Contacts of the helix formed by residues 214 - 228 (chain B) in PDB entry 1IB1
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 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B THR* 2.7 30.6 + - - -
165B PRO* 3.9 20.9 - - - -
168B LEU* 3.4 18.4 - - - +
211B TYR* 4.3 2.6 - - - +
212B LYS* 3.5 1.6 + - - -
213B ASP* 1.3 77.9 + - - +
215B THR* 1.3 64.2 + - - +
216B LEU 3.1 3.6 + - - -
217B ILE* 3.2 17.5 + - - +
218B MET* 3.2 17.1 + - - +
88F GLY 4.0 7.0 - - - -
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Residues in contact with THR 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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212B LYS* 3.3 21.8 + - - -
213B ASP 3.3 4.0 + - - -
214B SER* 1.3 74.7 - - - +
216B LEU* 1.3 58.1 + - - +
218B MET* 3.1 14.4 + - + +
219B GLN* 2.9 30.6 + - + +
41F THR* 5.0 0.9 - - - +
43F GLU* 3.5 43.4 + - + +
44F ASP* 3.4 23.4 + - - +
47F GLY 5.4 0.2 + - - -
90F LEU* 6.6 0.2 - - - -
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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
----------------------------------------------------------
213B ASP 5.0 0.2 + - - -
214B SER 3.2 0.6 - - - -
215B THR* 1.3 75.6 - - - +
217B ILE* 1.3 51.3 - - - +
218B MET 3.0 4.9 - - - -
219B GLN* 2.9 11.9 + - + +
220B LEU* 2.8 55.5 + - + +
33F PRO* 4.6 3.1 - - + -
36F GLU* 3.6 24.0 - - - +
38F ARG* 3.6 40.2 - - - +
44F ASP* 4.5 2.1 + - - +
85F PHE* 3.8 20.3 - - + -
88F GLY* 3.5 30.2 + - - +
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Residues in contact with ILE 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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165B PRO* 3.4 37.2 - - + +
168B LEU* 3.7 36.6 - - + +
169B GLY* 3.8 5.8 - - - +
172B LEU* 4.4 8.5 - - + +
214B SER* 3.2 11.8 + - - +
216B LEU* 1.3 73.5 - - - +
218B MET* 1.3 58.1 + - - +
220B LEU* 3.7 11.3 - - + +
221B LEU* 3.2 26.4 + - + +
32F LEU* 4.1 13.2 - - + -
87F GLU 3.9 13.2 - - - +
88F GLY* 3.6 29.6 - - - +
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Residues in contact with MET 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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163B THR* 5.5 1.3 - - - -
168B LEU* 3.9 20.9 - - + -
196B PHE* 3.5 37.8 - - + +
199B ALA* 3.4 30.7 - - + -
200B ILE* 3.7 25.6 - - + +
203B LEU* 4.3 14.6 - - + -
214B SER* 3.2 17.9 + - - +
215B THR* 3.1 13.6 + - + +
216B LEU 3.0 0.6 - - - -
217B ILE* 1.3 75.8 - - - +
219B GLN* 1.3 66.1 + - - +
220B LEU 3.1 1.1 - - - -
221B LEU* 3.1 11.3 + - + +
222B ARG 2.9 18.9 + - - -
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Residues in contact with GLN 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 THR* 2.9 19.5 + - + +
216B LEU* 2.9 13.7 + - + +
218B MET* 1.3 75.2 - - - +
220B LEU* 1.3 60.1 + - + +
222B ARG* 3.0 36.2 - - - +
223B ASP* 2.9 64.2 + - - +
41F THR* 5.9 3.4 - - + +
43F GLU* 5.4 17.2 + - + +
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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
----------------------------------------------------------
172B LEU* 3.7 27.4 - - + -
216B LEU* 2.8 38.9 + - + +
217B ILE* 3.7 12.6 - - - +
219B GLN* 1.3 78.9 - - + +
221B LEU* 1.3 61.9 + - - +
223B ASP* 3.4 8.6 + - - +
224B ASN* 3.1 27.5 + - - +
30F HIS* 3.8 32.2 - - + +
31F TPO 4.2 5.2 - - - +
33F PRO* 3.7 28.9 - - + -
38F ARG* 5.3 4.7 - - - +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 4.3 30.5 - - + +
