Contacts of the helix formed by residues 173 - 194 (chain A) in PDB entry 4O6M
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 THR 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A SER 3.7 12.6 - - - +
172A VAL* 1.3 75.0 - - - +
174A PRO* 1.3 75.6 - - - +
175A ASN 3.5 1.3 + - - -
176A GLN* 3.0 25.1 + - - +
177A ILE* 3.2 25.0 + - - +
220A ILE* 4.6 0.2 - - - -
226A MET* 3.7 18.8 - - + -
410A SO4 2.7 40.7 + - - +
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Residues in contact with PRO 174 (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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173A THR* 1.3 87.6 - - - +
175A ASN* 1.3 63.0 + - - +
177A ILE* 3.2 7.5 + - + +
178A THR* 2.9 31.4 + - - -
217A ASP* 3.5 28.2 - - + +
220A ILE* 4.2 4.7 - - + -
221A ALA* 3.6 35.2 - - + +
226A MET* 3.7 31.9 - - + +
231A GLY* 6.1 1.8 - - - -
410A SO4 5.5 0.9 - - - +
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A THR* 3.2 1.2 + - - +
174A PRO* 1.3 80.7 - - - +
176A GLN* 1.3 57.7 + - - +
178A THR* 3.3 7.7 + - - -
179A VAL* 3.0 35.2 + - - +
228A SER* 4.6 6.6 + - - -
230A TYR* 4.0 20.4 - - - -
231A GLY* 3.2 28.8 - - - +
234A LEU* 4.4 11.6 - - + +
402A MPG 4.5 0.7 - - - -
404A MPG 4.2 10.2 - - + +
410A SO4 3.0 37.2 + - - +
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Residues in contact with GLN 176 (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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171A SER 4.0 3.2 + - - +
172A VAL* 3.3 15.2 - - + +
173A THR* 3.0 41.9 + - - +
175A ASN* 1.3 75.8 - - - +
177A ILE* 1.3 57.5 + - - +
179A VAL 3.4 0.3 + - - -
180A PHE* 2.9 30.7 + - - +
402A MPG 3.8 33.5 - - + +
403A MPG 4.0 21.4 - - + +
406A MPG 4.3 21.4 - - - +
410A SO4 3.9 8.3 + - - +
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 4.1 7.6 - - + -
172A VAL* 3.5 20.9 - - + -
173A THR 3.2 14.9 + - - +
174A PRO 3.2 6.1 + - - +
176A GLN* 1.3 72.1 - - - +
178A THR* 1.3 58.0 + - - +
180A PHE* 3.3 2.2 + - - +
181A SER* 2.8 35.0 + - - -
213A ILE* 3.8 24.9 - - + +
216A CYS* 3.9 12.8 - - + +
217A ASP* 3.6 24.5 - - + +
220A ILE* 3.7 34.8 - - + -
403A MPG 4.1 17.9 - - + -
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO 2.9 15.7 + - - -
175A ASN* 3.5 12.4 + - - -
177A ILE* 1.3 76.9 - - - +
179A VAL* 1.3 56.2 + - - +
181A SER* 3.4 6.5 + - - -
182A PHE* 3.0 25.8 + - - +
214A ASP* 5.0 0.5 - - - +
217A ASP* 2.6 27.3 + - - +
231A GLY 4.7 3.4 + - - +
234A LEU* 4.1 8.1 - - + -
235A ASP* 3.6 38.6 + - - +
238A LEU* 4.0 18.7 - - + +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN 3.0 19.0 + - - +
177A ILE 3.3 0.2 - - - -
178A THR* 1.3 73.5 - - - +
180A PHE* 1.3 66.2 + - - +
182A PHE* 3.3 10.9 + - + +
183A PHE* 3.0 22.3 + - + +
234A LEU* 4.3 11.2 - - + -
238A LEU* 4.4 4.7 - - + -
402A MPG 3.6 40.2 - - + -
404A MPG 3.8 37.2 - - + -
405A MPG 3.7 21.8 - - + -
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLN 2.9 17.9 + - - +
177A ILE 3.7 2.5 - - - +
179A VAL* 1.3 76.6 - - - +
181A SER* 1.3 64.8 + - - +
183A PHE* 3.2 21.8 + + - +
184A LEU* 3.0 50.4 + - + +
213A ILE* 4.3 13.9 - - + -
402A MPG 3.8 19.9 - - + +
403A MPG 3.8 51.6 - - + -
406A MPG 4.5 15.5 - - + -
