Contacts of the helix formed by residues 225 - 243 (chain A) in PDB entry 1MUK
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 ALA 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ILE 6.0 0.2 - - - +
96A ASN* 3.5 37.7 - - - +
143A GLN* 4.5 3.6 - - - +
223A THR* 3.0 11.7 - - + +
224A SER* 1.3 81.1 + - - +
226A ILE* 1.3 65.6 + - + +
227A PRO 3.5 0.4 - - - -
228A PRO* 3.1 15.5 - - - +
229A LEU* 3.2 15.6 + - - +
261A ALA* 4.3 14.1 - - + +
266A TYR* 4.2 10.9 - - + -
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Residues in contact with ILE 226 (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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63A ILE* 4.0 27.6 - - + +
64A TYR* 5.0 1.6 - - + -
193A ILE* 4.1 12.1 - - + -
197A ILE* 3.8 25.8 - - + -
206A PRO* 4.2 1.1 - - + -
221A ARG 5.0 0.2 - - - +
222A MET* 3.5 22.4 - - + -
223A THR* 3.3 29.8 + - + +
225A ALA* 1.3 79.0 - - + +
227A PRO* 1.3 70.5 - - + +
229A LEU* 3.3 8.3 + - + +
230A LEU* 2.9 52.5 + - + +
261A ALA* 5.5 0.2 - - + -
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Residues in contact with PRO 227 (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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143A GLN 5.8 0.2 - - - -
144A ALA* 3.7 35.0 - - + +
207A TYR* 3.8 41.8 + - + +
216A TRP* 3.9 13.5 - - + -
222A MET* 3.9 2.5 - - + -
223A THR 3.7 5.8 - - - +
224A SER 3.4 9.2 - - - +
226A ILE* 1.3 93.9 - - + +
228A PRO* 1.3 74.3 - - + +
230A LEU* 3.7 1.8 - - + +
231A SER* 2.9 24.5 + - - -
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Residues in contact with PRO 228 (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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143A GLN* 3.3 42.8 - - + +
224A SER 3.7 4.0 - - - +
225A ALA* 3.1 14.6 - - - +
227A PRO* 1.3 98.8 - - + +
229A LEU* 1.3 62.2 + - - +
231A SER* 2.7 24.7 + - - +
232A ASP* 3.0 9.9 + - - +
266A TYR* 3.8 27.4 - - + -
375A ILE* 4.0 14.0 - - + +
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Residues in contact with LEU 229 (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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63A ILE* 4.6 2.0 - - + -
193A ILE* 4.1 37.2 - - + -
225A ALA 3.2 11.9 + - - +
226A ILE* 3.5 14.8 - - + +
228A PRO* 1.3 77.8 - - - +
230A LEU* 1.3 62.6 + - + +
232A ASP* 3.1 4.3 + - - +
233A LEU* 3.1 36.3 + - + +
257A CYS* 3.6 42.0 - - + +
258A LEU* 4.1 11.4 - - + +
261A ALA* 4.2 16.4 - - + -
266A TYR* 3.5 14.8 - - + +
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Residues in contact with LEU 230 (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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43A TYR* 5.7 0.2 - - - +
151A LEU* 3.7 13.5 - - + -
190A PHE* 3.5 28.4 - - + -
193A ILE* 4.2 20.6 - - + -
194A CYS* 3.7 27.6 - - - -
206A PRO* 4.0 11.4 - - + -
207A TYR* 4.3 12.6 - - + -
226A ILE* 2.9 43.1 + - + +
227A PRO 3.7 4.0 - - - +
229A LEU* 1.3 74.7 - - + +
231A SER* 1.3 63.5 + - - +
233A LEU* 3.2 9.9 + - + +
234A VAL* 3.0 27.7 + - - +
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Residues in contact with SER 231 (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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147A ILE* 4.2 16.6 - - - -