171B ALA* 4.4 2.5 - - + -
172B LEU* 3.8 37.9 - - + +
175B SER* 4.7 0.4 - - - +
192B ALA* 3.8 32.5 - - + +
195B ALA* 4.5 13.9 - - + -
196B PHE* 4.4 17.7 - - + +
217B ILE 3.2 19.6 + - - +
218B MET* 3.1 12.9 + - + +
220B LEU* 1.3 79.5 - - - +
222B ARG* 1.3 61.4 + - - +
224B ASN* 3.2 6.7 + - + +
225B LEU* 3.1 25.3 + - - +
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Residues in contact with ARG 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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196B PHE* 3.7 39.4 - - + -
200B ILE* 6.1 0.4 - - - +
218B MET 2.9 10.4 + - - +
219B GLN* 3.0 49.4 - - - +
221B LEU* 1.3 73.6 - - - +
223B ASP* 1.3 67.4 + - - +
225B LEU* 3.0 13.6 + - + +
226B THR* 2.8 35.6 + - - +
43F GLU* 6.3 1.0 - - - +
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Residues in contact with ASP 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 GLN* 2.9 39.6 + - - +
220B LEU* 3.6 8.3 - - - +
222B ARG* 1.3 79.2 - - - +
224B ASN* 1.3 57.8 + - - +
226B THR* 3.2 9.0 + - - -
227B LEU* 2.8 29.3 + - - +
27F GLN* 5.7 1.6 + - - -
30F HIS* 3.6 27.7 + - + +
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Residues in contact with ASN 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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172B LEU* 3.2 18.0 - - + +
175B SER* 5.0 0.6 + - - +
176B VAL* 3.7 12.9 - - - +
192B ALA* 5.7 1.1 - - + -
220B LEU 3.1 8.4 + - - +
221B LEU* 3.5 9.9 - - - +
223B ASP* 1.3 79.0 - - - +
225B LEU* 1.3 57.9 + - + +
227B LEU* 3.2 8.4 - - - +
228B TRP* 2.8 59.6 + - + -
29F ARG* 3.8 5.0 - - - -
30F HIS* 2.9 54.3 + - - +
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Residues in contact with LEU 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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189B CYS* 3.9 31.8 - - + +
192B ALA* 3.8 24.5 - - + +
193B LYS* 3.9 32.1 - - + +
196B PHE* 4.9 7.9 - - + -
221B LEU 3.1 17.7 + - - +
222B ARG* 3.0 17.6 + - + +
224B ASN* 1.3 74.6 - - - +
226B THR* 1.3 65.8 + - - +
228B TRP* 2.9 26.2 + - + +
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Residues in contact with THR 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 ARG* 2.8 23.4 + - - +
223B ASP* 3.4 12.8 + - - -
225B LEU* 1.3 72.7 - - - +
227B LEU* 1.3 63.3 + - - +
228B TRP 4.3 2.4 - - - -
27F GLN* 6.0 3.8 - - - +
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Residues in contact with LEU 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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223B ASP 2.8 14.1 + - - +
224B ASN* 3.2 13.5 - - - +
226B THR* 1.3 80.5 - - - +
228B TRP* 1.3 83.2 + - + +
27F GLN* 3.6 45.7 - - + +
28F ARG 4.5 1.8 - - - +
29F ARG* 3.7 32.8 - - + +
30F HIS* 6.2 0.9 - - + -
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Residues in contact with TRP 228 (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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175B SER* 4.0 15.7 - - - -
176B VAL* 3.9 19.3 - - + -
179B TYR* 3.5 63.3 - + + -
188B ALA* 4.2 17.7 - - + -
189B CYS* 3.8 35.4 - - - -
192B ALA* 4.7 5.4 - - + -
224B ASN* 2.8 54.5 + - + +
225B LEU* 2.9 17.2 + - + +
226B THR 4.3 2.2 - - - -
227B LEU* 1.3 104.1 - - + +
29F ARG* 4.2 10.0 - - + +
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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