Contacts of the helix formed by residues 213 - 227 (chain B) in PDB entry 4OE4
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 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B GLN* 4.1 2.0 - - - -
153B LYS* 3.4 20.6 - - - -
157B GLN 5.5 0.2 - - - -
160B ILE* 4.9 6.5 - - + -
161B ASP* 3.3 22.2 - - + +
165B GLU* 3.7 24.0 - - - -
210B PRO 4.4 7.5 + - - +
211B PHE 4.5 0.9 - - - -
212B ASN* 1.3 116.0 + - - +
214B THR* 1.3 64.8 - - - +
215B ALA* 4.7 0.7 - - + -
216B ILE* 3.1 39.8 + - + +
217B ALA* 3.5 8.0 + - - +
243B ASN* 5.4 0.4 + - - -
346B PHE* 4.9 3.8 - + - -
349B GLN 4.4 1.6 - - - -
350B LYS* 4.2 35.4 - - + -
351B CYS 5.7 0.2 - - - -
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Residues in contact with THR 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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143B MET* 4.0 15.7 - - + -
147B THR* 3.0 18.4 + - - -
151B GLN* 3.2 11.3 + - - +
161B ASP* 2.9 8.2 + - - -
162B CYS* 3.7 24.0 - - + -
166B LEU* 4.0 13.2 - - + -
213B PHE* 1.3 71.6 - - - +
215B ALA* 1.3 60.4 - - - +
217B ALA* 3.2 14.4 + - - +
218B ALA* 3.2 11.1 + - - +
242B SER* 3.1 26.5 + - - +
243B ASN* 4.3 11.2 - - - +
246B LEU* 4.4 5.0 - - + +
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Residues in contact with ALA 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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161B ASP* 2.7 24.8 + - - +
165B GLU* 3.8 16.8 - - + +
166B LEU* 3.4 40.1 - - - +
169B PHE* 3.3 17.2 - - + -
213B PHE* 3.1 1.8 - - + -
214B THR* 1.3 72.7 - - - +
216B ILE* 1.3 58.1 + - + +
217B ALA 3.3 0.2 - - - -
218B ALA* 3.3 3.6 + - - +
219B ASN 2.9 22.2 + - - -
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Residues in contact with ILE 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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165B GLU* 6.2 0.2 - - - +
169B PHE* 4.9 10.1 - - + -
210B PRO* 3.6 25.8 - - + -
212B ASN* 4.0 16.2 - - - +
213B PHE* 3.1 35.1 + - + +
215B ALA* 1.3 75.5 - - + +
217B ALA* 1.3 55.7 + - - +
219B ASN* 3.1 9.2 + - + +
220B LEU* 2.8 44.1 + - + +
286B THR* 3.9 23.1 - - + +
351B CYS* 5.9 3.4 - - + -
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B SER* 3.9 18.3 - - - -
210B PRO* 4.9 1.7 - - - +
213B PHE 3.5 5.0 + - - +
214B THR 3.2 12.2 + - - +
216B ILE* 1.3 79.7 - - - +
218B ALA* 1.3 61.6 + - - +
220B LEU* 3.2 1.1 + - - +
221B ILE* 3.1 30.2 + - - +
233B TRP* 3.8 13.7 - - + -
243B ASN* 3.5 30.5 - - - +
246B LEU* 4.3 5.2 - - + -
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.7 26.9 - - + +
169B PHE* 5.4 0.9 - - + -
170B PHE* 3.4 31.0 - - + -
214B THR 3.2 3.0 + - - -
215B ALA 3.5 8.5 - - - +
216B ILE 3.2 0.2 - - - -
217B ALA* 1.3 78.6 - - - +
219B ASN* 1.3 58.8 + - - +
221B ILE* 3.6 3.8 - - - +
222B GLY* 2.8 31.7 + - - -
246B LEU* 3.8 16.4 - - + +
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Residues in contact with ASN 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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169B PHE* 3.7 30.7 - - + -
170B PHE* 5.3 0.2 - - - -
173B TYR* 2.4 45.2 + - - -
215B ALA 2.9 14.3 + - - +
216B ILE* 3.1 12.7 + - - +
218B ALA* 1.3 77.4 - - - +
220B LEU* 1.3 78.1 + - - +
223B ALA* 3.2 26.7 + - - +
284B HIS* 3.9 7.5 + - - -
286B THR* 5.4 1.2 + - - -
548B ILE* 4.9 2.1 - - - +
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Residues in contact with LEU 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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207B ALA* 4.0 17.8 - - + +
208B VAL 3.5 11.4 - - - +
209B SER* 3.4 36.8 - - - -
210B PRO* 3.8 2.5 - - + -
216B ILE* 2.8 33.0 + - + +
217B ALA* 3.2 4.9 + - - +
219B ASN* 1.3 81.2 - - - +
