Contacts of the helix formed by residues 208 - 225 (chain D) in PDB entry 7CE1
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 PHE 208 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LYS* 3.9 43.3 - - + -
144D ILE 3.9 15.7 - - - +
145D GLU* 4.4 7.0 - - + -
146D PRO* 4.9 0.4 - - - +
204D PRO* 4.8 0.4 - - + -
205D PRO* 2.9 34.8 + - + +
206D SER 3.8 1.4 - - - +
207D ARG* 1.3 107.4 - - - +
209D ALA* 1.3 66.0 + - - +
210D PHE* 3.4 33.0 - + + -
211D HIS* 3.1 20.2 - - + +
212D ASP* 3.8 3.3 + - - +
237D ILE* 5.4 2.2 - - + -
238D GLU* 3.3 23.6 - - + -
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Residues in contact with ALA 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ILE 3.1 16.1 + - - +
145D GLU* 4.3 6.9 - - - +
146D PRO* 4.6 8.1 - - + -
166D ARG 3.1 33.2 - - - +
167D SER* 4.8 1.6 - - - -
207D ARG 3.8 1.3 + - - -
208D PHE* 1.3 74.3 - - - +
210D PHE* 1.3 63.4 + - + +
212D ASP* 3.3 14.8 + - - +
213D HIS* 3.5 26.8 + - + +
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Residues in contact with PHE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D LYS* 6.1 2.5 - - - -
144D ILE 5.3 3.8 - - - -
177D ASP* 4.7 9.4 + - - +
180D ASN* 3.2 34.2 - - - +
204D PRO* 3.3 36.3 - - + -
208D PHE* 3.5 35.0 - + + -
209D ALA* 1.3 76.7 - - + +
211D HIS* 1.3 64.6 + - - +
212D ASP 3.2 0.2 - - - -
213D HIS* 3.4 20.0 - - + +
214D ALA* 2.9 26.7 + - - +
237D ILE* 4.3 13.0 - - + -
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Residues in contact with HIS 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D VAL* 3.4 28.3 - - + +
204D PRO* 2.9 39.8 - - + +
205D PRO 3.6 11.4 - - - +
206D SER* 3.1 31.8 + - - -
208D PHE 3.1 17.3 + - - +
209D ALA 3.1 0.8 - - - -
210D PHE* 1.3 82.8 - - - +
212D ASP* 1.3 67.3 + - - +
215D ARG* 3.2 29.8 + - + +
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Residues in contact with ASP 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D PHE 3.8 2.4 + - - +
209D ALA* 3.3 9.9 + - - +
210D PHE 3.2 0.4 - - - -
211D HIS* 1.3 85.3 + - - +
213D HIS* 1.3 69.0 + - + +
215D ARG* 4.0 4.1 - - - +
216D LYS* 3.1 24.6 + - - +
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Residues in contact with HIS 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ARG* 3.1 51.8 - - + +
177D ASP* 4.3 6.5 - - - -
178D PHE 5.3 1.3 - - - -
180D ASN* 4.4 4.3 - - + +
181D GLU* 3.1 34.8 + - + +
209D ALA* 3.5 18.0 + - + +
210D PHE* 3.2 27.7 + - + +
212D ASP* 1.3 79.3 - - + +
214D ALA* 1.3 63.9 + - - +
216D LYS* 3.4 3.3 + - - +
217D GLY 3.0 17.7 + - - -
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Residues in contact with ALA 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D ASN* 4.1 16.4 - - + +
181D GLU 4.5 0.2 - - - +
183D TYR* 6.2 1.8 - - + -
184D ALA* 3.2 20.7 - - + +
201D ILE* 5.8 8.5 - - + -
203D VAL* 4.5 12.8 - - + -
204D PRO* 5.0 5.2 - - + -
210D PHE 2.9 16.0 + - - +
211D HIS 3.9 3.8 - - - +
213D HIS* 1.3 77.5 - - - +
215D ARG* 1.3 52.3 + - - +
217D GLY 3.1 0.9 + - - -
218D PHE* 2.6 34.7 + - - +
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Residues in contact with ARG 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D ILE* 6.3 1.3 - - + -
203D VAL* 5.0 7.4 - - + +
211D HIS* 3.2 23.4 + - + +
212D ASP* 4.2 4.9 - - - +
214D ALA* 1.3 76.5 - - - +
216D LYS* 1.3 60.9 + - - +
218D PHE* 3.9 9.2 - - + -
219D THR* 2.9 39.9 + - + +
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Residues in contact with LYS 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D GLU* 3.5 19.1 - - - +
212D ASP 3.1 19.4 + - - +
