Contacts of the helix formed by residues 173 - 189 (chain F) in PDB entry 5JLH
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 HIS 173 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135F TYR* 3.4 34.9 - + - +
137F TYR* 3.5 8.7 + - - -
142F CYS* 4.1 3.6 - - - -
153F ILE* 3.5 19.1 - - + +
154F TYR* 3.2 33.0 - + - -
158F ILE* 4.7 0.2 - - + -
162F TYR* 3.2 33.2 - + + +
171F PRO 3.3 2.9 + - - +
172F PRO* 1.3 75.0 - - - +
174F VAL* 1.3 80.0 + - + +
175F TYR* 3.0 42.8 + + - +
176F ALA* 3.3 17.7 - - + +
177F VAL* 3.5 7.6 + - - +
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Residues in contact with VAL 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F TYR* 3.3 35.4 - - + +
142F CYS* 4.9 4.9 - - - -
144F VAL* 5.5 0.7 - - + -
154F TYR* 5.6 0.7 - - + -
173F HIS* 1.3 78.7 + - + +
175F TYR* 1.3 55.9 + - + +
176F ALA 2.9 4.7 - - - -
177F VAL* 2.8 23.5 + - + +
178F THR* 2.8 35.2 + - + +
207F ASN* 3.3 21.3 - - - +
211F VAL* 3.3 33.9 - - + -
693F VAL* 5.3 10.8 - - + -
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Residues in contact with TYR 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F TYR* 3.2 44.1 + + - +
155F THR 4.8 1.0 + - - -
158F ILE* 4.3 3.8 - - + -
159F VAL* 4.2 20.6 - - + -
162F TYR* 3.2 35.0 - + + -
173F HIS* 3.0 25.8 + + - +
174F VAL* 1.3 79.6 - - + +
176F ALA* 1.3 56.0 + - - +
178F THR* 3.4 9.3 - - + +
179F GLU* 2.9 28.9 + - - +
210F LYS* 3.1 35.6 + - + +
211F VAL* 4.8 1.1 - - - -
213F GLN* 4.1 11.8 + - - +
214F TYR* 3.3 33.8 - + + -
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Residues in contact with ALA 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F TYR* 3.0 27.4 - - - +
162F TYR* 4.8 2.5 - - + -
165F LYS 5.6 0.7 - - - +
167F ARG* 4.6 13.7 - - + +
170F VAL* 4.4 20.9 - - + -
173F HIS* 3.3 13.6 + - + +
174F VAL 2.9 2.0 + - - -
175F TYR* 1.3 77.2 - - - +
177F VAL* 1.3 57.8 + - - +
179F GLU* 3.1 13.7 + - - +
180F GLY* 2.8 24.3 + - - -
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Residues in contact with VAL 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F TYR* 3.7 20.2 - - + +
140F LEU 5.9 2.0 - - - +
142F CYS* 3.7 27.4 - - + -
167F ARG* 5.6 7.9 - - - +
173F HIS 3.5 1.1 + - - +
174F VAL* 2.8 40.9 + - + +
176F ALA* 1.3 72.7 - - - +
178F THR* 1.3 59.0 + - - +
180F GLY* 2.9 16.1 + - - +
181F ALA* 3.0 12.5 + - - +
194F ILE* 4.9 4.4 - - + +
691F SER* 4.1 20.9 + - - +
692F PHE 5.1 1.6 - - - +
693F VAL* 4.2 20.0 - - + -
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Residues in contact with THR 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F VAL* 2.8 23.7 + - + +
175F TYR* 3.4 17.9 - - + +
177F VAL* 1.3 73.7 - - - +
179F GLU* 1.3 64.9 + - - +
181F ALA* 3.1 8.3 + - - +
182F TYR* 2.9 29.3 + - - +
194F ILE* 4.7 8.2 - - - +
211F VAL* 3.5 29.2 - - + +
214F TYR* 3.6 24.4 - - + -
215F LEU* 4.8 3.3 - - - +
474F LEU* 4.3 14.6 - - - +
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Residues in contact with GLU 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F TYR* 2.6 33.6 - - - +
163F ARG 4.0 0.2 - - - -
164F GLY* 2.5 13.7 + - - +
165F LYS 2.5 46.8 + - - +
170F VAL* 5.7 1.2 - - - +
175F TYR 2.9 20.3 + - - +
176F ALA* 3.2 10.6 - - - +
178F THR* 1.3 74.6 - - - +
180F GLY* 1.3 64.2 + - - +
182F TYR* 3.9 1.5 - - - +
183F ARG* 2.9 36.7 + - + +
214F TYR* 3.0 23.6 - - - +
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Residues in contact with GLY 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F ALA 2.8 13.8 + - - -
177F VAL* 2.9 6.2 + - - -
179F GLU* 1.3 76.2 - - - +
181F ALA* 1.3 56.4 + - - +
183F ARG* 3.9 3.8 - - - +
