Contacts of the helix formed by residues 207 - 221 (chain B) in PDB entry 1EWV
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 SER 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B THR 3.4 12.2 + - - -
190B ILE* 4.1 15.1 - - - +
193B SER* 4.5 2.0 - - - -
203B ARG* 3.9 7.2 - - - +
206B PRO* 1.4 77.5 - - - +
208B ASP* 1.3 69.5 + - - +
209B THR* 3.2 23.1 + - - +
210B LEU* 2.9 28.5 - - - +
211B GLN* 3.0 5.8 + - - +
474B ASP* 2.9 28.5 + - - +
475B ALA 5.2 0.2 + - - -
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Residues in contact with ASP 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B THR* 3.1 45.9 + - - +
189B SER* 3.8 5.4 + - - -
190B ILE* 4.4 5.2 - - + -
207B SER* 1.3 72.4 + - - +
209B THR* 1.4 53.6 + - - +
210B LEU 2.8 5.4 - - - -
211B GLN* 2.6 24.3 + - - +
212B ALA* 2.5 34.8 + - - +
236B TYR* 4.0 9.8 - - - +
239B SER* 4.0 1.7 - - - -
240B GLY* 3.5 35.3 + - - +
290B PHE* 3.7 8.1 - - + -
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Residues in contact with THR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE* 3.3 34.3 - - + +
207B SER* 3.2 15.3 + - - -
208B ASP* 1.4 75.7 - - - +
210B LEU* 1.3 59.9 + - - +
212B ALA* 4.7 0.4 - - - -
213B ARG* 2.9 28.8 + - - +
243B ALA* 3.4 32.5 - - + +
247B LEU* 3.8 9.7 - - - +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PRO* 3.4 26.5 - - + -
207B SER* 2.9 18.9 + - - +
208B ASP 2.7 1.0 + - - -
209B THR* 1.3 80.4 + - - +
211B GLN* 1.3 64.3 + - - +
212B ALA 3.2 0.2 - - - -
213B ARG* 3.1 20.5 + - + +
214B ALA* 3.4 7.4 + - - +
475B ALA 4.1 6.7 - - - +
476B PRO* 3.7 4.5 - - + -
477B GLY* 3.6 24.5 - - - +
479B TYR* 4.6 3.4 - - + -
500B TRP* 3.1 35.9 - - + -
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Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B THR* 5.9 1.2 - - - +
207B SER 3.0 6.6 + - - +
208B ASP* 2.6 32.7 + - - +
210B LEU* 1.3 74.5 - - - +
212B ALA* 1.3 60.9 + - - +
214B ALA* 3.4 10.9 + - - +
215B MET* 3.6 12.2 + - - +
236B TYR* 3.6 7.7 + - - -
290B PHE* 3.9 7.9 - - + -
317B SER* 3.0 14.2 - - - -
318B ASP* 2.8 47.8 + - - -
340B ILE* 3.3 23.4 - - + +
479B TYR* 3.2 29.2 + - + +
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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
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208B ASP 2.5 16.8 + - - +
209B THR* 4.3 3.1 - - - +
211B GLN* 1.3 68.4 - - - +
213B ARG* 1.3 56.1 + - - +
214B ALA 2.9 5.2 - - - -
215B MET* 2.7 33.9 + - - +
216B LEU* 2.8 11.7 + - - +
240B GLY 3.9 6.3 - - - +
243B ALA* 4.8 0.2 - - + -
244B PHE* 3.9 25.9 - - + +
247B LEU* 4.9 0.9 - - + -
290B PHE* 3.4 30.6 - - + -
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Residues in contact with ARG 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 THR 2.9 23.9 + - - +
210B LEU* 3.3 14.1 - - + +
212B ALA* 1.3 76.0 - - - +
214B ALA* 1.3 52.8 + - - +
216B LEU* 3.6 19.2 + - - +
217B ASP* 2.6 69.5 + - - +
220B LYS* 5.0 0.8 - - - +
247B LEU* 3.8 30.3 - - + +
251B GLU* 3.3 35.8 + - - -
500B TRP* 4.5 13.0 - - + -
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU 3.4 4.2 + - - +
211B GLN 3.6 10.3 - - - +
212B ALA 2.7 4.8 + - - -
213B ARG* 1.3 73.9 - - - +
215B MET* 1.3 60.4 + - - +
216B LEU 3.1 1.1 - - - -
217B ASP* 2.7 17.9 + - - +
218B ILE* 2.8 19.1 + - + +
340B ILE* 4.6 13.0 - - + -
479B TYR* 4.9 4.0 - - + -
481B ILE* 6.0 0.2 - - + -
500B TRP* 3.2 48.0 - - + +
505B LEU* 5.9 0.4 - - + -
