Contacts of the helix formed by residues 171 - 189 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169D SER* 3.8 3.1 - - - -
170D ARG* 1.3 111.4 - - + +
172D THR* 1.3 64.3 + - - +
173D LYS* 4.1 9.4 - - + +
174D THR* 2.9 26.7 + - + +
175D LYS* 3.2 14.0 + - - +
4H G 3.8 24.7 - - - -
32J T 6.2 4.5 - - + -
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Residues in contact with THR 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D PHE* 1.3 73.5 - - - +
173D LYS* 1.3 69.1 + - - +
175D LYS* 3.1 12.2 + - - +
176D THR* 2.7 36.7 + - - +
247D GLU* 5.7 2.5 - - - +
251D ASN* 3.6 24.9 - - - +
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Residues in contact with LYS 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D PHE* 4.1 5.1 - - + +
172D THR* 1.3 80.6 - - - +
174D THR* 1.3 54.6 + - + +
176D THR* 3.0 2.8 + - - -
177D LEU* 2.6 54.5 + - + +
251D ASN* 3.3 38.0 + - + +
252D SER* 3.4 26.3 + - - +
253D GLU* 4.7 8.4 - - - +
276D LYS* 3.0 33.3 - - - +
5H T 5.9 3.4 - - - +
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Residues in contact with THR 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D SER* 3.8 1.4 - - - -
171D PHE* 2.9 34.1 + - + -
173D LYS* 1.3 80.5 - - + +
175D LYS* 1.3 61.0 + - - -
177D LEU* 3.1 11.1 + - + -
178D TYR* 2.8 44.9 + - + +
4H G 3.0 53.7 + - - +
5H T 4.4 9.0 - - - +
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Residues in contact with LYS 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PHE 3.6 21.1 - - - +
166D GLU* 3.1 49.4 + - - +
169D SER* 3.3 15.0 - - - +
171D PHE 3.2 14.1 + - - +
172D THR* 3.1 12.5 + - - +
174D THR* 1.3 80.4 + - - +
176D THR* 1.3 71.5 + - - +
178D TYR* 3.6 1.4 + - - +
179D GLN* 3.1 48.2 + - - +
247D GLU* 5.8 1.8 + - - +
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Residues in contact with THR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D THR* 2.7 27.2 + - - +
173D LYS* 3.2 11.4 - - - -
175D LYS* 1.3 78.8 - - - +
177D LEU* 1.3 57.6 + - + +
179D GLN* 3.9 4.9 - - - +
180D PHE* 2.8 32.6 + - - +
244D TYR* 4.9 0.6 - - - +
247D GLU* 2.9 39.5 + - + +
248D PHE* 3.2 23.1 - - + +
251D ASN* 3.6 17.2 + - + +
252D SER* 5.7 0.4 - - - +
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D LYS* 2.6 46.0 + - + +
174D THR* 3.6 10.8 - - + +
176D THR* 1.3 74.7 - - + +
178D TYR* 1.3 64.9 + - + +
180D PHE* 3.7 3.3 - - + +
181D LEU* 2.8 28.7 + - - +
248D PHE* 3.7 23.8 - - + -
252D SER* 3.5 23.8 - - - +
275D LEU* 4.4 11.4 - - + +
276D LYS* 6.1 3.1 - - + +
279D LEU* 3.9 30.1 - - + +
5H T 5.6 4.5 - - - +
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Residues in contact with TYR 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PHE* 3.5 40.6 - + + -
169D SER* 3.7 13.2 - - - -
174D THR* 2.8 42.6 + - + +
175D LYS 4.0 2.0 - - - +
177D LEU* 1.3 74.4 - - - +
179D GLN* 1.3 58.0 + - - +
182D PHE* 2.9 31.8 + - - +
279D LEU* 3.9 16.6 - - + -
282D SER* 3.4 27.5 + - - -
283D TYR* 3.5 40.2 - + + -
286D ALA* 3.9 8.3 - - + -
4H G 3.1 33.9 + - - -
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Residues in contact with GLN 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LEU* 3.0 52.0 + - + +
163D ASN* 4.5 1.2 - - - +
165D PHE* 4.0 9.6 - - + -
166D GLU* 3.7 30.0 + - - +
175D LYS* 3.1 41.7 + - - +
176D THR* 4.0 3.0 - - - +
178D TYR* 1.3 74.2 - - - +
180D PHE* 1.3 65.8 + - - +
182D PHE* 4.6 0.4 - - - -
183D LEU* 3.1 21.5 + - - +
244D TYR* 3.7 30.0 + - + -
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Residues in contact with PHE 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D THR 2.8 19.2 + - - +
177D LEU* 3.7 3.1 - - - +
179D GLN* 1.3 78.7 - - - +
181D LEU* 1.3 57.9 + - - +
183D LEU* 3.8 0.9 - - - +
184D ALA* 2.7 37.2 + - + +
195D ILE* 4.4 8.7 - - + -
203D PHE* 6.2 0.2 - + - -
232D PHE* 3.3 44.0 - + - -
244D TYR* 3.8 22.6 - - + +
245D LEU* 3.7 21.5 - - + -
248D PHE* 3.6 55.2 - + + -
274D LEU* 3.9 17.7 - - + -
275D LEU* 4.2 10.1 - - + -
