Contacts of the helix formed by residues 209 - 226 (chain B) 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 ALA 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE 3.5 12.2 + - - +
145B GLU 4.0 0.2 - - - -
146B PRO* 3.9 29.9 - - + +
166B ARG 3.5 26.5 - - - +
167B SER* 4.9 1.6 - - - -
168B ASP* 5.2 3.1 - - + +
208B PHE* 1.3 70.0 - - - +
210B PHE* 1.3 59.3 + - + +
211B HIS 3.0 10.4 + - - -
212B ASP* 3.2 17.7 + - - +
213B HIS* 4.0 15.8 + - + -
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Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LYS* 6.6 0.7 - - - -
144B ILE 5.4 2.0 - - - -
177B ASP* 4.7 8.1 - - - +
180B ASN* 4.1 29.8 - - + +
204B PRO* 3.4 30.1 - - + -
208B PHE* 3.6 29.8 - + + -
209B ALA* 1.3 75.4 - - + +
211B HIS* 1.3 56.1 + - - +
212B ASP 3.2 0.9 - - - -
213B HIS* 3.3 22.5 + - + +
214B ALA* 2.8 37.8 + - + +
237B ILE* 5.7 0.7 - - + -
264B ILE* 4.0 20.2 - - + -
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Residues in contact with HIS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 3.9 24.4 - - + +
204B PRO* 2.6 44.3 + - + +
205B PRO 3.7 2.9 - - - +
206B SER* 3.5 31.5 + - - -
208B PHE 3.1 20.3 + - - +
209B ALA 3.0 0.2 - - - -
210B PHE* 1.3 80.8 - - - +
212B ASP* 1.3 82.3 + - - +
214B ALA* 3.5 2.9 + - - +
215B ARG* 3.2 29.1 + - + +
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Residues in contact with ASP 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE 5.4 0.6 - - - +
209B ALA 3.2 10.5 + - - +
210B PHE 3.2 0.6 - - - -
211B HIS* 1.3 95.4 - - - +
213B HIS* 1.3 65.3 + - + +
215B ARG* 4.4 4.3 - - - +
216B LYS* 2.8 34.2 + - + +
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Residues in contact with HIS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 3.2 56.4 + - + +
177B ASP* 4.7 2.0 + - - -
180B ASN* 4.7 4.0 - - + -
181B GLU* 3.4 30.6 - - + +
209B ALA* 4.0 11.4 + - + -
210B PHE* 3.0 32.6 + - + +
212B ASP* 1.3 80.3 - - + +
214B ALA* 1.3 62.7 + - - +
216B LYS* 4.1 3.4 - - - +
217B GLY 3.3 17.0 + - - -
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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
----------------------------------------------------------
180B ASN* 4.3 15.8 - - + +
184B ALA* 3.2 7.4 - - + +
201B ILE* 4.3 2.9 - - + +
203B VAL* 4.5 13.2 - - + -
204B PRO* 4.8 2.9 - - + -
210B PHE* 2.8 20.6 + - + +
211B HIS* 3.7 6.7 - - - +
213B HIS* 1.3 74.9 - - - +
215B ARG* 1.3 57.0 + - - +
218B PHE* 3.0 30.6 + - - +
264B ILE* 4.3 26.0 - - + -
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 4.3 11.4 - - + -
203B VAL* 4.8 4.9 - - + -
211B HIS* 3.2 20.7 + - + +
212B ASP* 4.1 4.9 - - - +
214B ALA* 1.3 78.1 - - - +
216B LYS* 1.3 60.9 + - - +
218B PHE* 4.2 5.2 - - - -
219B THR* 2.9 39.5 + - - +
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Residues in contact with LYS 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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181B GLU* 5.9 1.3 - - + -
212B ASP 2.8 23.5 + - - +
213B HIS* 4.1 5.4 - - - +
215B ARG* 1.3 71.4 - - - +
217B GLY* 1.3 59.8 + - - +
219B THR* 4.4 2.1 - - - -
220B ARG* 3.0 31.2 + - - +
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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
----------------------------------------------------------
181B GLU* 3.6 25.4 - - - +
184B ALA* 3.8 6.1 - - - -
185B TYR* 3.5 14.2 - - - +
213B HIS 3.3 9.5 + - - -
214B ALA 4.0 1.6 - - - -
216B LYS* 1.3 80.1 - - - +
218B PHE* 1.3 57.6 + - - +
220B ARG* 3.8 4.2 - - - +
221B GLY* 2.9 24.6 + - - -