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Residues in contact with SER 181 (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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177A ILE 2.8 22.4 + - - -
178A THR* 3.6 6.3 - - - -
180A PHE* 1.3 79.4 - - - +
182A PHE* 1.3 61.3 + - - +
184A LEU* 3.2 7.7 + - - +
185A SER 3.2 9.2 + - - -
210A HIS* 2.8 45.2 + - - -
213A ILE* 4.4 7.9 - - - -
214A ASP* 3.0 38.6 + - - +
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Residues in contact with PHE 182 (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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178A THR 3.0 14.7 + - - +
179A VAL* 3.3 11.4 + - + +
181A SER* 1.3 74.9 - - - +
183A PHE* 1.3 64.8 + - + +
185A SER* 2.6 24.2 + - - -
186A LEU* 3.2 41.2 + - + +
210A HIS* 4.4 1.1 - - - -
238A LEU* 3.8 29.8 - - + -
241A TYR* 3.7 32.3 - + + -
242A SER* 3.3 24.0 - - - -
245A ILE* 4.5 4.9 - - + -
404A MPG 4.3 26.2 - - + -
405A MPG 6.5 0.2 - - + -
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Residues in contact with PHE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 3.0 13.6 + - + +
180A PHE* 3.2 34.7 + + - +
182A PHE* 1.3 78.3 - - + +
184A LEU* 1.3 70.5 + - + +
186A LEU* 3.1 20.2 + - + +
187A VAL* 3.0 44.2 + - + +
402A MPG 4.8 9.9 - - + -
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Residues in contact with LEU 184 (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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180A PHE* 3.0 37.8 + - + +
181A SER* 3.2 10.1 + - - +
183A PHE* 1.3 85.4 - - + +
185A SER* 1.3 58.7 + - - +
187A VAL* 3.2 8.2 + - + +
188A GLY 3.0 23.9 + - - -
206A ILE* 3.3 26.1 - - + +
209A LEU* 4.1 20.2 - - + -
210A HIS* 4.2 18.8 - - + +
213A ILE* 3.7 31.4 - - + -
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Residues in contact with SER 185 (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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181A SER 3.2 2.2 + - - -
182A PHE* 2.6 23.8 + - - -
184A LEU* 1.3 78.9 - - - +
186A LEU* 1.3 58.8 + - - +
188A GLY* 3.4 1.2 + - - -
189A SER* 2.9 32.2 + - - -
207A ILE* 4.0 11.7 - - - +
210A HIS* 3.8 21.7 + - - -
242A SER* 2.7 38.8 + - - -
245A ILE* 6.0 0.2 - - - +
246A ILE* 4.2 7.4 - - - +
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Residues in contact with LEU 186 (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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182A PHE* 3.2 40.6 + - + +
183A PHE* 3.1 19.2 + - + +
185A SER* 1.3 81.3 + - - +
187A VAL* 1.3 60.3 + - - +
189A SER* 3.3 4.5 + - - -
190A ALA* 2.9 29.3 + - - +
245A ILE* 3.7 39.0 - - + -
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Residues in contact with VAL 187 (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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183A PHE* 3.0 51.4 + - + +
184A LEU* 3.2 14.3 + - + +
186A LEU* 1.3 74.6 - - - +
188A GLY* 1.3 63.6 + - - +
190A ALA* 3.3 7.1 + - - +
191A LEU* 3.0 28.1 + - + +
206A ILE* 4.0 24.0 - - + -
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Residues in contact with GLY 188 (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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184A LEU 3.0 11.8 + - - -
185A SER 3.4 3.1 + - - -
187A VAL* 1.3 77.0 - - - +