221B ILE* 1.3 59.1 + - + +
224B PRO* 3.1 13.0 - - - +
284B HIS* 2.8 58.2 + - + +
285B PHE 4.2 0.4 - - - -
286B THR* 3.5 20.4 - - - +
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Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 5.4 0.4 - - + -
170B PHE* 5.4 1.3 - - + -
207B ALA* 3.9 8.5 - - + -
217B ALA 3.1 17.4 + - - +
218B ALA* 3.6 5.4 - - - +
220B LEU* 1.3 79.1 - - + +
222B GLY* 1.3 63.4 + - - +
223B ALA 3.5 0.2 - - - -
224B PRO* 3.3 5.4 - - - +
225B ALA* 3.2 29.9 + - - +
231B VAL* 4.0 7.4 - - + +
233B TRP* 3.5 62.4 - - + -
246B LEU* 4.2 9.6 - - + -
250B LEU* 3.7 30.1 - - + -
260B ILE* 4.1 16.4 - - + -
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Residues in contact with GLY 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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128B PHE* 3.8 26.6 - - - -
170B PHE* 4.2 7.0 - - - -
173B TYR* 4.9 4.3 - - - -
218B ALA 2.8 21.9 + - - -
221B ILE* 1.3 73.5 - - - +
223B ALA* 1.3 59.2 + - - +
226B LEU* 2.9 34.2 + - - +
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Residues in contact with ALA 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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173B TYR* 3.8 21.6 - - + -
219B ASN* 3.2 16.3 + - - +
222B GLY* 1.3 77.7 - - - +
224B PRO* 1.4 71.5 - - + +
226B LEU* 3.4 5.4 + - - +
227B MET* 3.4 20.8 + - - +
284B HIS* 4.4 6.3 - - + -
548B ILE* 4.4 9.6 - - + -
549B LEU* 3.8 24.2 - - + +
552B PHE* 4.4 5.6 - - + -
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Residues in contact with PRO 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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205B VAL* 3.9 23.1 - - + -
220B LEU 3.1 27.8 - - - +
221B ILE 3.3 7.4 - - - +
223B ALA* 1.4 92.1 - - + +
225B ALA* 1.3 62.5 + - - +
227B MET 3.1 7.1 + - - -
229B ASN* 2.8 32.8 + - + +
231B VAL* 4.1 10.5 - - + -
284B HIS* 3.9 7.6 - - - +
552B PHE* 3.6 30.2 - - + -
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Residues in contact with ALA 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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116B TRP* 2.7 35.5 + - + +
128B PHE* 3.8 20.6 - - + -
221B ILE 3.2 21.2 + - - +
224B PRO* 1.3 78.4 - - - +
226B LEU* 1.3 63.1 + - - +
228B GLY 3.0 3.5 + - - -
229B ASN 3.3 16.6 - - - +
231B VAL* 4.4 2.6 - - + +
259B VAL* 4.6 1.1 - - + -
260B ILE* 4.1 16.8 - - + -
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Residues in contact with LEU 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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116B TRP* 4.9 0.4 - - - -
121B PHE* 4.2 9.0 - - + -
124B ARG* 2.9 29.0 + - + +
125B SER* 3.8 29.2 - - - +
128B PHE* 3.8 28.2 - - + -
173B TYR* 3.5 44.9 - - + +
174B VAL* 3.8 14.1 - - + +
177B ALA* 4.0 10.5 - - + -
181B TYR* 4.1 0.7 + - - -
222B GLY 2.9 18.4 + - - +
223B ALA* 3.8 4.7 - - - +
225B ALA* 1.3 77.7 - - - +
227B MET* 1.3 61.9 + - - +
228B GLY 3.1 0.2 - - - -
549B LEU* 5.1 0.7 - - + -
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Residues in contact with MET 227 (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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124B ARG* 3.8 1.2 + - - -
177B ALA* 3.7 24.2 - - + -
180B LEU* 3.8 26.9 - - + -
181B TYR* 3.4 41.2 + - + +
198B TYR* 5.2 1.0 - - + +
199B ARG 4.9 0.2 - - - -
200B PRO* 3.5 19.2 - - - +
223B ALA 3.4 14.6 - - - +
224B PRO 3.1 7.1 + - - +
225B ALA 3.1 1.2 - - - -
226B LEU* 1.3 80.6 - - - +
228B GLY* 1.3 59.6 + - - +
229B ASN* 3.5 7.6 - - - +
549B LEU* 4.0 30.5 - - + +
552B PHE* 4.2 2.2 - - + +
553B VAL* 3.6 27.8 - - + +
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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