151A LEU* 3.8 14.5 - - - +
207A TYR* 5.2 0.9 - - - -
227A PRO 2.9 15.0 + - - -
228A PRO* 2.7 21.1 + - - +
230A LEU* 1.3 77.3 - - - +
232A ASP* 1.3 60.8 + - - +
234A VAL* 3.6 0.7 + - - +
235A ASN* 3.4 28.5 + - - -
375A ILE* 3.8 12.5 - - - +
801A VAL* 3.7 16.4 - - - +
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Residues in contact with ASP 232 (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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228A PRO 3.0 2.4 + - - -
229A LEU 3.1 8.5 + - - +
231A SER* 1.3 81.9 + - - +
233A LEU* 1.3 64.6 + - - +
235A ASN* 3.2 9.3 + - - +
236A LEU* 3.0 30.3 + - + +
257A CYS* 3.6 17.4 - - - -
266A TYR* 2.6 23.0 + - - +
373A SER* 2.7 30.0 + - - -
374A GLY* 2.8 27.0 + - - -
375A ILE* 3.6 13.2 + - - +
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Residues in contact with LEU 233 (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 PRO* 3.3 24.5 - - + +
189A CYS* 3.7 24.2 - - + -
190A PHE* 3.9 18.4 - - + +
193A ILE* 4.5 1.6 - - + -
229A LEU* 3.1 40.5 + - + +
230A LEU* 3.2 14.1 + - + +
232A ASP* 1.3 77.0 - - - +
234A VAL* 1.3 56.7 + - - +
236A LEU* 3.3 3.7 + - + -
237A ALA* 2.8 27.1 + - - +
254A VAL* 3.9 41.1 - - + -
257A CYS* 5.1 3.4 - - + -
258A LEU* 5.6 1.3 - - + -
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Residues in contact with VAL 234 (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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151A LEU* 4.2 14.1 - - + +
154A PHE* 3.9 11.7 - - + -
155A VAL* 3.8 21.8 - - + +
158A LEU* 6.3 0.2 - - + -
187A LEU* 6.2 1.1 - - + -
190A PHE* 3.8 25.8 - - + -
230A LEU 3.0 20.1 + - - +
231A SER 4.0 4.3 - - - +
232A ASP 3.3 0.2 - - - -
233A LEU* 1.3 75.7 - - - +
235A ASN* 1.3 64.8 + - - +
237A ALA* 3.1 7.6 + - + +
238A ILE* 3.0 44.5 + - + +
801A VAL* 3.7 17.0 - - + -
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Residues in contact with ASN 235 (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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231A SER* 3.4 16.7 + - - -
232A ASP* 3.2 16.2 + - - +
234A VAL* 1.3 77.2 - - - +
236A LEU* 1.3 59.5 + - + +
238A ILE* 3.4 5.5 + - - +
239A LEU* 2.9 44.0 + - + +
374A GLY* 5.1 4.9 + - - -
799A PRO* 3.7 24.3 - - + +
800A ILE* 3.1 17.2 + - + +
801A VAL* 3.0 36.7 + - - +
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Residues in contact with LEU 236 (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 PRO* 3.6 15.2 - - + +
232A ASP* 3.0 24.8 + - + +
233A LEU* 3.7 5.4 - - + +
235A ASN* 1.3 77.9 - - + +
237A ALA* 1.3 64.3 + - - +
239A LEU* 3.8 7.0 - - + +
240A GLN* 2.9 26.7 + - - +
245A LEU* 4.8 4.3 - - + +
250A VAL* 4.4 10.2 - - + +
253A GLY* 4.3 7.0 - - - +
254A VAL* 3.9 35.7 - - + +
257A CYS* 4.8 6.3 - - - -
370A ALA 3.6 24.0 - - - +
371A CYS* 3.9 23.1 - - + +
372A THR 5.3 2.0 - - - +
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Residues in contact with ALA 237 (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 LEU* 3.9 13.7 - - + -
184A ASN* 2.9 43.6 + - - +
186A PRO* 3.5 4.7 - - + +
187A LEU* 4.0 15.5 - - + +
