Contacts of the helix formed by residues 185 - 201 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41K CYS* 3.7 1.6 - - - -
42K LYS* 3.9 22.9 - - - +
43K ASP* 3.6 13.9 - - - +
184K MET* 1.3 75.5 - - - +
186K CYS* 1.3 65.9 + - - +
187K ARG* 3.9 9.2 + - - +
188K ASP* 3.2 37.0 + - - +
189K ILE* 3.2 15.2 + - - +
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Residues in contact with CYS 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K CYS* 2.1 48.6 - - - -
43K ASP* 3.1 15.9 + - - +
44K GLY* 3.4 26.0 - - - -
45K VAL 3.8 3.1 - - - -
46K VAL* 4.2 6.7 - - + +
185K THR* 1.3 74.2 - - - +
187K ARG* 1.3 64.7 - - - +
189K ILE* 2.9 16.3 + - - +
190K VAL* 3.3 15.2 + - - +
215K TRP* 3.7 19.8 - - + -
216K VAL 4.3 4.3 - - - -
217K GLY* 5.0 0.7 - - - -
219K LEU* 4.2 5.8 - - + -
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Residues in contact with ARG 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K ASP* 5.0 0.2 + - - -
185K THR* 4.1 8.9 - - - +
186K CYS* 1.3 80.3 - - - +
188K ASP* 1.3 63.4 + - - +
190K VAL* 3.8 11.8 + - - +
191K LYS* 4.4 8.0 + - - +
215K TRP* 4.0 18.1 - - - -
219K LEU* 4.4 14.9 - - + +
231K ILE* 3.4 49.3 - - - +
234K GLU* 3.9 21.0 + - - -
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Residues in contact with ASP 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K MET* 3.8 23.4 - - + +
185K THR* 3.2 29.5 + - - +
187K ARG* 1.3 76.7 - - - +
189K ILE* 1.3 66.2 + - - +
190K VAL 3.3 0.7 + - - -
191K LYS* 3.3 27.7 + - - +
192K GLU* 3.7 6.9 + - - +
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Residues in contact with ILE 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K ILE* 4.0 31.6 - - + +
41K CYS* 3.6 22.9 - - + -
46K VAL* 3.9 16.4 - - + -
179K LEU* 5.4 0.7 - - + -
181K MET* 4.6 9.4 - - - -
184K MET* 3.7 34.3 - - + -
185K THR 3.2 14.4 - - - +
186K CYS 2.9 8.5 + - - +
188K ASP* 1.3 78.5 - - - +
190K VAL* 1.3 53.7 + - - +
192K GLU* 2.7 28.4 + - + +
193K VAL* 2.8 34.6 + - + +
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Residues in contact with VAL 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K VAL* 4.2 18.6 - - + -
186K CYS 3.5 4.3 - - - +
187K ARG 4.1 6.5 - - - +
188K ASP 3.3 0.4 - - - -
189K ILE* 1.3 75.7 - - - +
191K LYS* 1.3 65.1 + - + +
193K VAL* 3.4 4.0 - - - +
194K ALA* 3.2 20.1 + - - +
213K LEU* 3.9 28.9 - - + -
215K TRP* 3.1 44.9 - - + -
227K VAL* 4.5 15.9 - - + -
231K ILE* 4.6 8.5 - - + +
235K ALA* 4.2 9.9 - - + -
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Residues in contact with LYS 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K ARG* 4.4 7.6 + - - +
188K ASP* 3.3 19.5 + - - +
190K VAL* 1.3 76.9 - - - +
192K GLU* 1.3 56.9 + - + +
194K ALA* 2.8 24.4 + - - +
195K LYS* 2.9 13.5 + - - +
234K GLU* 3.6 31.2 + - - +
235K ALA* 3.9 18.8 - - + +
238K TYR* 3.5 52.3 - - + -
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Residues in contact with GLU 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K LEU* 3.4 35.9 - - + +
184K MET* 4.0 25.7 - - + +
188K ASP 4.0 6.3 - - - +
189K ILE* 2.7 16.2 + - + +
191K LYS* 1.3 73.8 - - + +
193K VAL* 1.3 66.0 + - - +
195K LYS* 3.4 26.0 + - - +
196K ILE* 3.1 25.6 - - - +
238K TYR* 2.9 25.4 + - - -
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Residues in contact with VAL 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ILE* 4.3 17.6 - - + +
39K ILE* 3.6 31.6 - - + +
46K VAL* 3.9 14.8 - - + +
48K GLY* 4.0 18.2 - - - +
179K LEU* 5.0 1.2 - - - +
189K ILE* 2.8 22.1 + - + +
190K VAL* 3.4 9.4 - - - +
192K GLU* 1.3 73.6 - - - +
194K ALA* 1.3 57.6 + - - +
196K ILE* 2.6 29.1 + - - +