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Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D LEU 2.8 21.9 + - - +
178D TYR 3.7 2.7 - - - +
180D PHE* 1.3 76.9 - - + +
182D PHE* 1.3 66.4 + - - +
184D ALA* 3.0 5.6 + - - +
185D THR* 2.7 47.8 + - + +
192D PHE* 3.8 28.9 - - + -
195D ILE* 4.1 9.9 - - + -
275D LEU* 3.8 20.6 - - + -
279D LEU* 4.1 19.3 - - + -
280D VAL* 5.3 0.4 - - - -
283D TYR* 3.8 37.2 - - + -
304D SER* 5.3 2.0 - - - -
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Residues in contact with PHE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D THR* 3.4 41.3 - - + -
161D ILE* 3.7 30.1 - - + -
162D LEU* 3.8 18.8 - - + -
165D PHE* 4.7 3.8 - - + -
178D TYR 2.9 20.0 + - - +
179D GLN 3.9 2.5 - - - +
181D LEU* 1.3 72.8 - - - +
183D LEU* 1.3 75.7 + - - +
185D THR* 2.7 26.7 + - - -
186D PHE* 3.0 8.7 + - + +
283D TYR* 3.1 26.9 + - + +
306D ILE* 3.8 26.0 - - + -
307D GLY* 4.2 5.8 - - - -
310D LEU* 3.7 26.7 - - + -
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TRP* 4.7 1.8 - - + -
158D THR* 4.5 9.0 - - + -
162D LEU* 4.5 8.1 - - + -
179D GLN 3.1 15.3 + - - +
180D PHE* 3.9 3.1 - - + +
182D PHE* 1.3 83.7 - - - +
184D ALA* 1.3 62.5 + - - +
186D PHE* 3.2 13.0 + - + -
187D ILE* 2.9 50.9 + - + +
239D ILE* 3.8 24.5 - - + -
241D PRO* 3.6 36.3 - - + -
244D TYR* 3.8 25.4 - - + -
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Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D PHE* 2.7 27.5 + - + +
181D LEU 3.2 5.2 - - - +
183D LEU* 1.3 74.6 - - - +
185D THR* 1.3 63.5 + - - +
187D ILE* 3.9 2.2 - - - +
188D ASN* 3.0 33.3 + - - +
195D ILE* 3.9 29.2 - - + -
232D PHE* 4.2 21.8 - - + -
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Residues in contact with THR 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D LEU* 2.7 45.5 + - + +
182D PHE* 2.7 21.8 + - - -
184D ALA* 1.3 72.3 - - - +
186D PHE* 1.3 57.1 + - - +
189D CYS* 2.8 25.5 + - - -
190D GLY 3.1 26.1 + - - +
191D ARG 4.2 6.7 - - - +
192D PHE* 4.7 1.8 - - - -
195D ILE* 3.7 13.7 - - + -
283D TYR* 5.2 1.0 + - + +
304D SER* 4.2 14.3 + - - +
307D GLY* 3.5 21.0 - - - -
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Residues in contact with PHE 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ILE* 3.7 24.2 - - + -
155D TRP* 4.0 28.5 - + - -
158D THR* 3.9 22.9 - - + -
182D PHE* 3.0 14.6 + - + +
183D LEU* 3.6 11.4 - - + +
185D THR* 1.3 79.3 + - - +
187D ILE* 1.3 79.0 + - + +
189D CYS 3.1 9.5 + - - -
307D GLY* 3.6 17.5 - - - +
310D LEU* 3.7 13.2 - - + -
311D MET* 3.3 76.1 - - + +
314D PHE* 4.5 4.7 - + + -
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Residues in contact with ILE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TRP* 4.3 6.7 - - + -
183D LEU* 2.9 38.9 + - + +
184D ALA* 3.9 4.5 - - - +
186D PHE* 1.3 94.0 - - + +
188D ASN* 1.3 61.2 + - - +
231D TYR* 4.1 13.7 - - + +
232D PHE* 5.4 1.1 - - + -
233D PHE* 3.1 38.4 - - + -
241D PRO* 4.2 16.8 - - + -
311D MET* 4.2 2.0 - - - -
354D TYR* 2.7 30.7 + - - -
358D VAL* 3.7 18.6 - - + +
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Residues in contact with ASN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ALA* 3.0 28.2 + - - +
187D ILE* 1.3 81.6 - - - +
189D CYS* 1.3 71.8 + - - +
190D GLY 4.2 3.1 - - - +
195D ILE* 4.3 1.7 - - + +
228D ARG* 2.9 33.6 + - - +
230D ILE* 3.3 29.8 - - + +
231D TYR* 2.5 56.0 + - - +
232D PHE* 5.1 0.2 - - - -
327D VAL* 3.1 9.2 - - - +
354D TYR* 5.6 0.4 - - - -
355D PHE* 5.5 0.3 - - - -
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Residues in contact with CYS 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D THR 2.8 11.4 + - - -
186D PHE 3.1 6.9 + - - -
188D ASN* 1.3 80.3 - - - +
190D GLY* 1.3 60.0 + - - +
228D ARG* 3.7 0.2 + - - -
308D ARG* 3.3 38.4 + - - +
311D MET* 3.9 15.0 - - + -
312D THR* 3.8 21.5 - - - -
315D LEU* 5.9 1.1 - - - -
324D THR* 5.1 2.7 - - - -
327D VAL* 3.8 18.2 - - + -
328D GLY* 3.5 24.5 - - - -
330D TRP* 4.1 7.4 - - - -
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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