Contacts of the helix formed by residues 185 - 201 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E CYS* 3.7 1.6 - - - -
42E LYS* 3.9 23.1 - - - +
43E ASP* 3.6 13.2 - - - +
184E MET* 1.3 74.0 - - - +
186E CYS* 1.3 65.2 + - - +
187E ARG* 4.0 8.1 + - - +
188E ASP* 3.1 36.8 + - - +
189E ILE* 3.2 15.6 + - - +
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Residues in contact with CYS 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E CYS* 2.1 48.6 - - - -
43E ASP* 3.1 15.9 + - - +
44E GLY* 3.4 26.5 - - - -
45E VAL 3.8 2.9 - - - -
46E VAL* 4.2 6.9 - - - +
185E THR* 1.3 71.7 - - - +
187E ARG* 1.3 67.4 + - - +
189E ILE* 2.9 15.1 + - - +
190E VAL* 3.3 15.4 + - - +
215E TRP* 3.7 20.6 - - + -
216E VAL 4.3 3.4 - - - -
217E GLY* 4.9 1.3 - - - -
219E LEU* 4.2 5.6 - - + -
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Residues in contact with ARG 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ASP* 5.0 0.2 + - - -
185E THR* 4.1 8.1 - - - +
186E CYS* 1.3 79.5 - - - +
188E ASP* 1.3 62.8 + - - +
190E VAL* 3.8 11.3 + - - +
191E LYS* 4.4 8.0 + - - +
215E TRP* 3.9 18.7 - - - -
219E LEU* 4.3 15.1 - - + +
231E ILE* 3.4 49.7 - - - +
234E GLU* 3.9 21.6 + - - -
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Residues in contact with ASP 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E MET* 3.8 24.6 - - + +
185E THR* 3.1 29.8 + - - +
187E ARG* 1.3 76.1 - - - +
189E ILE* 1.3 66.9 + - - +
190E VAL 3.3 0.7 + - - -
191E LYS* 3.3 27.7 + - - +
192E GLU* 3.7 6.8 + - - +
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Residues in contact with ILE 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ILE* 4.0 32.3 - - + +
41E CYS* 3.6 20.9 - - + -
46E VAL* 3.9 16.4 - - + -
179E LEU* 5.4 0.9 - - + -
181E MET* 4.6 9.4 - - - -
184E MET* 3.7 34.1 - - + -
185E THR 3.2 14.8 - - - +
186E CYS 2.9 8.3 + - - +
188E ASP* 1.3 76.8 - - - +
190E VAL* 1.3 53.0 + - - +
192E GLU* 2.7 29.4 + - + +
193E VAL* 2.8 33.0 + - + +
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Residues in contact with VAL 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E VAL* 4.2 17.9 - - + -
186E CYS 3.5 4.5 - - - +
187E ARG 4.1 6.3 - - - +
188E ASP 3.3 0.8 - - - -
189E ILE* 1.3 75.4 - - - +
191E LYS* 1.3 66.2 + - + +
193E VAL* 3.4 3.6 - - - +
194E ALA* 3.2 19.2 + - - +
213E LEU* 3.9 29.6 - - + +
215E TRP* 3.1 45.1 - - + -
227E VAL* 4.5 14.8 - - + -
231E ILE* 4.6 9.6 - - + +
235E ALA* 4.1 10.7 - - + +
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Residues in contact with LYS 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ARG* 4.4 7.6 + - - +
188E ASP* 3.3 19.3 + - - +
190E VAL* 1.3 77.3 - - - +
192E GLU* 1.3 57.2 + - + +
194E ALA* 2.8 24.6 + - - +
195E LYS* 2.9 13.2 + - - +
234E GLU* 3.6 30.3 + - - +
235E ALA* 3.9 18.8 - - + +
238E TYR* 3.5 51.4 - - + -
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Residues in contact with GLU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E LEU* 3.4 37.8 - - + +
184E MET* 4.0 25.1 - - + +
188E ASP 4.0 6.5 - - - +
189E ILE* 2.7 16.1 + - + +
191E LYS* 1.3 72.5 - - + +
193E VAL* 1.3 65.0 + - - +
195E LYS* 3.3 27.2 + - - +
196E ILE* 3.1 25.4 - - - +
238E TYR* 2.9 24.9 + - - -
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Residues in contact with VAL 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 4.3 16.9 - - + +
39E ILE* 3.6 32.3 - - + +
46E VAL* 3.9 14.6 - - + +
48E GLY* 4.0 17.3 - - - +
179E LEU* 5.1 0.8 - - - +
189E ILE* 2.8 21.8 + - + +
190E VAL* 3.4 9.2 - - - +
192E GLU* 1.3 74.3 - - - +
194E ALA* 1.3 59.3 + - - +
196E ILE* 2.6 29.0 + - - +
