Contacts of the helix formed by residues 175 - 191 (chain R) 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 ASP 175 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334J ARG* 3.1 52.7 + - + +
336J MET 4.6 2.6 + - - +
338J LEU* 4.7 14.8 + - + +
173R ASP* 3.3 0.6 + - - -
174R TRP* 1.3 78.4 - - - +
176R ARG* 1.3 64.2 + - - +
177R ARG 3.3 0.2 - - - -
178R ASN* 3.6 12.6 + - - +
179R ARG* 3.3 34.0 + - - +
207R THR* 6.1 0.7 - - - -
209R THR* 4.2 16.9 + - - +
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Residues in contact with ARG 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J ARG* 2.7 49.5 - - - +
134R LEU* 5.2 7.9 - - - +
135R GLY* 4.2 16.0 - - - +
138R LEU* 4.8 8.4 - - - +
139R ASP* 2.9 35.1 + - - +
142R PHE* 4.0 9.2 - - + -
168R ILE* 3.9 25.8 - - + -
172R GLY* 5.5 2.8 - - - -
173R ASP* 3.2 34.6 + - - +
175R ASP* 1.3 78.6 - - - +
177R ARG* 1.3 58.0 + - - +
178R ASN 3.1 0.4 - - - -
179R ARG* 2.8 33.1 - - + +
180R LEU* 2.9 15.1 + - - +
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Residues in contact with ARG 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192K LYS* 5.1 3.8 + - - +
168R ILE* 2.9 51.0 + - + +
169R GLU* 4.7 7.8 + - - +
171R GLY 4.3 6.3 + - - -
173R ASP 3.6 15.9 + - - +
174R TRP* 3.4 56.6 - - + +
175R ASP 3.3 0.6 - - - -
176R ARG* 1.3 79.2 - - - +
178R ASN* 1.3 56.6 + - - +
180R LEU* 3.3 9.7 - - + +
181R LYS* 2.9 46.6 + - - +
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Residues in contact with ASN 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337J ASN* 3.6 12.8 + - - +
338J LEU 5.1 1.4 + - - +
174R TRP* 2.8 43.0 + - - +
175R ASP* 3.6 9.7 + - - +
176R ARG 3.1 1.0 - - - -
177R ARG* 1.3 74.7 - - - +
179R ARG* 1.3 71.2 + - - +
180R LEU 3.0 0.7 - - - -
181R LYS* 3.1 10.7 + - - +
182R VAL* 2.9 23.2 + - - +
203R ASP 5.6 1.0 - - - +
204R THR* 4.5 4.8 - - - +
207R THR* 2.7 46.1 + - - +
208R PHE* 5.9 1.3 - - - -
209R THR 6.2 0.9 - - - +
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Residues in contact with ARG 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J ARG* 6.1 0.4 - - - +
139R ASP* 6.0 0.2 - - - -
142R PHE* 4.5 9.4 - - + -
175R ASP* 3.3 30.9 + - - -
176R ARG* 2.8 39.3 - - + +
178R ASN* 1.3 75.6 - - - +
180R LEU* 1.3 56.1 + - - +
182R VAL* 2.6 29.5 + - - +
183R TYR* 2.9 24.4 + - + -
209R THR* 3.4 39.6 + - - +
210R SER* 2.6 64.6 + - - +
212R GLU* 3.8 15.8 + - - +
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Residues in contact with LEU 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142R PHE* 2.9 39.0 - - + -
161R THR* 5.4 13.7 - - - +
164R ALA* 4.4 14.4 - - + -
165R LYS* 5.8 4.9 - - + +
168R ILE* 5.6 5.6 - - + -
176R ARG 2.9 19.5 + - - +
177R ARG* 3.3 12.8 - - + +
178R ASN 3.0 0.2 - - - -
179R ARG* 1.3 76.7 - - - +
181R LYS* 1.3 62.5 + - + +
183R TYR* 3.1 10.2 + - + +
184R GLN* 2.9 55.9 + - + +
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Residues in contact with LYS 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174R TRP* 3.5 34.2 - - + -
177R ARG* 2.9 33.9 + - - +
178R ASN* 3.1 11.4 + - - +
180R LEU* 1.3 76.1 - - + +
182R VAL* 1.3 61.4 + - - +
184R GLN* 4.2 10.3 - - - +
185R GLY* 2.9 24.7 + - - -
200R LEU* 3.2 36.7 - - + +
201R PHE* 4.7 0.2 - - - -
203R ASP* 6.0 5.4 - - + +
204R THR* 4.1 16.4 - - + +
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Residues in contact with VAL 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R ASN 2.9 17.6 + - - +
179R ARG* 2.6 21.4 + - - +
181R LYS* 1.3 70.1 - - - +
183R TYR* 1.3 63.1 + - + +
186R LEU* 2.9 23.5 + - + +
201R PHE* 3.5 10.5 - - + -
204R THR* 3.8 25.6 - - + +
207R THR 5.3 2.0 - - - +
208R PHE* 4.2 32.8 - - + -
210R SER* 5.0 5.2 - - - +
213R LEU* 4.4 17.0 - - + -
214R MET* 4.7 15.0 - - + -
219R PHE* 4.8 2.9 - - + -
