Contacts of the helix formed by residues 203 - 219 (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 GLY 203 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201F GLY* 3.2 7.2 - - - +
202F ALA* 1.3 79.7 - - - +
204F LYS* 1.3 57.7 + - - +
205F THR* 3.1 3.4 - - - -
206F GLU* 3.0 35.6 + - - +
207F ASN* 2.7 35.5 + - - +
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Residues in contact with LYS 204 (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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196F CYS* 3.3 33.4 + - + -
197F THR 3.2 19.8 + - - +
198F GLY* 3.4 3.0 - - - -
199F GLU* 3.3 35.2 - - + +
200F SER 5.0 2.2 - - - +
201F GLY 5.6 0.4 - - - +
202F ALA* 3.3 6.5 - - + -
203F GLY* 1.3 79.4 - - - +
205F THR* 1.3 54.7 + - - +
207F ASN* 3.4 8.1 + - - +
208F THR* 2.7 35.9 + - - -
478F ASP* 2.6 32.2 + - + +
479F ILE 3.2 20.6 + - - -
695F CYS* 3.8 19.7 - - + -
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Residues in contact with THR 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F GLY* 3.1 1.1 - - - -
204F LYS* 1.3 79.6 - - - +
206F GLU* 1.3 53.9 + - - +
208F THR* 2.9 11.3 + - - -
209F LYS* 2.7 37.9 + - + +
238F LEU 5.5 0.9 - - - +
242F ASN* 3.2 40.4 + - - +
264F LYS* 4.2 10.7 + - + +
266F ILE* 5.7 7.4 - - + -
478F ASP* 3.9 17.5 + - - +
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Residues in contact with GLU 206 (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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146F ASN* 5.5 2.4 + - - -
202F ALA 5.0 0.2 - - - +
203F GLY* 3.0 25.0 + - - +
205F THR* 1.3 80.6 - - - +
207F ASN* 1.3 61.0 + - - +
209F LYS* 3.1 46.1 + - + +
210F LYS* 3.3 17.5 + - - +
242F ASN* 6.0 2.5 - - - +
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Residues in contact with ASN 207 (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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134F ILE* 5.8 0.2 - - - +
135F TYR* 3.7 11.0 + - - -
144F VAL* 4.1 23.4 - - - +
154F TYR* 5.1 3.0 + - - -
174F VAL* 3.3 38.4 - - - +
203F GLY 2.7 15.7 + - - +
204F LYS* 3.5 12.3 - - - +
206F GLU* 1.3 70.9 - - - +
208F THR* 1.3 55.4 + - - +
210F LYS* 2.7 34.7 + - - +
211F VAL* 2.9 9.6 + - - +
693F VAL* 5.6 2.8 - - - +
695F CYS* 5.7 2.8 - - - -
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Residues in contact with THR 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196F CYS* 4.4 12.5 - - - -
204F LYS 2.7 18.7 + - - -
205F THR* 2.9 16.1 + - + -
207F ASN* 1.3 76.7 - - - +
209F LYS* 1.3 55.8 + - - +
211F VAL* 3.1 14.1 + - + +
212F ILE* 3.0 35.5 + - + +
266F ILE* 4.7 11.9 - - + -
476F ILE* 3.8 43.7 - - + +
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Residues in contact with LYS 209 (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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205F THR* 2.7 24.4 + - + +
206F GLU* 3.2 33.9 - - + +
207F ASN 3.1 0.2 - - - -
208F THR* 1.3 76.6 - - - +
210F LYS* 1.3 61.8 + - + +
212F ILE* 3.2 16.8 + - + +
213F GLN* 2.8 27.6 + - - +
234F LEU* 5.6 0.3 - - - +
238F LEU* 6.1 3.6 - - + +
239F LEU* 3.1 40.4 - - + +
242F ASN* 4.8 11.6 - - - +
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Residues in contact with LYS 210 (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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150F GLN* 6.3 0.8 - - - +
151F LEU 5.5 4.2 + - - +
154F TYR* 3.5 51.7 + - + -
175F TYR* 3.1 25.0 - - + +
206F GLU* 3.6 17.9 - - - +
207F ASN* 2.7 16.7 + - - +
209F LYS* 1.3 80.0 - - + +
211F VAL* 1.3 61.2 + - - -
213F GLN* 3.2 18.5 + - - +
214F TYR 3.0 18.4 + - - -
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Residues in contact with VAL 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F VAL* 3.3 32.1 - - + -
175F TYR* 4.4 6.7 - - - -
178F THR* 3.5 26.9 - - - +
194F ILE* 5.8 6.7 - - + -
207F ASN* 2.9 18.7 + - - +
208F THR* 3.1 19.7 + - + +
210F LYS* 1.3 74.8 - - - +
212F ILE* 1.3 58.6 + - - +
