2.0 - - - -
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Residues in contact with PHE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B THR* 3.4 43.5 - - + -
161B ILE* 3.8 37.2 - - + -
162B LEU* 3.8 19.1 - - + -
165B PHE* 4.6 3.1 - - + -
178B TYR 2.8 20.2 + - - +
179B GLN* 4.0 2.7 - - - +
181B LEU* 1.3 72.3 - - - +
183B LEU* 1.3 75.4 + - - +
185B THR* 2.7 27.2 + - - -
186B PHE* 3.0 9.8 + - + +
283B TYR* 3.1 27.3 + - + +
304B SER 6.0 0.2 - - - -
306B ILE* 3.7 27.4 - - + -
307B GLY* 4.4 5.4 - - - -
310B LEU* 4.0 13.7 - - + -
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Residues in contact with LEU 183 (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 TRP* 4.6 2.2 - - + -
158B THR* 4.5 8.5 - - + -
162B LEU* 4.5 8.1 - - + -
179B GLN 3.1 15.7 + - - +
180B PHE* 3.9 2.7 - - - +
182B PHE* 1.3 83.6 - - - +
184B ALA* 1.3 62.6 - - - +
186B PHE* 3.2 13.1 + - + +
187B ILE* 2.9 51.3 + - + +
239B ILE* 3.8 24.7 - - + -
241B PRO* 3.6 35.7 - - + -
244B TYR* 3.8 24.5 - - + -
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Residues in contact with ALA 184 (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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180B PHE* 2.7 26.9 + - + +
181B LEU 3.2 5.6 - - - +
183B LEU* 1.3 74.3 - - - +
185B THR* 1.3 63.3 + - - +
187B ILE* 4.8 2.5 - - - -
188B ASN* 3.0 33.2 + - - +
195B ILE* 3.8 29.4 - - + -
232B PHE* 4.3 21.8 - - + -
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Residues in contact with THR 185 (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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181B LEU* 2.8 43.1 + - + +
182B PHE* 2.7 22.6 + - - -
184B ALA* 1.3 72.3 - - - +
186B PHE* 1.3 56.5 + - - +
189B CYS* 2.8 25.5 + - - -
190B GLY 3.1 26.6 + - - +
191B ARG 4.5 6.3 - - - +
192B PHE* 4.7 1.8 - - + -
195B ILE* 3.7 15.7 - - + -
283B TYR* 5.3 0.8 + - + -
304B SER* 4.2 16.0 + - - +
307B GLY* 3.7 18.0 + - - -
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Residues in contact with PHE 186 (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 ILE* 3.7 31.0 - - + -
155B TRP* 4.0 32.8 - + - -
158B THR* 3.9 26.5 - - + -
182B PHE* 3.0 12.3 + - + +
183B LEU* 3.5 11.2 - - + +
185B THR* 1.3 78.9 + - - +
187B ILE* 1.3 78.7 + - + +
189B CYS 3.2 8.8 + - - -
307B GLY* 3.8 24.0 - - - +
310B LEU* 4.0 9.4 - - + -
311B MET* 3.3 56.5 - - + +
314B PHE* 5.1 4.0 - + + -
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Residues in contact with ILE 187 (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 TRP* 4.2 8.3 - - + -
183B LEU* 2.9 39.2 + - + +
184B ALA* 3.8 5.2 - - - +
186B PHE* 1.3 91.1 - - + +
188B ASN* 1.3 59.7 + - - +
231B TYR* 4.1 14.6 - - + +
232B PHE* 5.4 1.3 - - + -
233B PHE* 3.1 40.2 - - + -
241B PRO* 4.2 14.8 - - + -
311B MET* 4.5 1.8 - - - -
354B TYR* 2.6 31.2 + - - -
355B PHE* 5.7 0.6 - - + -
358B VAL* 3.7 21.3 - - + +
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Residues in contact with ASN 188 (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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184B ALA* 3.0 29.6 + - - +
187B ILE* 1.3 81.9 - - - +
189B CYS* 1.3 72.5 + - - +
190B GLY 4.2 3.4 - - - +
195B ILE* 4.3 2.0 - - + +
228B ARG* 2.9 33.6 + - - +
230B ILE* 3.3 31.1 - - + +
231B TYR* 2.5 55.5 + - - +
327B VAL* 3.1 8.7 - - - +
350B ILE* 5.3 2.5 - - - +
354B TYR* 4.7 0.9 - - - -
355B PHE* 5.5 0.5 - - - -
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Residues in contact with CYS 189 (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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185B THR 2.8 12.6 + - - -
186B PHE 3.2 6.5 + - - -
187B ILE 3.4 0.2 - - - -
188B ASN* 1.3 81.5 - - - +
190B GLY* 1.3 58.5 + - - +
228B ARG* 3.7 0.5 + - - -
308B ARG* 3.6 28.9 + - - +
311B MET* 3.6 20.6 - - + -
312B THR* 3.8 23.1 - - - -
315B LEU* 5.6 2.0 - - - -
324B THR* 5.4 0.9 - - - -
327B VAL* 3.4 18.4 - - + -
328B GLY* 3.6 29.0 - - - -
330B TRP* 4.6 2.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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