Contacts of the helix formed by residues 184 - 200 (chain M) in PDB entry 1MVW
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 GLY 184 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127M ASN* 4.8 6.7 - - - -
180M GLU 4.4 0.2 + - - -
181M SER 4.6 3.0 + - - -
182M GLY 3.1 6.5 + - - -
183M ALA* 1.3 78.8 - - - +
185M LYS* 1.3 63.4 + - - +
186M THR 4.7 0.2 - - - -
187M VAL* 3.3 27.9 - - - +
188M ASN* 3.1 19.6 + - - -
240M ASN* 4.9 10.5 - - - -
674M CYS* 4.8 0.4 - - - -
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Residues in contact with LYS 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M ILE* 3.6 19.7 - - + +
178M THR* 4.3 3.1 - - - -
179M GLY* 2.9 46.2 - - - +
180M GLU 3.9 11.6 + - - +
181M SER* 4.9 8.2 + - - +
184M GLY* 1.3 75.5 - - - +
186M THR* 1.3 54.4 + - - +
187M VAL 3.0 2.2 - - - -
188M ASN* 2.6 29.1 + - - +
189M THR* 2.5 24.3 + - - +
243M SER* 5.8 0.8 + - - -
244M SER* 4.6 19.2 + - - +
463M ASP* 4.4 17.3 + - - +
464M ILE 3.8 17.0 + - - +
465M ALA* 4.6 9.1 - - - +
674M CYS* 4.2 6.7 - - + -
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Residues in contact with THR 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184M GLY* 3.7 0.4 - - - -
185M LYS* 1.3 75.5 + - - +
187M VAL* 1.3 58.3 + - - +
189M THR* 3.1 7.0 + - - -
190M MLY 2.6 47.1 + - + +
230M GLU* 3.6 23.6 - - + +
234M ASN* 4.6 4.2 + - - +
240M ASN* 5.5 2.4 + - - -
242M ASN* 4.5 9.3 + - - -
244M SER* 3.7 29.2 + - - +
248M MLY 3.3 31.6 - - - -
463M ASP* 3.8 4.6 + - - -
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Residues in contact with VAL 187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135M TYR* 5.5 6.7 - - + +
184M GLY* 3.3 32.8 - - - +
186M THR* 1.3 78.7 - - - +
188M ASN* 1.3 63.6 + - - +
190M MLY 3.6 16.4 + - - +
191M ARG* 3.0 47.0 + - - +
240M ASN* 5.5 5.8 - - - +
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Residues in contact with ASN 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M TYR* 4.4 1.0 + - - -
125M THR* 4.1 14.5 - - - +
135M TYR* 3.9 17.2 + - - -
155M ILE* 3.3 30.9 - - + +
177M ILE* 4.8 7.6 - - + -
184M GLY 3.1 15.8 + - - -
185M LYS* 2.6 11.8 + - - +
187M VAL* 1.3 75.9 - - - +
189M THR* 1.3 55.3 + - - +
191M ARG* 2.8 7.1 + - - +
192M VAL* 2.6 41.4 + - + +
674M CYS* 2.9 36.2 - - - +
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Residues in contact with THR 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M ILE* 4.4 10.3 - - + +
185M LYS* 2.5 26.4 + - - +
186M THR* 3.3 5.6 - - - -
188M ASN* 1.3 71.4 - - - +
190M MLY 1.3 65.7 + - - +
192M VAL* 3.0 10.2 + - - +
193M ILE* 2.9 30.6 + - + +
248M MLY 4.8 15.3 - - - -
250M ILE* 5.0 2.0 - - + -
461M VAL* 3.7 26.7 - - + +
463M ASP* 3.1 36.4 + - + +
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Residues in contact with MLY 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186M THR* 2.6 40.1 + - + +
187M VAL* 3.7 15.0 - - - +
189M THR* 1.3 71.8 - - - +
191M ARG* 1.3 100.4 + - - +
193M ILE* 2.8 25.4 + - - +
194M GLN* 2.9 20.4 + - - +
226M ASN* 4.1 30.5 - - + +
227M PRO* 6.1 2.2 - - - -
230M GLU* 2.8 44.4 - - - +
242M ASN* 4.0 8.3 - - - -
248M MLY 4.8 5.4 - - - -
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Residues in contact with ARG 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135M TYR* 3.1 49.5 - - + -
155M ILE* 5.8 4.9 - - + -
156M PHE* 4.4 16.1 - - + -
187M VAL* 3.0 37.1 + - - +
188M ASN* 2.8 6.5 + - - +
190M MLY 1.3 114.3 + - - +
192M VAL* 1.3 60.9 + - - +
194M GLN* 3.6 29.6 + - + +
195M TYR* 3.3 18.2 + - - +
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Residues in contact with VAL 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155M ILE* 4.4 26.0 - - + +
156M PHE* 5.9 0.2 - - - -
158M ILE* 6.5 0.7 - - + -