233A LEU 2.8 18.7 + - - +
234A VAL* 3.4 9.4 - - + +
236A LEU* 1.3 77.9 - - - +
238A ILE* 1.3 60.7 + - - +
241A GLN* 3.4 13.7 + - - +
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Residues in contact with ILE 238 (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 PHE* 4.1 9.4 - - + +
158A LEU* 3.7 24.0 - - + -
234A VAL* 3.0 37.3 + - + +
235A ASN* 3.7 4.5 - - - +
237A ALA* 1.3 73.3 - - - +
239A LEU* 1.3 52.7 + - - +
241A GLN* 3.1 3.3 + - - +
242A THR* 2.6 47.3 + - + +
800A ILE* 3.6 36.6 - - + -
801A VAL* 4.6 1.6 - - + -
841A TYR* 3.3 44.4 - - + +
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Residues in contact with LEU 239 (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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235A ASN* 2.9 37.3 + - + +
236A LEU* 3.9 4.3 - - + +
238A ILE* 1.3 69.6 - - - +
240A GLN* 1.3 61.0 + - - +
242A THR* 3.4 7.4 - - - +
243A ALA* 2.5 37.3 + - + +
244A GLY 3.5 0.9 + - - -
245A LEU* 3.7 16.1 - - + +
370A ALA* 4.0 24.7 - - + +
795A LEU* 4.2 35.4 - - + +
796A SER* 5.7 0.7 - - - -
798A HIS 6.2 0.2 - - - +
800A ILE* 3.5 31.0 - - + -
833A LEU* 5.0 9.4 - - + -
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Residues in contact with GLN 240 (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 ILE* 4.0 7.4 - - + +
179A PRO* 5.1 5.1 - - + +
183A HIS* 3.4 26.3 + - - +
184A ASN* 3.9 14.3 - - - +
185A CYS* 4.7 1.1 + - - +
186A PRO* 3.9 6.9 - - - +
236A LEU 2.9 18.0 + - - +
237A ALA 3.8 5.2 - - - +
238A ILE 3.3 0.2 - - - -
239A LEU* 1.3 76.0 - - - +
241A GLN* 1.3 71.8 + - - +
244A GLY* 3.5 18.2 - - - -
245A LEU* 3.9 23.0 - - - +
247A PRO* 3.6 29.0 - - + +
250A VAL* 3.3 32.8 - - + +
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Residues in contact with GLN 241 (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 LEU* 4.2 8.5 - - + -
162A GLU* 2.8 37.7 + - + +
178A ILE* 4.1 9.4 - - - +
179A PRO 2.8 28.8 + - - +
180A ASP* 4.1 5.8 - - - +
181A LEU* 3.6 27.9 - - + +
184A ASN* 3.1 18.0 + - - +
237A ALA 3.4 12.8 + - - +
238A ILE 3.1 7.6 + - - +
240A GLN* 1.3 94.2 + - - +
242A THR* 1.3 60.0 + - + +
244A GLY 4.3 0.7 - - - -
837A ARG* 3.7 30.7 + - - +
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Residues in contact with THR 242 (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 LEU* 5.3 1.6 - - + -
162A GLU* 5.4 2.9 - - - +
238A ILE* 2.6 43.8 + - + +
239A LEU* 3.4 5.2 - - - +
241A GLN* 1.3 80.5 - - + +
243A ALA* 1.3 58.6 + - - +
244A GLY 3.3 1.6 - - - -
833A LEU* 3.6 10.1 - - - +
834A GLN* 3.0 30.0 + - - +
837A ARG* 4.0 22.7 - - + +
838A TRP* 3.7 31.3 - - + -
841A TYR* 4.0 13.7 - - + -
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Residues in contact with ALA 243 (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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239A LEU* 2.5 20.6 + - - +
242A THR* 1.3 74.8 - - - +
244A GLY* 1.3 64.4 + - - +
245A LEU* 4.0 8.5 - - + -
363A ARG* 3.8 6.6 + - - -
366A ARG* 3.0 34.1 + - - +
795A LEU* 3.9 14.6 - - + -
833A LEU* 3.7 22.9 - - + -
834A GLN* 4.0 8.2 - - - +
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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