184F SER* 2.9 30.7 + - - -
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Residues in contact with ALA 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177F VAL 3.0 10.8 + - - +
178F THR* 3.1 9.6 + - - +
180F GLY* 1.3 77.3 - - - +
182F TYR* 1.3 57.4 + - - +
184F SER* 2.5 22.9 + - - -
185F MET* 2.9 13.2 + - - +
192F GLN* 3.2 16.7 - - + +
194F ILE* 4.1 14.6 - - + -
474F LEU* 4.0 28.0 - - + -
691F SER* 5.2 5.4 - - - -
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Residues in contact with TYR 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F THR* 2.9 16.3 + - - +
179F GLU* 3.9 5.2 - - - +
181F ALA* 1.3 76.2 - - - +
183F ARG* 1.3 86.1 + - + +
185F MET* 3.2 17.1 + - + +
186F LEU* 3.0 66.2 + - + +
214F TYR* 4.9 10.8 - + + -
215F LEU* 4.9 20.0 - - + -
218F VAL* 3.5 36.9 + - + +
219F ALA* 4.4 11.2 - - + +
270F PHE* 5.4 5.6 - + - -
273F ALA 5.2 0.5 + - - -
274F GLY* 3.7 24.6 + - - -
474F LEU* 5.8 4.2 - - + +
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Residues in contact with ARG 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F ARG* 4.2 25.5 - - - +
164F GLY* 3.7 35.0 - - - +
165F LYS 5.8 0.9 - - - +
179F GLU* 2.9 32.6 + - + +
180F GLY* 4.1 3.8 - - - +
182F TYR* 1.3 100.3 - - + +
184F SER* 1.3 57.9 + - - +
186F LEU* 4.1 14.8 - - - +
187F GLN* 2.8 34.8 + - + +
214F TYR* 5.8 0.2 + - - -
218F VAL* 5.4 1.6 - - - +
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Residues in contact with SER 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F GLY 2.9 17.0 + - - -
181F ALA* 2.5 21.1 + - - -
183F ARG* 1.3 75.7 - - - +
185F MET* 1.3 51.6 + - - +
187F GLN* 4.2 4.9 - - - -
188F ASP* 2.6 44.4 + - - +
192F GLN* 2.8 31.4 + - - -
689F ASN* 4.8 6.7 - - - -
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Residues in contact with MET 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F ALA 2.9 13.8 + - - +
182F TYR* 3.2 14.8 + - + +
184F SER* 1.3 74.8 + - - +
186F LEU* 1.3 81.5 + - + +
187F GLN 3.1 1.1 - - - -
189F ARG* 2.5 35.1 + - - -
190F GLU 3.5 26.2 - - - +
191F ASP* 4.8 1.1 - - - -
192F GLN* 4.2 4.7 - - + -
270F PHE* 3.3 49.8 - - + -
271F ASP 5.2 3.4 - - - +
274F GLY* 5.4 1.1 - - - -
472F SER* 4.1 21.8 - - - -
473F PHE 4.2 10.5 - - - +
474F LEU* 5.4 1.8 - - - -
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Residues in contact with LEU 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F TYR* 3.0 68.2 + - + +
183F ARG* 4.1 17.5 - - - +
185F MET* 1.3 87.9 - - + +
187F GLN* 1.3 63.1 + - - +
189F ARG* 4.1 5.8 + - - +
272F VAL 5.4 5.8 - - - +
273F ALA 5.1 8.1 - - - +
274F GLY* 4.7 9.0 - - - -
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Residues in contact with GLN 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F ARG* 2.8 21.7 + - + +
184F SER* 3.9 4.5 - - - +
186F LEU* 1.3 81.7 - - - +
188F ASP* 1.3 63.5 + - + +
189F ARG* 5.0 1.9 - - - +
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Residues in contact with ASP 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F SER* 2.6 28.0 + - - +
187F GLN* 1.3 74.6 - - + +
189F ARG* 1.3 71.6 + - - +
190F GLU* 3.0 43.1 + - + +
192F GLN* 5.0 4.8 + - - +
689F ASN* 5.2 5.9 + - - +
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Residues in contact with ARG 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F MET* 2.5 26.8 + - - -
186F LEU 4.1 5.1 + - - +
187F GLN 3.4 2.4 - - - +
188F ASP* 1.3 84.2 - - - +
190F GLU* 1.3 59.6 + - + +
191F ASP* 5.4 0.3 - - - +
472F SER* 4.4 10.6 + - - -
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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