159M SER* 4.0 14.4 - - - -
175M ILE* 4.7 11.7 - - + -
177M ILE* 4.4 14.1 - - + -
188M ASN 2.6 24.8 + - - +
189M THR* 3.0 10.1 + - - +
191M ARG* 1.3 75.1 - - - +
193M ILE* 1.3 63.3 + - + +
195M TYR* 2.8 27.5 - - - +
196M PHE* 3.1 31.0 + - + -
461M VAL* 4.8 10.1 - - + -
672M VAL* 6.4 0.9 - - + -
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Residues in contact with ILE 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189M THR* 3.0 19.7 - - + +
190M MLY 2.8 13.6 + - - +
192M VAL* 1.3 77.9 - - + +
194M GLN* 1.3 65.4 + - - +
196M PHE* 3.0 18.8 + - - +
197M ALA* 3.0 10.9 + - - +
222M ILE* 4.0 28.7 - - + +
223M ILE* 5.3 6.3 - - + -
226M ASN* 5.6 7.6 - - - +
248M MLY 5.6 2.7 - - - -
250M ILE* 3.1 37.2 - - + -
252M ILE* 3.9 24.5 - - + -
461M VAL* 4.7 8.1 - - + -
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Residues in contact with GLN 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190M MLY 2.9 18.6 + - - +
191M ARG* 3.8 36.8 + - + +
193M ILE* 1.3 74.3 - - - +
195M TYR* 1.3 54.5 + - - +
197M ALA* 2.9 6.0 + - - +
198M THR* 2.5 42.7 + - + +
223M ILE* 3.2 40.2 - - + +
226M ASN* 6.0 0.2 + - - -
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Residues in contact with TYR 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M VAL* 3.4 36.4 + - + -
143M TYR* 3.9 6.2 + - - +
144M ARG* 4.0 1.0 + - - -
156M PHE* 2.9 41.9 - + + -
159M SER* 2.8 33.9 - - - +
160M ASP* 2.4 31.8 + - + +
191M ARG 3.3 10.5 + - - +
192M VAL* 2.8 15.7 + - - +
194M GLN* 1.3 79.5 - - - +
196M PHE* 1.3 63.9 + + - +
198M THR* 3.0 13.9 + - - -
199M ILE* 2.9 54.8 + - + +
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Residues in contact with PHE 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159M SER* 3.1 33.9 - - - -
162M ALA* 4.3 5.4 - - + -
163M TYR* 4.0 15.0 - + + -
175M ILE* 4.2 4.9 - - + -
192M VAL* 3.1 38.2 + - + -
193M ILE* 3.0 7.6 + - - +
195M TYR* 1.3 81.6 - + - +
197M ALA* 1.3 68.1 + - - +
198M THR 3.2 0.2 + - - -
199M ILE* 3.6 12.1 + - + +
200M ALA* 3.3 23.7 + - - +
252M ILE* 4.6 17.9 - - + -
254M PHE* 3.6 28.9 - + + -
260M LEU* 4.7 2.2 - - + +
459M ILE* 3.7 43.1 - - + -
461M VAL* 4.9 1.6 - - + -
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Residues in contact with ALA 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193M ILE 3.0 10.9 + - - +
194M GLN* 2.9 11.5 + - - +
196M PHE* 1.3 80.7 - - - +
198M THR* 1.3 62.3 + - - +
200M ALA 3.8 0.2 - - - -
201M ALA* 3.0 27.5 + - - +
219M GLU* 4.3 24.2 - - + +
222M ILE* 5.2 5.8 - - + -
223M ILE* 4.9 7.2 - - + -
260M LEU* 3.9 20.0 - - + -
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Residues in contact with THR 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140M VAL* 5.1 11.7 - - + +
194M GLN* 2.5 33.0 + - + +
195M TYR* 3.0 12.8 + - - -
197M ALA* 1.3 75.9 - - + +
199M ILE* 1.3 61.8 + - - +
200M ALA 2.8 8.2 + - - -
201M ALA* 3.7 7.6 + - - +
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Residues in contact with ILE 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M VAL* 4.8 7.9 - - + +
144M ARG* 4.5 17.5 + - + -
160M ASP* 4.1 7.2 - - - +
163M TYR* 4.3 24.4 + - + -
195M TYR* 2.9 69.5 + - + +
196M PHE* 4.1 19.3 - - + +
198M THR* 1.3 75.0 - - - +
200M ALA* 1.3 63.5 + - + +
259M LYS* 4.5 5.0 + - - -
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Residues in contact with ALA 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163M TYR* 3.1 35.9 - - + +
196M PHE 3.3 11.5 + - - +
197M ALA 3.8 3.1 - - - -
198M THR 2.8 9.1 + - - -
199M ILE* 1.3 79.7 - - + +
201M ALA* 1.3 60.8 + - - +
254M PHE* 4.3 5.6 - - + -
258M GLY 3.6 7.0 - - - +
259M LYS* 3.7 11.8 - - - +
260M LEU* 3.1 28.6 + - - +
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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