Contacts of the helix formed by residues 203 - 215 (chain F) in PDB entry 4DEM
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 203 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200F VAL 3.9 16.6 - - - +
201F ARG 3.1 6.5 + - - +
202F PHE* 1.3 79.7 - - - +
204F GLU* 1.3 65.2 + - - +
205F LYS* 3.6 7.4 + - - +
206F ARG* 3.0 26.2 + - - +
207F TYR* 2.9 24.1 + - - +
281F CYS* 4.5 0.5 - - - -
286F VAL* 4.0 5.2 - - - +
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Residues in contact with GLU 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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203F THR* 1.3 74.2 - - - +
205F LYS* 1.3 63.9 + - - +
207F TYR* 3.4 5.0 + - + +
208F LYS* 3.0 45.7 + - + +
283F TRP* 6.4 0.7 - - + -
286F VAL* 3.8 16.5 - - + +
287F GLN* 4.0 10.1 + - - +
290F GLN* 2.4 42.0 + - - +
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Residues in contact with LYS 205 (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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203F THR* 3.2 7.1 + - - +
204F GLU* 1.3 80.7 - - - +
206F ARG* 1.3 62.7 + - - +
208F LYS* 3.4 9.2 + - - +
209F SER* 3.2 27.9 + - - +
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Residues in contact with ARG 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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187F LEU* 4.0 30.8 + - - +
190F LEU* 4.5 12.7 - - - +
191F THR* 2.8 31.4 + - + +
201F ARG* 3.8 22.7 - - - +
203F THR* 3.0 21.9 + - - +
205F LYS* 1.3 74.8 - - - +
207F TYR* 1.3 66.6 + - - +
209F SER* 3.2 10.1 + - - -
210F ILE* 2.9 43.9 + - + +
281F CYS* 4.7 2.0 - - - -
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Residues in contact with TYR 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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203F THR 2.9 17.7 + - - +
204F GLU* 3.5 8.7 - - + +
206F ARG* 1.3 76.2 - - - +
208F LYS* 1.3 72.0 + - + +
210F ILE* 3.1 7.2 + - + +
211F VAL* 3.1 49.2 + - + +
251F GLU* 5.1 0.7 - - + -
254F GLN 3.5 3.5 - - - -
255F ILE* 3.4 43.7 + - + +
258F ASP* 2.6 29.8 + - - -
281F CYS* 3.2 29.1 - - - -
282F SER 4.1 1.6 - - - -
283F TRP* 3.3 28.9 - + + -
286F VAL* 4.2 11.0 - - + -
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Residues in contact with LYS 208 (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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204F GLU* 3.0 37.9 + - + +
205F LYS* 3.8 7.9 - - - +
206F ARG 3.3 0.2 - - - -
207F TYR* 1.3 80.9 - - + +
209F SER* 1.3 62.8 + - - +
211F VAL* 3.6 9.7 + - - +
212F LYS* 3.1 25.4 + - - +
248F GLU* 5.7 3.1 - - - -
251F GLU* 3.4 38.9 + - - +
331F TYR* 5.7 1.4 + - - -
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Residues in contact with SER 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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187F LEU* 4.2 14.3 - - - +
205F LYS* 3.2 14.8 + - - +
206F ARG* 3.2 13.3 + - - -
208F LYS* 1.3 77.0 - - - +
210F ILE* 1.3 68.0 + - - +
212F LYS* 3.5 6.9 + - - +
213F TYR* 3.4 31.9 + - - +
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Residues in contact with ILE 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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184F GLY* 4.1 4.5 - - - +
187F LEU* 3.9 26.2 - - + +
188F ASP* 4.0 26.5 - - + +
191F THR* 3.9 21.8 - - - +
206F ARG* 2.9 33.5 + - + +
207F TYR* 3.1 7.6 + - + +
209F SER* 1.3 77.5 - - - +
211F VAL* 1.3 60.8 + - + +
213F TYR* 3.7 1.6 - - - +
214F LYS* 2.8 44.8 + - + +
281F CYS* 4.0 27.1 - - + +
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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
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207F TYR* 3.1 45.9 + - + +
208F LYS* 3.6 7.4 - - - +
210F ILE* 1.3 76.2 - - + +
212F LYS* 1.3 68.7 + - - +
214F LYS* 4.1 13.7 - - - -
215F THR* 3.0 19.9 + - - -
216F ALA* 3.1 9.7 + - - +
250F GLY 5.2 0.3 - - - +
251F GLU* 4.0 33.0 - - + -
254F GLN* 3.4 34.8 - - + -
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Residues in contact with LYS 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 LYS 3.1 19.2 + - - +
209F SER* 3.7 7.9 - - - +
211F VAL* 1.3 81.1 - - - +
213F TYR* 1.3 84.4 + - + +
216F ALA* 3.4 20.1 + - + +
217F PHE* 3.2 39.8 + - + -
247F LEU* 4.3 22.4 - - + -
251F GLU* 6.1 1.6 - - - -
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Residues in contact with TYR 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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179F TYR* 6.5 0.9 - + - -
180F GLN* 3.2 31.5 - - + +
181F THR* 3.2 21.5 + - - -
183F ILE* 4.0 18.8 - - + -
184F GLY* 3.4 19.7 - - - -
187F LEU* 4.9 7.4 - - + -
209F SER* 3.4 20.4 + - - +
210F ILE 3.3 1.4 + - - -
211F VAL 3.3 0.2 - - - -
212F LYS* 1.3 114.8 + - + +
214F LYS* 1.3 63.3 + - - +
215F THR 3.5 0.7 + - - -
217F PHE* 3.9 24.4 - + - +
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Residues in contact with LYS 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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181F THR* 3.5 13.0 - - - +
184F GLY* 3.6 17.0 - - - -
185F GLN* 3.9 7.2 - - - +
188F ASP* 2.9 31.3 + - + +
210F ILE* 2.8 36.3 + - + +
211F VAL* 4.1 5.6 - - - -
213F TYR* 1.3 74.8 - - - +
215F THR* 1.3 62.8 + - - +
218F TYR* 3.3 9.9 - - - -
254F GLN* 3.8 29.6 - - - +
258F ASP* 4.9 2.0 + - - -
280F LYS* 5.9 0.2 - - - +
401F YS4 2.6 63.1 + - + +
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Residues in contact with THR 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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74F ARG* 5.4 0.4 - - - +
211F VAL 3.0 10.0 + - - -
213F TYR 3.3 0.4 - - - -
214F LYS* 1.3 84.6 - - - +
216F ALA* 1.3 68.2 + - - +
217F PHE 3.5 2.0 + - - -
218F TYR* 3.6 7.8 + - + -
219F SER* 3.1 33.2 + - - +
220F PHE* 4.9 0.2 - - + -
250F GLY 4.1 10.8 - - - +
253F PHE* 3.7 27.1 - - + -
254F GLN* 2.7 34.1 + - + +
401F YS4 3.5 11.1 - - + -
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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