Contacts of the helix formed by residues 185 - 201 (chain X) in PDB entry 5GJQ
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41X CYS* 3.7 2.9 - - - -
42X LYS* 4.3 20.9 - - - +
43X ASP* 3.3 19.1 - - - +
183X GLU 4.6 1.8 - - - +
184X MET* 1.3 80.1 - - - +
186X CYS* 1.3 67.7 + - - +
187X ARG* 2.8 14.2 + - - +
188X ASP* 2.8 35.8 + - - +
189X ILE* 2.9 11.0 + - - +
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Residues in contact with CYS 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X CYS* 3.2 18.5 - - - -
43X ASP* 3.0 44.0 + - - +
44X GLY* 3.6 13.2 - - - -
45X VAL 4.1 3.1 - - - -
46X VAL* 4.0 9.0 - - + +
185X THR* 1.3 71.8 - - - +
187X ARG* 1.3 63.3 + - - +
189X ILE* 3.0 13.6 + - - +
190X VAL* 3.1 22.2 + - - +
215X TRP* 3.3 25.6 - - + -
216X VAL 4.9 2.7 - - - -
217X GLY* 5.0 2.7 - - - -
219X LEU* 5.4 6.7 - - + -
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Residues in contact with ARG 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X THR* 2.8 12.9 + - - +
186X CYS* 1.3 82.1 - - - +
188X ASP* 1.3 67.4 + - - +
189X ILE 3.1 1.0 + - - -
190X VAL* 3.5 12.3 + - - +
191X LYS* 4.3 20.0 + - - +
215X TRP* 3.8 16.9 - - + -
219X LEU* 4.2 23.7 - - + +
231X ILE* 3.6 42.7 - - - +
234X GLU* 4.8 6.1 + - - -
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Residues in contact with ASP 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X MET* 3.8 24.2 - - + +
185X THR* 2.8 33.2 + - - +
187X ARG* 1.3 81.0 - - - +
189X ILE* 1.3 63.5 + - - +
190X VAL 3.7 0.2 + - - -
191X LYS* 3.8 16.7 + - - +
192X GLU* 3.8 15.9 + - - +
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Residues in contact with ILE 189 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X ILE* 3.7 36.3 - - + +
41X CYS* 4.0 15.5 - - + -
46X VAL* 4.0 11.9 - - + -
179X LEU* 4.9 2.7 - - + -
181X MET* 4.2 5.4 - - + -
184X MET* 3.6 38.4 - - + -
185X THR 2.9 21.9 + - - +
186X CYS* 3.5 9.9 - - - +
187X ARG 3.0 0.6 - - - -
188X ASP* 1.3 76.9 - - - +
190X VAL* 1.3 68.1 + - - +
192X GLU* 2.8 15.9 + - + +
193X VAL* 2.9 29.1 + - + -
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Residues in contact with VAL 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X VAL* 4.2 20.0 - - + -
186X CYS 3.1 17.1 + - - +
187X ARG 3.8 6.3 - - - +
188X ASP 3.4 0.4 - - - -
189X ILE* 1.3 76.5 - - - +
191X LYS* 1.3 64.3 + - + +
193X VAL* 3.2 3.7 + - - +
194X ALA* 3.0 22.2 + - - +
213X LEU* 4.0 23.2 - - + +
215X TRP* 3.5 32.1 - - + -
227X VAL* 4.7 7.6 - - + -
231X ILE* 4.4 15.5 - - + +
235X ALA* 3.9 17.0 - - + -
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Residues in contact with LYS 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187X ARG* 4.3 23.8 + - - +
188X ASP* 3.8 13.1 + - - +
189X ILE 3.2 0.4 - - - -
190X VAL* 1.3 79.4 - - + +
192X GLU* 1.3 59.7 + - + +
194X ALA* 3.4 2.3 + - - +
195X LYS* 2.9 29.1 + - - +
231X ILE* 5.6 3.0 - - + +
234X GLU* 3.0 35.9 + - - -
235X ALA* 3.8 26.5 - - + +
238X TYR* 3.7 43.2 - - + -
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Residues in contact with GLU 192 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179X LEU* 3.5 45.1 - - + +
184X MET* 4.1 10.5 - - + +
188X ASP 3.8 13.0 - - - +
189X ILE* 2.8 9.9 + - - +
191X LYS* 1.3 74.3 - - + +
193X VAL* 1.3 62.1 + - - +
195X LYS* 3.3 29.0 + - - +
196X ILE* 2.9 39.0 + - - +
238X TYR* 2.9 25.5 + - - -
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Residues in contact with VAL 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X ILE* 3.9 18.1 - - + +
39X ILE* 3.5 32.5 - - + -
46X VAL* 4.0 11.9 - - + +
47X PHE 4.4 0.4 - - - -
48X GLY* 3.7 33.0 - - - +
179X LEU* 6.2 0.4 - - + -
189X ILE* 2.9 24.5 + - + +
190X VAL* 3.4 8.1 - - - +
192X GLU* 1.3 74.3 - - - +
194X ALA* 1.3 66.7 + - - +
196X ILE* 3.1 4.6 + - - +