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Residues in contact with TYR 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142R PHE* 3.6 43.7 - + + +
146R ARG* 3.5 24.3 + - + -
149R LEU* 5.1 11.2 - - + -
179R ARG* 2.9 32.4 + - + -
180R LEU* 3.4 8.1 - - + +
182R VAL* 1.3 78.1 - - + +
184R GLN* 1.3 64.5 + - - +
186R LEU* 3.1 2.1 + - - +
187R TYR* 2.8 23.5 + - - +
210R SER* 4.7 2.0 - - - -
212R GLU* 3.7 15.3 - - + +
213R LEU* 2.6 51.8 - - + +
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Residues in contact with GLN 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161R THR* 4.0 32.5 + - - +
162R GLU* 5.7 1.0 + - - -
165R LYS* 5.8 4.0 - - - +
180R LEU* 2.9 41.5 + - + +
181R LYS* 4.2 7.5 - - - +
183R TYR* 1.3 72.2 - - - +
185R GLY* 1.3 56.9 + - - +
187R TYR* 3.2 13.1 - - + +
188R CYS* 2.9 39.8 + - - -
196R GLN* 5.2 5.0 - - - +
200R LEU* 4.5 16.5 - - + +
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Residues in contact with GLY 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181R LYS 2.9 20.3 + - - -
184R GLN* 1.3 72.9 - - - +
186R LEU* 1.3 54.6 + - - +
188R CYS* 2.7 28.0 + - - +
189R VAL 2.9 4.7 + - - -
197R ALA* 4.4 1.1 - - - -
200R LEU* 4.5 8.5 - - - +
201R PHE* 2.0 37.4 - - - -
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Residues in contact with LEU 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17R LEU* 4.9 2.2 - - + -
149R LEU* 5.5 9.9 - - + -
182R VAL* 2.9 18.3 + - + +
183R TYR* 3.5 4.0 - - - +
185R GLY* 1.3 67.8 - - - +
187R TYR* 1.3 63.5 + - - +
189R VAL* 3.2 9.3 + - + +
190R ALA* 2.9 19.1 + - - +
201R PHE* 1.9 25.2 - - + -
213R LEU* 3.5 31.2 - - + -
214R MET* 4.9 11.0 - - + -
222R TYR* 5.2 12.3 - - + -
286R TRP* 4.5 10.3 - - + +
287R LEU* 2.8 51.1 - - + +
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Residues in contact with TYR 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149R LEU* 6.3 3.4 - - + -
154R ASN* 3.9 37.4 - - + +
157R ILE* 4.7 25.8 - - + -
158R THR* 5.6 8.0 - - - -
183R TYR 2.8 12.4 + - - +
184R GLN* 3.2 18.4 - - + +
186R LEU* 1.3 74.2 - - - +
188R CYS* 1.3 69.9 + - - +
190R ALA* 2.4 42.4 + - + +
191R ILE* 3.2 37.8 + - + +
287R LEU* 5.6 0.2 - - - -
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Residues in contact with CYS 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184R GLN* 2.9 30.0 + - - -
185R GLY* 2.7 15.8 + - - +
187R TYR* 1.3 86.1 - - - +
189R VAL* 1.3 59.6 + - - +
191R ILE* 3.0 15.2 + - - +
193R ASP* 2.6 38.8 + - + +
196R GLN* 3.6 35.0 - - - -
197R ALA* 3.5 13.5 - - + +
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Residues in contact with VAL 189 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185R GLY 2.9 6.5 + - - -
186R LEU* 3.4 11.7 - - + +
188R CYS* 1.3 70.7 - - - +
190R ALA* 1.3 58.5 + - - +
191R ILE 2.6 21.3 - - - +
194R PHE* 3.5 21.8 - - + -
197R ALA* 3.8 4.0 - - + -
201R PHE* 3.5 28.0 - - + -
222R TYR* 5.8 5.8 - - + -
226R VAL* 3.7 24.2 - - + -
287R LEU* 3.0 27.1 - - + +
288R PHE* 3.8 26.0 - - + -
291R HIS* 3.6 2.8 + - - -
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Residues in contact with ALA 190 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186R LEU 2.9 11.0 + - - +
187R TYR* 2.4 38.2 + - + +
189R VAL* 1.3 67.8 - - - +
191R ILE* 1.3 57.7 + - + +
286R TRP* 5.8 0.7 - - + -
287R LEU* 3.1 29.3 - - + +
291R HIS* 3.5 8.6 - - - -
39Y TRP* 5.6 1.4 - - - +
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Residues in contact with ILE 191 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154R ASN* 5.4 4.5 - - - -
187R TYR* 3.2 48.2 + - + +
188R CYS* 3.0 6.2 + - - +
189R VAL 2.6 16.4 - - - +
190R ALA* 1.3 79.7 - - + +
192R ARG* 1.3 74.3 + - + +
193R ASP* 2.9 30.7 + - + +
194R PHE* 3.6 4.0 - - - -
291R HIS* 2.8 12.1 + - - -
39Y TRP* 3.7 40.6 - - + +
40Y GLU* 3.9 15.0 - - + +
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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