Contacts of the helix formed by residues 171 - 189 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A SER* 3.8 3.3 - - - +
170A ARG* 1.3 112.6 - - + +
172A THR* 1.3 63.9 + - - +
173A LYS* 4.1 9.9 - - + +
174A THR* 3.0 28.7 + - + +
175A LYS* 3.3 13.7 + - - +
3E A 6.1 0.2 - - - -
4E G 3.9 19.1 - - - -
32H T 5.6 7.2 - - + -
33H C 4.3 20.9 - - - -
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 1.3 73.2 - - - +
173A LYS* 1.3 68.4 + - - +
175A LYS* 3.1 12.3 + - - +
176A THR* 2.7 36.2 + - - +
247A GLU* 5.7 2.0 - - - +
251A ASN* 3.6 26.0 - - - +
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 4.1 6.2 - - + +
172A THR* 1.3 79.6 - - - +
174A THR* 1.3 54.5 + - + +
176A THR* 3.0 2.4 + - - -
177A LEU* 2.7 53.5 + - + +
251A ASN* 3.3 37.6 - - + +
252A SER* 3.4 25.6 + - - +
253A GLU* 4.9 11.0 - - - +
276A LYS* 3.0 34.3 - - - +
5E T 5.6 5.6 + - - +
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 3.8 1.4 - - - -
171A PHE* 3.0 26.2 + - + -
173A LYS* 1.3 80.7 - - + +
175A LYS* 1.3 68.0 + - - -
177A LEU* 4.2 9.2 - - + -
178A TYR* 2.8 47.2 + - + +
4E G 2.8 42.8 + - - +
5E T 3.8 23.3 - - - +
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Residues in contact with LYS 175 (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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165A PHE 3.6 22.0 - - - +
166A GLU* 3.1 49.0 + - - +
169A SER* 3.3 19.7 + - - +
171A PHE 3.3 9.2 + - - +
172A THR* 3.1 12.1 + - - +
174A THR* 1.3 81.1 + - - +
176A THR* 1.3 71.1 + - - +
178A TYR* 3.6 1.7 + - - +
179A GLN* 3.1 49.9 + - - +
247A GLU* 5.8 1.8 + - - +
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Residues in contact with THR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR* 2.7 23.3 + - - +
173A LYS* 3.2 11.0 - - - -
175A LYS* 1.3 85.1 - - - +
177A LEU* 1.3 59.5 + - + +
179A GLN* 3.8 3.6 - - - +
180A PHE* 2.8 32.4 + - - +
244A TYR* 4.9 1.4 - - - +
247A GLU* 2.9 41.1 + - + +
248A PHE* 3.2 24.0 - - + +
251A ASN* 3.5 18.0 + - + +
252A SER* 6.1 0.4 - - - -
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Residues in contact with LEU 177 (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 LYS* 2.7 45.9 + - + +
174A THR* 3.6 8.7 - - + +
176A THR* 1.3 74.2 - - + +
178A TYR* 1.3 57.6 + - - +
180A PHE* 3.2 3.5 + - - +
181A LEU* 2.8 35.2 + - - +
248A PHE* 3.7 24.0 - - + -
252A SER* 3.6 23.3 - - - +
275A LEU* 4.4 11.9 - - + -
276A LYS* 6.1 3.4 - - + +
279A LEU* 3.9 30.8 - - + +
5E T 5.2 8.1 - - - +
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Residues in contact with TYR 178 (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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165A PHE* 3.5 38.8 - + + -
169A SER* 3.7 13.2 - - - -
174A THR* 2.8 38.1 + - + +
175A LYS 4.0 1.6 - - - +
177A LEU* 1.3 73.6 - - + +
179A GLN* 1.3 59.1 + - - +
182A PHE* 2.9 28.9 + - - +
279A LEU* 3.9 11.7 - - + -
282A SER* 3.1 42.9 + - - -
283A TYR* 3.5 35.9 - + + -
286A ALA* 3.9 9.9 - - + -
4E G 3.2 33.9 + - - -
5E T 5.6 0.4 - - - -
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Residues in contact with GLN 179 (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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162A LEU* 3.0 51.7 + - + +
163A ASN* 4.4 3.8 - - - +
165A PHE* 4.0 10.1 - - + -
166A GLU* 3.7 29.6 + - - +
175A LYS* 3.1 42.2 + - - +
176A THR* 4.0 3.1 - - - +
178A TYR* 1.3 74.9 - - - +
180A PHE* 1.3 65.8 + - - +
182A PHE* 4.6 0.4 - - - -
183A LEU* 3.1 21.5 + - - +
244A TYR* 3.6 29.1 + - + -
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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
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176A THR 2.8 22.7 + - - +
177A LEU 3.6 3.6 - - - +
179A GLN* 1.3 74.6 - - - +
181A LEU* 1.3 56.3 + - - +
183A LEU* 3.8 1.0 - - - +
184A ALA* 2.7 38.3 + - + +
195A ILE* 4.3 9.0 - - + -
203A PHE* 6.2 0.2 - + - -
232A PHE* 3.2 44.4 - + - -
244A TYR* 3.7 22.1 - - + +
245A LEU* 3.7 20.9 - - + -
248A PHE* 3.6 52.7 - + + -
274A LEU* 3.8 20.6 - - + -
275A LEU* 4.2 9.6 - - + -
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Residues in contact with LEU 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 LEU 2.8 20.5 + - - +
178A TYR 3.7 2.5 - - - +
180A PHE* 1.3 76.5 - - - +