214F TYR* 3.2 7.8 + - - +
215F LEU* 2.9 31.1 + - + +
474F LEU* 5.4 1.6 - - + -
476F ILE* 4.5 18.4 - - + -
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Residues in contact with ILE 212 (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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208F THR* 3.0 27.2 + - + +
209F LYS* 3.3 17.9 - - + +
211F VAL* 1.3 77.0 - - + +
213F GLN* 1.3 56.2 + - - +
215F LEU* 2.9 12.3 + - + +
216F ALA* 2.9 27.4 + - - +
234F LEU* 3.6 29.5 - - + +
238F LEU* 3.7 33.7 - - + -
266F ILE* 5.7 7.9 - - + -
268F ILE* 4.1 24.0 - - + -
476F ILE* 5.0 1.8 - - + -
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Residues in contact with GLN 213 (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 26.6 + - - +
155F THR 5.0 1.0 + - - -
156F GLU* 4.3 13.3 + - - -
175F TYR* 4.1 12.4 + - - +
209F LYS 2.8 14.0 + - - +
210F LYS* 3.3 22.1 - - - +
212F ILE* 1.3 74.5 - - - +
214F TYR* 1.3 64.0 + - - +
216F ALA* 3.2 2.9 + - - +
217F HIS* 3.1 42.4 + - + +
234F LEU* 3.8 15.3 - - + -
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Residues in contact with TYR 214 (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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159F VAL* 3.3 37.2 - - + -
162F TYR* 4.7 4.7 - - + -
163F ARG* 5.0 4.2 - - + +
175F TYR* 3.3 54.9 - + + -
178F THR* 3.6 23.1 - - + -
179F GLU* 3.0 34.4 - - + +
182F TYR* 4.9 10.7 - + + +
183F ARG* 5.8 0.3 + - - -
210F LYS 3.0 6.5 + - - -
211F VAL* 3.3 9.0 - - - +
213F GLN* 1.3 75.5 - - - +
215F LEU* 1.3 66.4 + - + +
217F HIS* 3.1 3.4 + - - +
218F VAL* 2.9 61.7 + - + +
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Residues in contact with LEU 215 (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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178F THR* 4.8 6.1 - - - +
182F TYR* 4.9 14.6 - - + -
211F VAL* 2.9 17.1 + - + +
212F ILE* 2.9 13.1 + - + +
214F TYR* 1.3 86.6 - - + +
216F ALA* 1.3 56.6 + - - +
218F VAL* 4.0 2.0 - - - +
219F ALA* 3.0 37.5 + - + +
268F ILE* 3.8 18.2 - - + -
270F PHE* 3.1 37.7 - - + -
276F ILE* 3.7 14.5 - - + +
474F LEU* 3.7 30.3 - - + -
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Residues in contact with ALA 216 (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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212F ILE 2.9 5.3 + - - -
213F GLN 3.5 4.3 - - - +
214F TYR 3.2 0.2 - - - -
215F LEU* 1.3 75.2 - - - +
217F HIS* 1.3 68.0 + - + +
219F ALA* 2.7 25.9 - - - +
220F SER* 3.1 6.6 + - - -
234F LEU* 3.4 46.0 - - + +
276F ILE* 5.6 5.8 - - - -
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Residues in contact with HIS 217 (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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156F GLU* 2.8 43.9 + - - +
159F VAL* 4.6 19.1 - - + -
160F GLU* 5.5 6.7 - - - +
163F ARG* 4.6 2.9 + - - -
213F GLN* 3.1 42.4 + - + +
214F TYR 3.9 3.1 - - - +
216F ALA* 1.3 82.9 - - + +
218F VAL* 1.3 64.5 + - - +
220F SER* 3.3 12.5 + - - -
234F LEU* 6.0 0.8 - - - +
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Residues in contact with VAL 218 (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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159F VAL* 4.7 3.6 - - + -
163F ARG* 3.5 38.1 + - + +
182F TYR* 3.5 43.2 + - + +
183F ARG* 5.4 4.3 - - - +
214F TYR* 2.9 56.7 + - + +
215F LEU* 4.0 3.4 - - - +
217F HIS* 1.3 80.4 - - - +
219F ALA* 1.3 58.8 + - - +
220F SER* 3.5 4.9 + - - +
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Residues in contact with ALA 219 (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* 4.4 12.6 - - + +
215F LEU* 3.0 24.1 + - + +
216F ALA* 2.7 19.1 - - - +
218F VAL* 1.3 76.1 - - - +
220F SER* 1.3 57.7 + - - +
221F SER 3.8 8.0 - - - +
270F PHE* 5.8 0.2 - - + -
274F GLY 3.2 26.9 - - - +
275F TYR* 4.3 6.5 - - - -
276F ILE* 4.8 10.9 - - + +
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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