Contacts of the helix formed by residues 185 - 201 (chain M) in PDB entry 5DSV
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 185 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41M CYS* 3.7 1.8 - - - -
42M LYS* 3.9 23.3 - - - +
43M ASP* 3.6 12.8 - - - +
184M MET* 1.3 74.9 - - - +
186M CYS* 1.3 66.8 + - - +
187M ARG* 3.9 9.5 + - - +
188M ASP* 3.2 37.7 + - - +
189M ILE* 3.2 15.6 + - - +
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Residues in contact with CYS 186 (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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41M CYS* 2.1 49.7 - - - -
43M ASP* 3.1 16.1 + - - +
44M GLY* 3.4 26.0 - - - -
45M VAL 3.8 2.9 - - - -
46M VAL* 4.4 6.5 - - - -
185M THR* 1.3 71.5 - - - +
187M ARG* 1.3 68.3 + - - +
189M ILE* 2.9 15.4 + - - +
190M VAL* 3.3 15.6 + - - +
215M TRP* 3.7 19.6 - - + -
216M VAL 4.3 3.8 - - - -
217M GLY* 5.0 0.9 - - - -
219M LEU* 4.2 5.8 - - + -
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Residues in contact with ARG 187 (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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43M ASP* 5.0 0.2 + - - -
185M THR* 4.1 8.5 - - - +
186M CYS* 1.3 79.7 - - - +
188M ASP* 1.3 63.0 + - - +
190M VAL* 3.8 11.3 + - - +
191M LYS* 4.5 7.4 + - - +
215M TRP* 4.0 19.2 - - - -
219M LEU* 4.3 15.1 - - + +
231M ILE* 3.4 49.7 - - - +
234M GLU* 3.9 21.4 + - - -
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Residues in contact with ASP 188 (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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184M MET* 3.8 23.5 - - + +
185M THR* 3.2 28.6 + - - +
187M ARG* 1.3 76.7 - - - +
189M ILE* 1.3 67.2 + - - +
190M VAL 3.3 0.7 + - - -
191M LYS* 3.4 27.6 + - - +
192M GLU* 3.7 6.6 + - - +
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Residues in contact with ILE 189 (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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39M ILE* 4.0 31.6 - - + +
41M CYS* 3.6 21.3 - - + -
46M VAL* 3.9 15.9 - - + -
179M LEU* 5.4 0.9 - - + -
181M MET* 4.6 9.4 - - - -
184M MET* 3.7 35.0 - - + -
185M THR 3.2 14.8 - - - +
186M CYS 2.9 8.1 + - - +
188M ASP* 1.3 76.6 - - - +
190M VAL* 1.3 52.8 + - - +
192M GLU* 2.7 28.4 + - + +
193M VAL* 2.8 34.8 + - + +
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Residues in contact with VAL 190 (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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46M VAL* 4.2 17.9 - - + -
186M CYS 3.5 4.0 - - - +
187M ARG 4.1 6.3 - - - +
188M ASP 3.3 0.6 - - - -
189M ILE* 1.3 76.2 - - - +
191M LYS* 1.3 64.4 + - - +
193M VAL* 3.4 4.4 - - - +
194M ALA* 3.2 19.8 + - - +
213M LEU* 4.0 30.0 - - + +
215M TRP* 3.1 45.5 - - + -
227M VAL* 4.5 15.0 - - + -
231M ILE* 4.6 8.3 - - + +
235M ALA* 4.2 10.1 - - + -
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Residues in contact with LYS 191 (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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187M ARG* 5.0 7.0 + - - +
188M ASP* 3.4 19.1 + - - +
190M VAL* 1.3 77.1 - - - +
192M GLU* 1.3 57.2 + - + +
194M ALA* 2.8 23.7 + - - +
195M LYS* 2.9 13.7 + - - +
234M GLU* 3.6 31.0 + - - +
235M ALA* 3.9 19.4 - - + +
238M TYR* 3.5 51.4 - - + -
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Residues in contact with GLU 192 (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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179M LEU* 3.4 37.7 - - + +
184M MET* 4.0 24.9 - - + -
188M ASP 4.0 6.5 - - - +
189M ILE* 2.7 16.3 + - + +
191M LYS* 1.3 74.5 - - + +
193M VAL* 1.3 64.6 + - - +
195M LYS* 3.4 25.7 + - - +
196M ILE* 3.1 26.6 - - - +
238M TYR* 2.9 25.2 + - - -
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Residues in contact with VAL 193 (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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37M ILE* 4.3 17.8 - - + +
39M ILE* 3.6 32.3 - - + +
46M VAL* 3.9 15.0 - - + +
47M PHE 4.7 0.2 - - - -
48M GLY* 4.0 17.3 - - - +
179M LEU* 5.1 0.6 - - - +
189M ILE* 2.8 21.0 + - + +
190M VAL* 3.4 9.0 - - - +