182A PHE* 1.3 66.7 + - - +
184A ALA* 3.0 6.0 + - - +
185A THR* 2.8 47.5 + - + +
192A PHE* 3.8 31.6 - - + -
195A ILE* 4.1 9.9 - - + -
275A LEU* 3.8 21.3 - - + -
279A LEU* 4.1 15.7 - - + -
280A VAL* 5.3 0.2 - - - -
283A TYR* 3.8 35.4 - - + -
304A SER* 5.2 3.1 - - - -
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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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158A THR* 3.4 45.1 - - + -
161A ILE* 3.7 36.8 - - + -
162A LEU* 3.8 18.6 - - + -
165A PHE* 4.7 3.6 - - + -
178A TYR 2.9 19.5 + - - +
179A GLN 3.9 2.7 - - - +
181A LEU* 1.3 73.2 - - - +
183A LEU* 1.3 75.6 + - - +
185A THR* 2.7 26.4 + - - -
186A PHE* 3.0 8.0 + - + +
283A TYR* 3.1 26.2 + - + +
306A ILE* 3.6 28.0 - - + -
307A GLY* 4.2 5.8 - - - -
310A LEU* 3.9 14.1 - - + -
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Residues in contact with LEU 183 (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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155A TRP* 4.6 2.0 - - + -
158A THR* 4.5 9.2 - - + -
162A LEU* 4.5 8.3 - - + -
179A GLN 3.1 15.7 + - - +
180A PHE* 3.9 2.2 - - + +
182A PHE* 1.3 84.5 - - - +
184A ALA* 1.3 57.7 + - - +
186A PHE* 3.2 12.8 + - + +
187A ILE* 2.9 58.8 + - + +
239A ILE* 3.8 24.7 - - + -
241A PRO* 3.6 35.9 - - + -
244A TYR* 3.8 24.5 - - + -
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Residues in contact with ALA 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* 2.7 28.0 + - + +
181A LEU* 3.1 5.8 - - - +
183A LEU* 1.3 74.5 - - - +
185A THR* 1.3 63.5 + - - +
187A ILE* 4.8 2.2 - - - -
188A ASN* 3.0 33.6 + - - +
195A ILE* 3.8 28.9 - - + -
232A PHE* 4.3 22.0 - - + -
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Residues in contact with THR 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 LEU* 2.8 43.2 + - + +
182A PHE* 2.7 22.1 + - - -
184A ALA* 1.3 72.9 - - - +
186A PHE* 1.3 56.6 + - - +
189A CYS* 2.8 26.2 + - - -
190A GLY 3.1 25.2 + - - +
191A ARG 4.3 6.5 - - - +
192A PHE* 4.7 2.0 - - - -
195A ILE* 3.7 14.8 - - + -
283A TYR* 6.0 0.2 - - - +
304A SER* 4.0 17.0 + - - +
307A GLY* 3.6 18.6 - - - -
308A ARG 4.8 0.2 - - - -
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Residues in contact with PHE 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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154A ILE* 3.7 22.9 - - + -
155A TRP* 4.0 30.5 - + - -
158A THR* 4.0 25.6 - - + -
182A PHE* 3.0 11.2 + - + +
183A LEU* 3.6 11.9 - - + +
185A THR* 1.3 79.5 + - - +
187A ILE* 1.3 77.2 + - + +
189A CYS 3.2 9.2 + - - -
307A GLY* 3.6 24.7 - - - +
310A LEU* 3.7 17.3 - - + -
311A MET* 3.3 59.8 - - + +
314A PHE* 4.7 5.6 - + + -
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Residues in contact with ILE 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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155A TRP* 4.2 7.2 - - + -
183A LEU* 2.9 39.8 + - + +
184A ALA* 3.8 4.9 - - - +
186A PHE* 1.3 92.0 - - + +
188A ASN* 1.3 60.3 + - - +
231A TYR* 4.1 12.8 - - + +
232A PHE* 5.4 2.0 - - + -
233A PHE* 3.1 38.1 - - + -
241A PRO* 4.2 16.8 - - + -
311A MET* 4.0 2.6 - - - +
354A TYR* 2.7 31.2 + - - -
355A PHE* 5.7 0.8 - - + -
358A VAL* 3.7 21.3 - - + +
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Residues in contact with ASN 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 ALA* 3.0 28.3 + - - +
187A ILE* 1.3 82.0 - - - +
189A CYS* 1.3 73.8 + - - +
190A GLY 4.2 3.6 - - - +
195A ILE* 4.3 1.8 - - + +
228A ARG* 2.9 33.4 + - - +
230A ILE* 3.3 30.3 - - + +
231A TYR* 2.5 55.5 + - - +
232A PHE* 5.1 0.2 - - - -
327A VAL* 3.3 7.9 - - - +
350A ILE* 5.6 0.3 - - - +
354A TYR* 4.7 0.9 - - - -
355A PHE* 5.5 0.3 - - - -
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Residues in contact with CYS 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 THR 2.8 11.5 + - - -
186A PHE 3.2 6.6 + - - -
188A ASN* 1.3 80.9 - - - +
190A GLY* 1.3 58.9 + - - +
228A ARG* 3.7 1.2 + - - -
308A ARG* 3.3 31.9 + - - +
311A MET* 3.5 25.6 - - + -
312A THR* 3.6 25.1 - - - -
315A LEU* 5.6 2.2 - - - -
324A THR 5.5 0.2 - - - -
327A VAL* 3.8 10.5 - - + -
328A GLY* 3.7 25.2 - - - -
330A TRP* 4.2 5.2 - - - -
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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