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Residues in contact with PHE 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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184B ALA* 3.4 16.9 - - + +
188B VAL* 3.9 17.0 - - + +
199B ILE* 3.3 35.0 - - + -
200B ALA 3.9 2.7 - - - -
201B ILE* 3.3 41.1 - - + -
214B ALA 3.0 19.4 + - - +
215B ARG 3.9 1.6 - - - +
217B GLY* 1.3 76.5 - - - +
219B THR* 1.3 64.4 + - - +
221B GLY* 3.2 1.7 + - - -
222B ILE* 3.0 30.8 + - + +
229B GLU* 2.9 38.1 - - + -
262B VAL* 3.9 25.8 - - + -
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Residues in contact with THR 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 ARG* 2.9 27.3 + - - +
216B LYS* 4.4 2.5 - - - -
218B PHE* 1.3 76.2 - - - +
220B ARG* 1.3 62.6 + - - +
222B ILE* 3.0 25.5 - - + +
223B ARG* 3.4 11.3 + - - +
229B GLU* 4.5 11.4 + - - -
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Residues in contact with ARG 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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185B TYR* 6.2 0.9 - - + -
216B LYS 3.0 20.4 + - - +
217B GLY* 3.9 5.4 - - - +
219B THR* 1.3 76.0 - - - +
221B GLY* 1.3 62.0 + - - +
223B ARG* 3.5 4.9 + - - +
224B ASP* 3.1 30.4 + - - +
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Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 4.5 11.4 - - - +
188B VAL* 3.6 17.7 - - - +
217B GLY 2.9 19.1 + - - -
218B PHE 3.2 3.8 + - - -
219B THR 3.2 0.6 - - - -
220B ARG* 1.3 78.2 - - - +
222B ILE* 1.3 55.0 + - - +
224B ASP* 3.4 5.3 + - - +
225B PHE* 2.9 30.5 + - - +
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Residues in contact with ILE 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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188B VAL* 3.9 11.6 - - + +
199B ILE* 5.7 2.7 - - + -
218B PHE* 3.0 23.7 + - + +
219B THR* 3.0 31.4 - - + +
221B GLY* 1.3 70.0 - - - +
223B ARG* 1.3 63.5 + - - +
225B PHE* 4.5 1.1 - - - +
226B GLY* 3.1 20.8 + - - -
227B VAL 2.9 20.6 - - - +
228B SER* 3.6 4.3 - - - -
229B GLU* 3.1 46.2 - - + +
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Residues in contact with ARG 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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219B THR 3.4 12.4 + - - +
220B ARG* 3.8 10.8 - - - +
221B GLY 3.3 0.6 - - - -
222B ILE* 1.3 82.5 - - - +
224B ASP* 1.3 65.6 + - - +
226B GLY* 3.4 9.9 + - - -
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Residues in contact with ASP 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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220B ARG* 3.1 19.7 + - - +
221B GLY* 3.9 4.7 - - - +
223B ARG* 1.3 83.0 - - - +
225B PHE* 1.3 59.1 + - - +
226B GLY 3.3 0.2 - - - -
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Residues in contact with PHE 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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188B VAL* 3.8 26.9 - - + +
189B GLU* 5.3 2.7 - - - -
192B ALA* 4.5 15.1 - - + +
221B GLY 2.9 17.4 + - - +
222B ILE 4.7 0.4 - - - +
224B ASP* 1.3 76.2 - - - +
226B GLY* 1.3 56.8 + - - +
227B VAL* 3.1 23.5 + - + +
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Residues in contact with GLY 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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222B ILE 3.1 11.7 + - - -
223B ARG 3.4 8.0 + - - -
224B ASP 3.3 3.2 - - - -
225B PHE* 1.3 78.1 - - - +
227B VAL* 1.3 60.8 + - - +
228B SER 4.4 0.2 + - - -
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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