192M GLU* 1.3 73.7 - - - +
194M ALA* 1.3 57.9 + - - +
196M ILE* 2.5 30.9 + - - +
197M ILE* 3.1 14.4 + - + +
213M LEU* 4.0 23.1 - - + -
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Residues in contact with ALA 194 (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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190M VAL 3.6 9.6 - - - +
191M LYS 2.8 11.0 + - - +
193M VAL* 1.3 76.7 - - + +
195M LYS* 1.3 66.4 + - - +
197M ILE* 3.6 4.6 + - - +
198M TYR* 3.0 30.0 + - - -
211M LEU* 3.7 27.6 - - + -
213M LEU* 5.0 3.1 - - + -
235M ALA* 4.1 23.3 - - + +
236M GLU* 4.6 0.4 - - - +
239M ALA* 3.6 5.4 - - + -
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Residues in contact with LYS 195 (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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191M LYS 2.9 11.3 + - - +
192M GLU* 3.4 32.0 + - - +
194M ALA* 1.3 73.8 - - - +
196M ILE* 1.3 53.7 + - + +
198M TYR* 2.9 7.8 + - - +
199M ILE* 2.8 59.4 + - + +
238M TYR* 3.9 22.8 + - + +
239M ALA* 3.5 15.9 - - + +
242M SER* 4.0 31.6 + - - +
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Residues in contact with ILE 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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37M ILE* 4.3 11.9 - - + -
39M ILE* 5.7 0.9 - - + -
172M ALA* 4.0 24.2 - - + +
175M GLU* 3.7 41.5 - - + +
176M ILE* 3.9 14.1 - - + -
179M LEU* 3.7 24.5 - - + -
192M GLU* 3.1 19.5 - - - +
193M VAL* 2.5 15.9 + - - +
195M LYS* 1.3 74.8 - - + +
197M ILE* 1.3 63.6 + - - +
199M ILE* 3.6 13.0 - - + +
200M VAL* 3.1 23.8 + - + +
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Residues in contact with ILE 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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35M THR* 4.6 10.1 - - + +
37M ILE* 4.2 19.5 - - + -
48M GLY 3.9 25.1 - - - +
49M VAL* 4.3 0.2 - - - -
50M GLU* 3.9 32.5 - - + +
193M VAL* 3.1 20.9 + - + +
194M ALA* 3.7 8.1 - - - +
196M ILE* 1.3 76.0 - - - +
198M TYR* 1.3 53.2 + - + +
200M VAL* 3.3 3.6 + - - +
201M HIS* 2.8 33.6 + - - +
209M PHE* 4.0 12.1 - - + -
211M LEU* 3.5 29.8 - - + -
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Residues in contact with TYR 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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194M ALA* 3.0 20.6 + - - +
195M LYS 2.9 8.5 + - - +
197M ILE* 1.3 80.0 - - + +
199M ILE* 1.3 66.6 + - - +
200M VAL 3.3 0.2 + - - -
201M HIS* 3.8 17.4 + - - +
203M GLU* 5.2 4.2 - - - +
209M PHE* 3.5 41.2 + + - -
210M GLU 6.0 0.2 - - - -
211M LEU* 4.3 18.5 - - + +
236M GLU* 3.1 27.7 + - + -
239M ALA* 3.7 21.3 - - + +
240M LYS* 3.2 39.8 + - + -
243M LEU* 4.1 30.1 - - + +
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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
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175M GLU* 3.5 39.5 - - + +
195M LYS* 2.8 52.1 + - + +
196M ILE* 3.6 14.8 - - + +
198M TYR* 1.3 74.5 - - - +
200M VAL* 1.3 70.8 + - + +
201M HIS 3.9 3.5 - - - +
243M LEU* 4.6 14.4 - - + +
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Residues in contact with VAL 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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35M THR* 3.9 20.9 - - + +
50M GLU* 4.7 1.3 - - - +
167M LYS* 6.3 0.2 - - + -
168M ALA* 3.7 29.1 - - + +
171M ALA* 3.9 11.9 - - + -
172M ALA* 3.7 32.5 - - + +
175M GLU* 4.7 1.1 - - + -
196M ILE* 3.1 20.8 + - + +
197M ILE* 3.9 2.7 - - - +
199M ILE* 1.3 84.3 - - + +
201M HIS* 1.3 72.5 + - - +
202M ASP* 3.4 5.4 + - - +
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Residues in contact with HIS 201 (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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50M GLU* 3.4 37.4 + - + -
197M ILE 2.8 18.3 + - - +
198M TYR 3.9 10.4 - - - +
199M ILE 3.9 5.9 - - - +
200M VAL* 1.3 82.7 - - - +
202M ASP* 1.3 84.2 + - - +
203M GLU* 3.6 20.8 + - + +
206M ASP* 3.8 10.2 - - + +
207M LYS 3.6 16.9 + - - -
208M ALA 4.5 0.6 + - - -
209M PHE* 3.0 57.7 - + + +
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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