189A SER* 1.3 60.8 + - - +
191A LEU* 3.1 3.3 + - - -
192A PHE* 3.1 24.0 + - - -
203A ALA* 3.3 20.8 - - - +
206A ILE* 3.8 10.9 - - - +
207A ILE* 3.9 17.3 - - - -
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Residues in contact with SER 189 (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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185A SER 2.9 18.4 + - - -
186A LEU* 3.6 5.8 - - - -
188A GLY* 1.3 75.4 - - - +
190A ALA* 1.3 62.3 + - - +
192A PHE* 3.2 22.1 + - - +
193A LEU* 3.2 12.0 + - - +
207A ILE* 4.5 0.8 - - - +
245A ILE* 3.5 18.9 - - - +
246A ILE* 3.4 25.6 - - - +
249A SER* 3.4 25.9 - - - -
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Residues in contact with ALA 190 (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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186A LEU 2.9 17.4 + - - +
187A VAL* 3.3 7.8 + - - +
189A SER* 1.3 76.7 - - - +
191A LEU* 1.3 62.8 + - + +
193A LEU* 3.1 27.7 + - + +
194A LEU* 3.5 13.2 + - - +
408A MPG 4.0 18.6 - - + +
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Residues in contact with LEU 191 (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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187A VAL* 3.0 24.6 + - + +
188A GLY 3.1 6.7 + - - +
190A ALA* 1.3 74.5 - - + +
192A PHE* 1.3 66.2 + - - +
194A LEU* 3.2 28.5 + - + -
199A THR* 3.4 46.9 + - + +
200A THR 4.5 0.2 + - - -
202A LEU* 4.0 12.8 - - + -
203A ALA* 3.7 14.6 - - + +
206A ILE* 3.2 35.2 - - + -
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Residues in contact with PHE 192 (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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188A GLY 3.1 23.6 + - - -
189A SER* 3.2 12.8 + - - +
191A LEU* 1.3 74.6 - - - +
193A LEU* 1.3 62.9 + - - +
194A LEU 3.1 1.2 + - - -
195A ASN* 3.2 12.6 + - - -
200A THR* 4.0 25.0 + - + -
203A ALA* 3.6 23.3 - - + +
204A GLY 4.3 3.6 - - - -
207A ILE* 4.1 17.7 - - + -
246A ILE* 4.2 9.2 - - + -
249A SER* 4.2 11.7 - - - +
250A ILE* 3.8 41.1 - - + -
253A VAL* 3.5 13.1 - - - +
308A ILE* 3.9 8.3 - - + -
312A SER* 3.4 26.9 - - - -
317A PRO* 4.4 6.3 - - + -
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Residues in contact with LEU 193 (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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189A SER* 3.2 13.9 + - - +
190A ALA* 3.1 15.2 + - - +
192A PHE* 1.3 77.6 - - - +
194A LEU* 1.3 60.3 + - - +
195A ASN* 3.1 6.6 + - - +
249A SER* 3.8 33.0 - - - +
252A TYR* 4.0 25.8 - - + -
253A VAL* 3.7 9.0 - - + +
408A MPG 3.4 47.0 - - + +
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Residues in contact with LEU 194 (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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190A ALA* 3.8 12.3 - - + +
191A LEU* 3.2 23.7 + - + +
192A PHE 3.1 1.4 + - - -
193A LEU* 1.3 73.7 - - - +
195A ASN* 1.3 71.5 + - - +
196A SER* 3.5 4.8 + - - +
199A THR* 3.7 26.9 + - + +
408A MPG 4.0 40.7 - - + +
409A MPG 4.7 12.8 - - + -
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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
------------------------------------------------------------
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