Contacts of the helix formed by residues 208 - 226 (chain B) in PDB entry 1EFU
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 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B MET* 3.4 36.7 - - + -
206B LYS 3.3 3.6 + - - -
207B PRO* 1.3 68.0 - - - +
209B GLU* 1.3 64.5 + - - +
211B ALA* 3.1 1.9 + - - +
212B GLU* 2.8 61.4 + - - +
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Residues in contact with GLU 209 (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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207B PRO* 3.1 28.6 + - - +
208B LYS* 1.3 81.3 + - - +
210B ILE* 1.3 70.1 + - + +
212B GLU* 3.9 9.4 + - - +
213B LYS* 3.4 27.5 + - - +
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Residues in contact with ILE 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 LYS* 5.0 4.3 - - + -
207B PRO* 2.8 40.1 + - + +
209B GLU* 1.3 81.1 - - + +
211B ALA* 1.3 58.7 - - - +
213B LYS* 3.2 5.3 + - - +
214B MET* 2.9 44.2 + - - +
132D ARG* 3.6 41.1 - - + +
133D ARG* 3.6 40.6 - - + +
262D GLU 4.1 6.7 - - - +
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Residues in contact with ALA 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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198B LEU* 4.1 2.9 - - + -
201B ALA* 3.9 15.2 - - + +
202B MET* 3.8 24.7 - - - -
206B LYS* 3.8 30.0 - - + +
207B PRO 3.0 6.2 + - - +
208B LYS 3.6 6.3 - - - +
210B ILE* 1.3 78.2 - - - +
212B GLU* 1.3 57.6 + - - +
214B MET* 3.5 3.0 + - - +
215B VAL* 3.0 34.8 + - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B TYR* 3.9 17.5 + - - +
198B LEU* 3.9 29.3 - - + +
202B MET* 4.7 0.6 - - + +
208B LYS* 2.8 56.0 + - + +
209B GLU* 4.2 9.0 - - - +
211B ALA* 1.3 74.6 - - - +
213B LYS* 1.3 65.2 + - + +
215B VAL* 3.4 3.0 + - - +
216B GLU* 3.0 28.9 + - - +
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Residues in contact with LYS 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 GLU 3.4 18.2 + - - +
210B ILE* 3.2 3.4 + - - +
212B GLU* 1.3 82.1 - - + +
214B MET* 1.3 61.7 + - - +
216B GLU* 3.3 27.2 + - - +
217B GLY* 3.3 15.8 + - - -
132D ARG* 5.8 0.2 - - - +
263D GLY* 2.9 38.0 - - - +
265D GLU* 3.0 28.5 + - + +
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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
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201B ALA* 5.8 0.4 - - + -
206B LYS* 3.2 39.9 - - + +
210B ILE* 2.9 24.3 + - + +
211B ALA* 3.7 4.9 - - - +
213B LYS* 1.3 75.8 - - - +
215B VAL* 1.3 64.8 + - + +
216B GLU 3.1 0.2 - - - -
217B GLY* 3.2 10.8 + - - -
218B ARG* 3.2 37.2 + - + +
262D GLU* 3.3 38.8 - - + +
263D GLY* 3.8 21.5 - - - +
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Residues in contact with VAL 215 (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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194B TYR* 3.5 44.6 - - + +
197B GLN* 3.6 11.4 - - + +
198B LEU* 3.5 26.2 - - + +
201B ALA* 3.9 4.3 - - + -
211B ALA 3.0 18.6 + - - +
212B GLU 3.8 4.3 - - - +
214B MET* 1.3 74.7 - - - +
216B GLU* 1.3 64.8 + - - +
218B ARG* 3.0 41.2 + - - +
219B MET* 3.2 14.7 + - + +
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Residues in contact with GLU 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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194B TYR* 4.4 12.8 - - + +
212B GLU 3.0 16.1 + - - +
213B LYS* 3.3 38.3 + - - +
215B VAL* 1.3 78.6 - - - +
217B GLY* 1.3 63.2 + - - +
219B MET* 3.4 16.9 + - - +
220B LYS* 4.1 8.0 + - - +
265D GLU* 3.8 21.0 - - - +
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Residues in contact with GLY 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 LYS 3.3 6.6 + - - -
214B MET 3.2 8.1 + - - -
216B GLU* 1.3 79.5 - - - +
218B ARG* 1.3 61.8 + - - +
219B MET 3.3 0.3 + - - -
220B LYS* 3.5 19.4 + - - +
221B LYS* 4.1 4.5 + - - +