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Residues in contact with MET 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLN* 4.1 10.8 - - - +
212B ALA* 2.7 20.9 + - - +
214B ALA* 1.3 73.4 - - - +
216B LEU* 1.3 61.6 + - - +
217B ASP 3.1 0.5 + - - -
218B ILE* 3.3 17.2 + - - +
219B VAL* 3.4 17.8 + - - +
244B PHE* 3.7 12.1 - - + -
288B VAL* 3.8 18.8 - - + -
289B CYS 3.1 28.3 - - - +
290B PHE* 4.6 8.1 - - + +
315B ILE* 3.1 32.2 - - + +
316B GLY 4.3 0.2 - - - -
317B SER* 3.8 25.1 - - - +
340B ILE* 3.8 21.5 - - + -
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Residues in contact with LEU 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 2.8 9.5 + - - +
213B ARG* 3.6 32.1 - - - +
215B MET* 1.3 77.2 - - - +
217B ASP* 1.3 63.2 + - - +
219B VAL* 3.6 4.8 + - - +
220B LYS* 3.1 48.5 + - + +
244B PHE* 3.4 22.7 - - + +
247B LEU* 3.4 46.9 - - + +
248B ALA* 3.9 11.0 - - + +
251B GLU* 4.6 3.8 - - + +
253B LEU* 5.0 8.0 - - + +
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Residues in contact with ASP 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 ARG* 2.6 54.9 + - - +
214B ALA* 2.7 13.8 + - - +
216B LEU* 1.3 80.3 - - - +
218B ILE* 1.3 58.2 + - - -
219B VAL 2.9 6.1 + - - -
220B LYS* 3.8 9.3 - - - +
221B ARG* 3.2 23.9 + - - +
500B TRP* 3.7 14.9 + - + +
503B GLY 5.5 1.8 - - - +
505B LEU* 3.6 16.7 - - + +
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Residues in contact with ILE 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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214B ALA* 2.8 19.3 + - + +
215B MET* 3.3 8.0 + - - +
217B ASP* 1.3 73.7 - - - +
219B VAL* 1.3 57.9 + - - +
221B ARG* 4.1 1.6 - - - -
222B TYR* 3.0 30.4 - - + -
224B TRP* 4.3 2.8 - - + -
315B ILE* 4.1 26.0 - - + -
338B ILE* 3.5 28.5 - - + -
340B ILE* 4.8 9.0 - - + -
481B ILE* 3.4 39.9 - - + -
505B LEU* 3.9 23.1 - - + -
507B ILE* 4.5 6.3 - - + -
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Residues in contact with VAL 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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215B MET 3.5 13.2 - - - +
216B LEU* 3.7 9.0 - - - +
217B ASP 2.9 0.4 - - - -
218B ILE* 1.3 78.5 - - - +
220B LYS* 1.4 64.2 + - - +
221B ARG 2.9 4.7 - - - -
222B TYR* 2.9 14.7 + - - +
223B ASN 3.4 7.3 + - - -
224B TRP* 3.7 43.2 + - + +
227B VAL* 4.7 7.6 - - + -
244B PHE* 4.9 10.1 - - + -
253B LEU* 3.9 20.6 - - + -
286B VAL* 4.8 4.7 - - + -
288B VAL* 5.3 2.2 - - + -
315B ILE* 3.8 25.1 - - + -
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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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213B ARG* 5.0 0.4 - - - +
216B LEU* 3.1 29.2 + - + +
217B ASP* 3.6 12.8 + - - +
219B VAL* 1.4 82.3 - - + +
221B ARG* 1.3 60.0 + - - +
222B TYR 3.1 1.8 + - - -
223B ASN* 3.6 15.6 + - - +
224B TRP 5.6 0.7 - - - +
251B GLU* 2.6 56.6 + - + +
253B LEU* 5.5 6.7 - - + -
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Residues in contact with ARG 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 ASP 3.2 19.0 + - - +
218B ILE* 4.1 2.2 - - - +
219B VAL 2.9 1.0 - - - -
220B LYS* 1.3 80.8 - - - +
222B TYR* 1.4 84.6 + - + +
223B ASN* 3.8 1.5 + - - -
505B LEU* 3.8 29.7 + - + +
506B ASN* 4.8 0.6 - - - +
507B ILE* 3.3 41.8 + - + +
509B ASP* 4.3 8.5 + - - +
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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