197K ILE* 3.0 14.3 + - + +
213K LEU* 4.0 23.3 - - + -
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Residues in contact with ALA 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K VAL 3.2 10.0 + - - +
191K LYS 2.8 12.0 + - - +
193K VAL* 1.3 77.1 - - + +
195K LYS* 1.3 66.3 + - - +
197K ILE* 3.6 4.0 + - - +
198K TYR* 3.0 30.0 + - - -
211K LEU* 3.7 27.6 - - + -
213K LEU* 5.0 3.1 - - + -
235K ALA* 4.1 22.2 - - + +
236K GLU* 4.6 0.4 - - - +
239K ALA* 3.6 4.7 - - + -
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Residues in contact with LYS 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191K LYS 2.9 11.6 + - - +
192K GLU* 3.4 31.2 + - - +
194K ALA* 1.3 73.0 - - - +
196K ILE* 1.3 54.0 + - + +
198K TYR* 2.9 8.7 + - - +
199K ILE* 2.8 58.6 + - + +
238K TYR* 3.9 23.2 + - + +
239K ALA* 3.5 16.6 - - + +
242K SER* 4.0 31.4 + - - +
243K LEU 6.1 0.2 - - - +
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Residues in contact with ILE 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ILE* 4.3 11.7 - - + -
39K ILE* 5.7 0.7 - - + -
172K ALA* 4.0 23.8 - - + +
175K GLU* 3.7 40.6 - - + +
176K ILE* 3.9 14.6 - - + -
179K LEU* 3.7 24.7 - - + -
192K GLU* 3.1 19.7 - - - +
193K VAL* 2.6 16.2 + - - +
195K LYS* 1.3 75.0 - - + +
197K ILE* 1.3 64.8 + - - +
199K ILE* 4.0 12.8 - - + -
200K VAL* 3.1 24.1 + - + +
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Residues in contact with ILE 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K THR* 4.6 9.2 - - + +
37K ILE* 4.2 20.4 - - + -
48K GLY 3.9 25.1 - - - +
50K GLU* 3.8 32.0 - - + +
193K VAL* 3.0 21.1 + - + +
194K ALA* 3.7 7.9 - - - +
196K ILE* 1.3 76.3 - - - +
198K TYR* 1.3 51.9 - - + +
200K VAL* 3.3 3.8 + - - +
201K HIS* 2.8 33.3 + - - +
209K PHE* 4.0 12.1 - - + -
211K LEU* 3.5 30.3 - - + -
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Residues in contact with TYR 198 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194K ALA 3.0 20.1 + - - +
195K LYS 2.9 8.9 + - - +
197K ILE* 1.3 78.6 - - + +
199K ILE* 1.3 66.2 + - - +
200K VAL 3.3 0.5 + - - -
201K HIS* 3.8 17.4 + - - +
203K GLU* 5.2 3.8 - - - +
209K PHE* 3.5 43.1 + + - -
211K LEU* 4.3 20.0 - - + +
236K GLU* 3.1 27.3 + - + -
239K ALA* 3.7 21.3 - - + +
240K LYS* 3.2 39.5 + - + -
243K LEU* 4.1 31.1 - - + +
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Residues in contact with ILE 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K ALA* 6.3 0.2 - - + -
175K GLU* 3.5 39.5 - - - +
195K LYS* 2.8 51.3 + - + +
196K ILE* 3.6 15.5 - - + +
198K TYR* 1.3 74.3 - - - +
200K VAL* 1.3 69.2 + - + +
201K HIS 3.9 3.8 - - - +
243K LEU* 4.6 15.1 - - + +
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Residues in contact with VAL 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K THR* 3.9 20.2 - - + +
50K GLU* 4.7 1.3 - - - +
168K ALA* 3.7 30.2 - - + +
171K ALA* 3.9 11.7 - - + +
172K ALA* 3.7 31.6 - - + +
175K GLU* 4.7 0.9 - - + -
196K ILE* 3.1 20.9 + - + +
197K ILE* 3.9 3.4 - - - +
199K ILE* 1.3 85.9 - - + +
201K HIS* 1.3 72.4 + - - +
202K ASP* 3.4 4.9 + - - +
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Residues in contact with HIS 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K GLU* 3.3 35.9 + - + -
52K LEU* 4.5 0.4 - - + +
197K ILE 2.8 18.5 + - - +
198K TYR 3.9 11.3 + - - +
199K ILE 3.9 6.2 - - - +
200K VAL* 1.3 80.5 - - - +
202K ASP* 1.3 84.1 + - - +
203K GLU* 3.6 19.8 + - + +
206K ASP* 3.8 12.0 - - + +
207K LYS 3.6 17.0 + - - -
208K ALA 4.5 0.2 + - - -
209K PHE* 3.0 58.1 - + + +
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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