197X ILE* 2.9 28.0 + - + +
213X LEU* 3.9 10.8 - - + -
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Residues in contact with ALA 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X VAL 3.0 13.4 + - - +
191X LYS 3.6 7.2 - - - +
193X VAL* 1.3 77.2 - - - +
195X LYS* 1.3 56.7 + - - +
197X ILE* 3.4 4.0 + - - +
198X TYR* 2.9 35.3 + - - -
211X LEU* 3.7 29.2 - - + -
213X LEU* 4.7 3.1 - - + +
235X ALA* 3.7 29.2 - - + +
236X GLU 4.4 0.2 - - - +
239X ALA* 3.9 4.7 - - + -
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Residues in contact with LYS 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175X GLU* 5.1 4.2 + - - -
191X LYS 2.9 18.6 + - - +
192X GLU* 3.3 31.9 + - - +
194X ALA* 1.3 75.6 - - - +
196X ILE* 1.3 58.7 + - + +
198X TYR* 3.1 5.2 + - - +
199X ILE* 2.9 53.2 + - + +
238X TYR* 4.0 24.2 + - + +
239X ALA* 3.7 12.3 - - - +
242X SER* 4.4 21.1 - - - -
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Residues in contact with ILE 196 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X ILE* 3.9 19.5 - - + -
39X ILE* 6.4 1.1 - - + -
172X ALA* 4.1 20.2 - - + +
175X GLU* 3.8 41.5 - - + +
176X ILE* 3.5 26.7 - - + -
179X LEU* 4.2 15.7 - - + -
192X GLU* 2.9 27.8 + - + +
193X VAL* 3.7 4.3 - - - +
195X LYS* 1.3 75.3 - - + +
197X ILE* 1.3 57.9 + - - +
199X ILE* 3.4 10.0 + - + +
200X VAL* 3.0 29.2 + - + +
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Residues in contact with ILE 197 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X THR* 4.7 9.0 - - - +
37X ILE* 3.9 34.5 - - + +
48X GLY 4.4 12.3 - - - +
50X GLU* 4.1 22.0 - - + +
193X VAL* 2.9 23.2 + - + +
194X ALA 3.5 7.4 - - - +
196X ILE* 1.3 77.0 - - - +
198X TYR* 1.3 64.2 + - + +
200X VAL* 3.3 8.6 + - + +
201X HIS* 3.0 24.1 + - - +
209X PHE* 3.8 19.7 - - + -
211X LEU* 3.8 30.3 - - + -
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Residues in contact with TYR 198 (chain X).
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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194X ALA 2.9 24.7 + - - +
195X LYS 3.1 6.5 + - - +
197X ILE* 1.3 76.6 - - + +
199X ILE* 1.3 63.4 + - - +
201X HIS* 3.8 15.2 + + - +
209X PHE* 3.7 34.3 - + - -
211X LEU* 4.5 9.0 - - + +
236X GLU* 3.9 29.9 + - + +
239X ALA* 3.4 26.7 - - + +
240X LYS* 3.6 35.9 - - + -
243X LEU* 4.0 37.7 - - + +
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Residues in contact with ILE 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171X ALA* 6.5 0.2 - - + -
175X GLU* 3.3 47.3 - - + +
195X LYS* 2.9 42.4 + - + +
196X ILE* 3.5 11.7 - - + +
198X TYR* 1.3 77.6 - - - +
200X VAL* 1.3 68.8 + - + +
201X HIS 3.2 7.4 + - - +
242X SER 6.1 0.9 - - - +
243X LEU* 4.3 17.3 - - + +
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Residues in contact with VAL 200 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X THR* 4.1 17.0 - - + +
37X ILE* 6.4 0.2 - - + -
50X GLU* 4.6 4.9 - - - +
168X ALA* 3.4 35.8 - - + +
171X ALA* 3.8 11.7 - - + -
172X ALA* 3.6 35.9 - - + +
175X GLU* 5.5 0.9 - - + -
196X ILE* 3.0 15.0 + - + +
197X ILE* 4.0 11.2 - - + +
199X ILE* 1.3 83.6 - - + +
201X HIS* 1.3 68.8 + - - +
202X ASP* 3.6 4.0 + - - +
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Residues in contact with HIS 201 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X GLU* 2.4 35.8 + - - +
52X LEU* 4.2 5.6 - - + -
197X ILE 3.0 17.5 + - - +
198X TYR* 3.9 11.5 - + - +
199X ILE 3.2 8.8 - - - +
200X VAL* 1.3 80.9 - - - +
202X ASP* 1.3 76.4 + - - +
203X GLU* 3.9 19.6 + - + +
206X ASP* 3.7 17.2 - - + +
207X LYS 3.3 19.7 + - - -
209X PHE* 3.3 40.2 - + + -
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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
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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