Contacts of the helix formed by residues 203 - 220 (chain B) in PDB entry 5UNG
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 LYS 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B PRO* 3.2 9.7 + - + +
202B GLU* 1.3 91.2 - - + +
204B TYR* 1.4 61.6 + - - +
205B ALA 3.5 2.0 - - - -
206B GLN* 3.5 35.1 + - + +
207B TRP* 3.2 37.5 + - + +
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Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ILE* 4.1 14.0 - - + +
197B MET* 2.7 32.7 + - - +
198B ALA* 4.4 2.9 - - - -
199B PHE* 3.5 37.4 - + + -
200B PRO 3.0 5.1 + - - +
201B PRO* 3.6 19.3 + - + +
202B GLU 3.8 0.4 - - - -
203B LYS* 1.4 74.4 - - - +
205B ALA* 1.4 59.5 + - - +
206B GLN* 4.1 0.2 + - - -
207B TRP* 3.4 2.6 + - - +
208B SER* 2.9 49.4 + - - -
283B TRP* 3.6 31.6 - + + -
1102B ILE* 3.9 35.4 - - + -
1106B LEU* 6.0 2.0 - - + -
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS 3.5 0.4 - - - -
204B TYR* 1.4 77.0 - - - +
206B GLN* 1.3 64.7 + - - +
208B SER 3.5 0.3 + - - -
209B ALA* 3.1 30.0 + - - +
283B TRP* 3.4 44.8 - - + +
284B MET* 5.5 1.6 - - - -
1106B LEU* 3.9 24.5 - - + +
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Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLU 4.7 2.7 + - - +
203B LYS* 3.5 49.1 - - + +
204B TYR 3.4 0.2 - - - -
205B ALA* 1.3 82.5 + - + +
207B TRP* 1.3 58.9 + - + +
209B ALA* 3.6 5.7 + - - +
210B GLY* 3.0 24.9 + - - -
284B MET* 6.3 0.9 - - - -
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Residues in contact with TRP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B PHE* 3.6 33.9 - + - -
199B PHE* 3.5 31.2 - + + -
200B PRO* 3.6 30.9 - - + +
203B LYS* 3.2 32.9 + - + +
204B TYR 3.7 1.1 - - - +
206B GLN* 1.3 77.3 - - + +
208B SER* 1.4 58.9 + - - +
210B GLY* 3.8 1.9 - - - +
211B ILE* 3.0 57.8 + - + +
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 3.5 17.0 - - - -
204B TYR* 2.9 43.2 + - - -
205B ALA 3.8 1.3 - - - -
207B TRP* 1.4 75.2 - - - +
209B ALA* 1.3 55.9 + - - +
211B ILE* 4.5 0.7 - - - +
212B ALA* 3.3 27.2 + - - +
283B TRP* 3.6 37.7 - - - -
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ALA 3.1 17.6 + - - +
206B GLN* 3.9 5.6 - - - +
208B SER* 1.3 74.2 - - - +
210B GLY* 1.3 59.5 + - - +
212B ALA* 3.8 1.4 - - - +
213B LEU* 3.2 34.6 + - - +
280B ALA* 3.6 30.1 - - - +
283B TRP* 4.5 1.7 - - + +
284B MET* 3.8 29.8 - - + -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLN 3.0 16.9 + - - -
207B TRP* 3.4 2.9 + - - -
209B ALA* 1.3 75.1 - - - +
211B ILE* 1.3 59.6 - - - +
213B LEU* 3.4 8.3 + - - +
214B MET* 3.1 24.8 + - - +
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B PRO* 4.5 17.9 - - + -
181B PHE* 5.2 0.4 - - + -
197B MET* 4.5 7.0 - - + -
199B PHE* 3.6 30.3 - - + -
207B TRP* 3.0 39.8 + - + +
208B SER 4.6 1.6 - - - +
210B GLY* 1.3 72.6 - - - +
212B ALA* 1.4 60.9 + - - +
214B MET* 3.2 26.0 + - + +
215B LYS* 2.9 46.3 + - - +
1201B 8ES 4.3 17.3 - - + -
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B SER 3.3 20.9 + - - +