197E ILE* 3.1 14.1 + - + +
213E LEU* 4.0 21.5 - - + -
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Residues in contact with ALA 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E VAL 3.2 9.4 + - - +
191E LYS 2.8 11.3 + - - +
193E VAL* 1.3 77.6 - - + +
195E LYS* 1.3 66.5 + - - +
197E ILE* 3.6 4.5 + - - +
198E TYR* 3.1 30.5 + - - -
211E LEU* 3.7 28.3 - - + -
213E LEU* 5.0 2.9 - - + -
235E ALA* 4.1 22.7 - - + +
236E GLU* 4.6 0.9 - - - +
239E ALA* 3.6 4.3 - - + -
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Residues in contact with LYS 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E LYS 2.9 11.8 + - - +
192E GLU* 3.3 33.1 + - - +
194E ALA* 1.3 75.0 - - - +
196E ILE* 1.3 53.2 + - + +
198E TYR* 2.9 8.3 + - - +
199E ILE* 2.8 59.2 + - + +
238E TYR* 3.9 22.7 + - + +
239E ALA* 3.5 15.7 - - + +
242E SER* 4.0 31.7 + - - +
245E GLU* 5.4 2.6 + - - -
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Residues in contact with ILE 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 4.3 13.2 - - + -
39E ILE* 5.6 1.1 - - + -
172E ALA* 4.0 23.8 - - + +
175E GLU* 3.7 41.5 - - + +
176E ILE* 3.9 14.4 - - + -
179E LEU* 3.7 24.7 - - + -
192E GLU* 3.1 19.1 - - - +
193E VAL* 2.6 15.5 + - - +
195E LYS* 1.3 74.7 - - + +
197E ILE* 1.3 64.9 + - - +
199E ILE* 3.6 13.6 - - + +
200E VAL* 3.1 23.8 + - + +
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Residues in contact with ILE 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E THR* 4.6 10.3 - - + +
37E ILE* 4.2 19.3 - - + -
48E GLY 3.9 25.8 - - - +
50E GLU* 3.8 32.8 - - + +
193E VAL* 3.1 22.2 + - + +
194E ALA* 3.8 8.1 - - - +
196E ILE* 1.3 76.3 - - - +
198E TYR* 1.3 58.7 + - + +
200E VAL* 3.3 3.5 + - - +
201E HIS* 2.8 29.1 + - - +
209E PHE* 4.0 12.1 - - + -
211E LEU* 3.5 30.3 - - + -
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Residues in contact with TYR 198 (chain E).
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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194E ALA 3.1 20.1 + - - +
195E LYS* 2.9 9.2 + - - +
197E ILE* 1.3 80.0 - - + +
199E ILE* 1.3 67.9 + - - +
200E VAL 3.3 0.2 + - - -
201E HIS* 3.8 17.2 + - - +
203E GLU* 5.2 4.3 - - - +
209E PHE* 3.5 43.7 + + - -
210E GLU 5.9 0.2 - - - -
211E LEU* 4.3 19.6 - - + +
236E GLU* 3.1 27.7 + - + -
239E ALA* 3.7 20.2 - - + +
240E LYS* 3.2 39.9 - - + -
243E LEU* 4.2 29.5 - - + +
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Residues in contact with ILE 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E GLU* 3.5 38.8 - - + +
195E LYS* 2.8 51.5 + - + +
196E ILE* 3.6 15.7 - - + +
198E TYR* 1.3 74.2 - - - +
200E VAL* 1.3 69.2 + - + +
201E HIS 3.9 3.6 - - - +
243E LEU* 4.7 14.7 - - + +
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Residues in contact with VAL 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E THR* 3.9 20.9 - - + +
50E GLU* 4.7 1.3 - - - +
168E ALA* 3.7 29.2 - - + +
171E ALA* 3.9 12.1 - - + +
172E ALA* 3.8 31.4 - - + +
175E GLU* 4.7 0.7 - - + -
196E ILE* 3.1 20.9 + - + +
197E ILE* 3.8 2.7 - - - +
198E TYR 3.1 0.2 - - - -
199E ILE* 1.3 87.3 - - + +
201E HIS* 1.3 72.9 - - - +
202E ASP* 3.4 4.7 + - - +
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Residues in contact with HIS 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLU* 3.3 36.3 + - + -
52E LEU* 4.5 1.0 - - + +
197E ILE 2.8 18.1 + - - +
198E TYR 3.9 11.2 - - - +
199E ILE 3.9 5.9 - - - +
200E VAL* 1.3 79.7 - - - +
202E ASP* 1.3 84.6 + - - +
203E GLU* 3.6 21.1 + - + +
206E ASP* 3.8 11.0 - - + +
207E LYS 3.6 16.8 + - - -
209E 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