Contacts of the helix formed by residues 203 - 216 (chain F) in PDB entry 4U8T
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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202F SER* 1.3 86.0 + - - +
204F PHE* 1.3 70.1 + - - +
206F GLY* 3.0 19.1 + - - -
207F ASN* 2.7 24.4 + - - +
260F TYR* 5.1 6.3 - - + +
297F ASP* 4.7 3.2 + - + +
-1R G 3.5 44.7 + - - +
0R 6MZ 4.3 27.8 + - + +
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Residues in contact with PHE 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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288D ASP* 3.5 42.6 - - + -
203F THR* 1.3 77.9 - - - +
205F TYR* 1.3 80.3 + + + +
207F ASN* 3.9 5.5 - - - +
208F LYS* 3.3 28.0 + - + +
-2O G 3.6 81.7 - + - +
-2R G 5.3 0.7 - - - +
-1R G 6.5 0.9 - - - -
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Residues in contact with TYR 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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205A TYR* 5.0 2.3 + - - -
203F THR* 3.2 1.2 + - - -
204F PHE* 1.3 92.8 - + + +
206F GLY* 1.3 60.2 + - - +
208F LYS* 3.3 18.6 + - - +
209F ARG* 2.9 32.9 + - - +
-2O G 3.2 47.4 + + - -
-2R G 3.6 31.8 + - + +
-1R G 3.3 71.7 + + + +
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Residues in contact with GLY 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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202F SER* 3.5 22.9 - - - -
203F THR* 3.0 12.0 + - - -
205F TYR* 1.3 75.5 - - - +
207F ASN* 1.3 59.7 + - - +
209F ARG* 3.3 7.8 + - - +
210F LEU* 3.0 35.0 + - - +
298F THR* 3.7 14.8 - - - -
-1R G 4.1 2.3 - - - -
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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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201F SER* 3.5 18.0 + - - -
202F SER* 2.9 31.7 + - - -
203F THR 2.7 20.2 + - - +
204F PHE* 3.9 5.0 - - - +
206F GLY* 1.3 68.1 - - - +
208F LYS* 1.3 60.9 + - - +
210F LEU* 3.9 3.5 - - - +
211F SER* 2.8 33.2 + - - -
245F LEU* 3.6 36.7 - - + +
262F HIS* 4.0 11.1 + - - +
264F PHE* 3.7 12.7 - - - -
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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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285D PRO 5.5 0.9 - - - -
286D ALA* 3.6 25.5 + - - +
288D ASP 6.1 0.4 - - - +
204F PHE* 3.3 24.3 + - + +
205F TYR* 3.3 22.9 + - + +
207F ASN* 1.3 77.6 - - - +
209F ARG* 1.3 62.3 + - - +
211F SER* 3.9 4.2 - - - -
212F GLU* 2.8 62.2 + - - +
245F LEU* 5.2 0.4 - - - +
-3O A 5.8 3.2 - - - -
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Residues in contact with ARG 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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181F PHE* 4.7 12.5 - - + -
205F TYR* 2.9 24.2 + - - +
206F GLY* 3.7 4.4 - - - +
207F ASN 3.2 0.2 - - - -
208F LYS* 1.3 78.4 - - - +
210F LEU* 1.3 60.9 + - - +
212F GLU* 4.1 6.2 - - - +
213F ALA* 3.2 23.2 + - - +
298F THR* 3.0 41.3 + - - +
-3Q A 3.4 21.8 + - - -
-1R G 2.7 51.9 + - - -
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Residues in contact with LEU 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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181F PHE* 4.0 37.5 - - + -
183F ILE* 4.1 18.8 - - + -
202F SER* 4.3 8.1 - - - -
206F GLY 3.0 21.3 + - - +
207F ASN* 3.9 3.8 - - - +
209F ARG* 1.3 74.0 - - - +
211F SER* 1.3 64.4 + - - +
213F ALA* 3.3 4.1 + - - +
214F TYR* 3.0 25.0 + - - +
223F ILE* 5.1 0.4 - - + -
225F LEU* 4.2 14.1 - - + -
241F MSE 3.8 19.7 - - - +
264F PHE* 3.6 32.5 - - + -
298F THR* 4.1 13.0 - - + -
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Residues in contact with SER 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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285D PRO* 3.5 28.7 - - - +
286D ALA* 3.6 7.7 + - - +
207F ASN 2.8 19.5 + - - -
208F LYS 3.9 4.0 - - - -
210F LEU* 1.3 77.6 - - - +
212F GLU* 1.3 61.7 + - - +
214F TYR* 3.2 5.7 + - - +
215F GLU* 3.2 23.2 + - - +
241F MSE 5.8 0.4 - - - -
244F ASN* 2.7 29.8 + - - -
245F LEU* 4.6 7.2 - - - +
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Residues in contact with GLU 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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286D ALA* 3.9 21.6 - - + +
208F LYS* 2.8 51.8 + - - +
209F ARG* 4.1 6.1 - - - +
211F SER* 1.3 77.8 - - - +
213F ALA* 1.3 56.5 + - - +
215F GLU* 3.6 5.6 + - - +
216F SER* 2.7 33.8 + - - +
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Residues in contact with ALA 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 ARG* 3.3 33.9 + - - +
181F PHE* 4.0 11.9 - - + -
209F ARG 3.2 16.9 + - - +
210F LEU 3.7 3.1 - - - +
211F SER 3.2 0.2 - - - -
212F GLU* 1.3 79.5 - - - +
214F TYR* 1.3 61.3 + - - +
216F SER* 3.6 9.7 + - - -
217F LEU* 3.5 13.0 - - - +
223F ILE* 3.4 23.2 - - + +
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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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210F LEU 3.0 17.6 + - - +
211F SER* 3.5 6.5 - - - +
213F ALA* 1.3 75.1 - - - +
215F GLU* 1.3 67.9 + - + +
216F SER 3.2 0.7 + - - -
217F LEU* 3.3 30.9 + - + +
222F LYS* 6.6 0.2 - - + -
223F ILE* 3.6 7.6 - - + +
241F MSE 3.2 42.8 - - + -
242F SER 3.6 6.1 + - - -
243F SER* 3.2 30.5 + - - -
244F ASN* 3.3 35.4 - - + -
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Residues in contact with GLU 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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302D PRO* 3.6 41.2 - - + +
303D ALA* 3.9 15.3 + - - +
304D THR* 4.9 3.6 + - - -
211F SER 3.2 13.0 + - - +
212F GLU* 4.0 6.3 - - - +
214F TYR* 1.3 82.1 - - + +
216F SER* 1.3 60.4 + - - +
217F LEU 3.1 6.2 + - - +
244F ASN* 3.9 17.0 - - - +
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Residues in contact with SER 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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179F ARG* 4.6 8.6 + - - -
212F GLU 2.7 21.3 + - - -
213F ALA* 3.7 10.2 - - - -
214F TYR 3.2 1.2 - - - -
215F GLU* 1.3 77.6 - - - +
217F LEU* 1.3 63.9 + - - +
218F PRO* 3.5 8.1 - - - +
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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