209B ALA 3.8 0.9 - - - +
210B GLY 3.4 0.2 - - - -
211B ILE* 1.4 76.0 - - - +
213B LEU* 1.4 61.5 + - - +
215B LYS* 3.4 18.8 + - + +
216B ASN* 3.3 27.7 + - - +
276B THR* 3.7 17.9 - - + +
279B ASP* 5.8 2.9 - - - +
280B ALA* 3.7 27.1 - - + +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ALA 3.2 20.2 + - - +
210B GLY* 3.5 12.6 - - - +
212B ALA* 1.4 73.7 - - - +
214B MET* 1.4 57.5 + - - +
216B ASN* 3.3 9.3 + - + +
217B ILE* 3.1 60.2 + - + +
277B PHE* 4.4 30.7 - - + -
280B ALA* 4.4 10.3 - - + -
284B MET* 5.1 12.8 - - + -
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Residues in contact with MET 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 5.5 0.5 - - - -
174B SER* 4.4 13.0 - - - +
177B PRO* 4.3 19.1 - - + -
210B GLY 3.1 13.7 + - - +
211B ILE* 3.2 32.1 + - + +
213B LEU* 1.4 74.1 - - - +
215B LYS* 1.4 58.7 + - - +
217B ILE* 4.7 6.1 - - - +
218B LEU* 3.1 54.8 + - + +
1201B 8ES 4.2 18.2 - - + -
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 5.6 1.3 - - - -
211B ILE* 2.9 36.7 + - - +
212B ALA* 3.4 10.3 - - - +
213B LEU 3.3 0.2 - - - -
214B MET* 1.4 76.2 - - - +
216B ASN* 1.4 55.5 + - - +
219B GLY* 3.1 23.8 + - - +
272B PHE* 4.9 4.7 - - + -
273B HIS* 3.2 18.9 - - + -
276B THR* 3.8 25.5 - - + +
1201B 8ES 3.4 73.9 + - + -
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Residues in contact with ASN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ALA 3.3 17.3 + - - +
213B LEU* 3.3 10.7 + - + +
215B LYS* 1.4 73.9 - - - +
217B ILE* 1.3 55.4 + - + +
220B PHE* 3.1 10.0 + - + +
221B ILE* 2.8 43.0 + - + +
273B HIS* 3.1 46.4 + - + +
276B THR* 3.9 8.5 - - - +
277B PHE* 3.5 33.8 - - + +
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LEU* 3.1 41.9 + - + +
214B MET* 4.3 5.2 - - - +
216B ASN* 1.3 76.7 - - + +
218B LEU* 1.3 61.3 + - + +
221B ILE* 3.6 19.3 - - + -
222B ILE* 2.9 52.4 + - + +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PHE* 3.9 20.2 - - + -
133B PHE* 4.1 19.5 - - + -
174B SER* 3.4 33.7 - - - +
214B MET* 3.1 38.2 + - + +
217B ILE* 1.3 77.2 - - + +
219B GLY* 1.3 59.0 + - - +
222B ILE* 4.3 18.1 - - + +
223B PRO* 3.4 16.8 - - - +
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Residues in contact with GLY 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B MET* 5.3 2.5 - - - -
129B PHE* 3.8 18.4 - - - -
132B ILE* 3.9 22.2 - - - +
215B LYS 3.1 15.8 + - - -
218B LEU* 1.3 77.3 - - - +
220B PHE* 1.4 61.0 + - - +
223B PRO* 3.7 9.8 - - - +
265B PHE* 4.1 5.4 - - - -
269B TRP* 5.4 0.5 - - - -
273B HIS* 3.8 13.3 + - - -
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LYS 3.9 0.2 + - - -
216B ASN* 3.1 9.8 + - + +
218B LEU 3.5 1.0 - - - -
219B GLY* 1.4 78.4 - - - +
221B ILE* 1.4 76.4 + - + +
223B PRO* 3.5 5.5 - - - +
224B LEU* 3.0 52.5 + - + +
265B PHE* 3.7 26.6 - + - -
266B ILE* 4.6 6.7 - - + -
269B TRP* 3.7 32.5 - - + -
270B LEU* 3.7 43.5 - - + -
273B HIS* 3.6 28.9 - + + -
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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