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Residues in contact with ARG 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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197B GLN* 3.1 54.2 + - - +
200B ILE* 5.4 0.4 - - - +
201B ALA* 3.8 7.7 - - - +
214B MET* 3.2 33.0 + - + +
215B VAL* 3.0 29.6 + - - +
217B GLY* 1.3 75.5 - - - +
219B MET* 1.3 64.1 + - + +
220B LYS 3.3 0.2 - - - -
221B LYS* 3.1 36.5 - - - +
222B PHE* 3.1 25.8 + - - +
178D GLU* 3.6 26.7 + - - -
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Residues in contact with MET 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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190B VAL* 3.7 34.5 - - + +
193B GLU* 3.8 6.1 - - + +
194B TYR* 3.6 32.8 - - + -
197B GLN* 3.4 35.9 - - + -
215B VAL* 3.2 16.9 + - + +
216B GLU* 3.6 11.2 - - - +
217B GLY 3.2 0.6 - - - -
218B ARG* 1.3 80.3 - - + +
220B LYS* 1.3 67.1 + - + +
222B PHE* 3.1 34.7 + - + +
223B THR* 3.3 14.4 + - - +
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Residues in contact with LYS 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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216B GLU 4.1 6.9 + - - +
217B GLY* 3.5 12.9 + - - +
218B ARG 3.3 0.4 - - - -
219B MET* 1.3 79.3 - - - +
221B LYS* 1.3 61.4 + - - +
223B THR* 3.2 20.1 + - - +
224B GLY* 3.3 8.1 + - - -
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Residues in contact with LYS 221 (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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217B GLY 4.1 2.5 + - - +
218B ARG* 3.1 51.6 + - - +
220B LYS* 1.3 75.7 - - - +
222B PHE* 1.3 55.1 + - - +
224B GLY* 3.6 2.1 - - - +
225B GLU* 2.8 58.6 + - + +
176D LYS* 5.8 4.2 - - - +
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Residues in contact with PHE 222 (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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185B VAL* 4.4 17.5 - - + -
189B VAL* 4.3 2.2 - - + -
190B VAL* 4.1 17.5 - - + -
193B GLU* 3.8 44.0 - - + -
218B ARG 3.1 13.9 + - - +
219B MET* 3.1 25.5 + - + +
221B LYS* 1.3 79.4 - - - +
223B THR* 1.3 71.7 + - + +
225B GLU* 3.3 13.3 + - + +
226B VAL* 3.3 34.2 + - + +
196D VAL* 4.5 4.0 - - + -
197D GLN* 5.0 5.2 - - - -
200D ILE* 4.2 22.0 - - + -
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Residues in contact with THR 223 (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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182B PRO* 3.8 27.6 - - - +
185B VAL* 4.0 13.5 - - + -
190B VAL* 4.0 23.1 - - + -
219B MET 3.3 8.0 + - - +
220B LYS* 3.2 16.5 + - - +
222B PHE* 1.3 92.6 - - + +
224B GLY* 1.3 59.1 + - - +
226B VAL* 3.4 8.8 - - - +
227B SER* 2.9 29.1 + - - -
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Residues in contact with GLY 224 (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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182B PRO* 4.9 4.0 - - - -
220B LYS 3.3 12.1 + - - -
221B LYS* 3.1 7.3 + - - -
223B THR* 1.3 78.4 + - - +
225B GLU* 1.3 61.6 + - - +
226B VAL 3.4 0.2 - - - -
227B SER* 3.6 7.6 - - - +
230B GLY* 3.0 38.2 - - - +
231B GLN* 3.3 4.7 + - - +
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Residues in contact with GLU 225 (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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221B LYS* 2.8 54.0 + - + +
222B PHE* 3.5 11.9 - - + +
224B GLY* 1.3 79.2 - - - +
226B VAL* 1.3 62.5 + - + +
231B GLN* 2.8 29.3 + - - +
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Residues in contact with VAL 226 (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 2.7 - - - -
178B GLU* 2.9 43.6 + - - +
179B PHE* 3.0 18.5 + - + -
185B VAL* 3.8 21.8 - - + -
222B PHE* 3.3 37.5 - - + +
223B THR* 3.4 16.2 - - - +
225B GLU* 1.3 81.0 - - + +
227B SER* 1.3 58.2 + - - +
231B GLN* 4.7 0.2 - - - +
197D GLN* 6.2 0.2 - - - +
200D ILE* 4.8 8.7 - - + -
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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