213D HIS* 3.7 3.4 - - - +
215D ARG* 1.3 76.4 - - - +
217D GLY* 1.3 58.2 + - - +
219D THR* 3.3 6.7 + - - -
220D ARG* 3.0 36.0 + - + +
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Residues in contact with GLY 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D GLU* 3.4 32.7 - - - +
184D ALA* 4.1 0.2 - - - -
185D TYR* 3.3 22.2 - - - +
213D HIS 3.0 10.5 + - - -
214D ALA 3.4 3.6 - - - -
216D LYS* 1.3 76.2 - - - +
218D PHE* 1.3 60.8 + - - +
220D ARG* 4.0 5.4 - - - -
221D GLY 3.1 16.5 + - - -
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Residues in contact with PHE 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ALA* 3.6 11.2 - - + +
188D VAL* 3.6 15.6 - - + +
199D ILE* 3.4 39.3 - - + -
200D ALA 4.9 0.2 - - - -
201D ILE* 3.3 46.4 - - + -
214D ALA 2.6 20.4 + - - +
215D ARG* 3.6 10.5 - - + +
216D LYS 3.2 0.2 - - - -
217D GLY* 1.3 74.9 - - - +
219D THR* 1.3 62.2 + - + +
221D GLY* 3.5 1.2 + - - -
222D ILE* 3.0 61.4 + - + +
229D GLU* 3.6 23.3 - - + -
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Residues in contact with THR 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D ARG* 2.9 27.4 + - + +
216D LYS* 3.3 8.8 + - - -
218D PHE* 1.3 83.2 - - + +
220D ARG* 1.3 70.4 + - - +
222D ILE* 4.1 5.2 - - - +
223D ARG* 3.2 31.1 + - - +
229D GLU* 4.9 8.5 - - - +
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Residues in contact with ARG 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D GLU* 3.4 44.3 + - - +
182D ALA* 5.5 1.2 - - - +
185D TYR* 3.4 37.3 - - - +
216D LYS* 3.0 16.7 + - + +
217D GLY* 4.0 6.2 - - - +
219D THR* 1.3 79.7 + - - +
221D GLY* 1.3 60.5 + - - +
223D ARG* 3.7 24.2 - - - +
224D ASP* 2.9 37.0 + - - +
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Residues in contact with GLY 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D TYR* 3.4 28.6 - - - -
188D VAL* 4.1 8.5 - - - +
217D GLY 3.1 15.3 + - - -
218D PHE 3.8 1.1 - - - -
220D ARG* 1.3 76.2 - - - +
222D ILE* 1.3 62.5 + - - +
224D ASP 3.5 0.5 + - - -
225D PHE* 2.9 35.9 + - - +
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Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D VAL* 4.1 15.7 - - + -
199D ILE* 4.5 6.5 - - + -
218D PHE* 3.0 62.3 + - + +
219D THR* 4.1 5.6 - - - +
220D ARG 3.4 0.2 - - - -
221D GLY* 1.3 77.1 - - - +
223D ARG* 1.3 59.2 + - - +
225D PHE 3.6 0.5 + - - -
226D GLY* 3.0 22.0 + - - -
227D VAL* 2.8 39.5 + - + +
228D SER* 4.4 4.0 - - - -
229D GLU* 3.6 24.0 - - + +
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Residues in contact with ARG 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D THR* 3.2 21.9 + - - +
220D ARG* 3.7 30.3 + - - +
222D ILE* 1.3 83.0 - - - +
224D ASP* 1.3 83.1 + - - +
226D GLY* 3.1 13.5 + - - -
227D VAL 5.2 0.2 - - - -
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Residues in contact with ASP 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D TYR* 3.7 19.8 + - + +
220D ARG* 2.9 25.8 + - - +
221D GLY 3.5 2.9 + - - +
222D ILE 3.4 0.2 - - - -
223D ARG* 1.3 99.8 + - - +
225D PHE* 1.3 72.6 + - + +
226D GLY 3.4 0.2 - - - -
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Residues in contact with PHE 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D TYR* 4.3 31.0 - + - -
188D VAL* 4.8 5.8 - - + -
189D GLU* 3.2 53.6 - - + -
192D ALA* 4.1 26.1 - - + +
221D GLY* 2.9 29.6 + - - +
222D ILE 4.5 0.9 - - - +
224D ASP* 1.3 82.9 - - + +
226D GLY* 1.3 62.4 + - - +
227D VAL* 3.4 14.5 + - + +
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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