Contacts of the helix formed by residues 217 - 231 (chain B) in PDB entry 2IG7
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 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B LEU 3.1 11.5 + - - -
214B GLU* 3.1 12.7 + - - +
215B MSE 5.2 0.2 + - - -
216B TYR* 1.3 79.1 - - - +
218B LEU* 1.3 60.4 + - - +
219B LYS 3.4 2.5 - - - -
220B ASP* 3.5 17.2 + - - +
221B GLU* 3.0 24.8 + - - +
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Residues in contact with LEU 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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196B LEU* 4.7 8.0 - - + +
212B LEU 3.7 15.7 - - - +
213B LEU* 3.0 46.6 + - + +
216B TYR* 3.7 19.1 - - + +
217B SER* 1.3 73.8 - - - +
219B LYS* 1.3 66.9 + - - +
221B GLU* 4.2 1.1 - - + -
222B MSE 2.9 23.0 + - - +
351B PHE* 3.5 22.7 - - + -
355B LEU* 4.3 3.6 - - + -
358B ILE* 4.2 2.7 - - + -
378B PHE* 3.5 54.3 - - + -
382B PHE* 5.4 2.0 - - + -
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Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 4.1 27.3 - - + +
200B GLN* 4.3 15.7 - - - +
213B LEU* 4.7 3.9 + - + +
217B SER 3.4 0.4 - - - -
218B LEU* 1.3 78.7 - - - +
220B ASP* 1.3 68.8 + - - +
222B MSE 3.6 12.4 + - + +
223B GLY* 3.8 6.4 + - - -
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Residues in contact with ASP 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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217B SER* 3.5 18.4 + - - +
218B LEU 3.3 0.2 - - - -
219B LYS* 1.3 83.4 - - - +
221B GLU* 1.3 62.7 + - - +
223B GLY* 3.2 5.6 + - - -
224B ASN* 3.1 28.2 + - - +
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Residues in contact with GLU 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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216B TYR 4.5 3.8 - - - +
217B SER 3.0 19.0 + - - +
218B LEU* 3.3 4.9 + - - +
220B ASP* 1.3 73.6 - - - +
222B MSE 1.3 61.8 + - - +
224B ASN* 3.0 23.6 + - - +
225B LEU* 2.8 28.6 + - - +
351B PHE* 3.8 12.8 - - + -
381B TYR* 2.7 41.4 + - + +
382B PHE* 3.8 17.0 - - + -
385B LYS* 2.6 31.3 + - - -
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Residues in contact with MSE 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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189B PHE* 3.7 20.0 - - + -
192B MSE 4.0 34.8 - - + +
193B GLU* 4.1 23.1 - - + -
196B LEU* 3.4 30.3 - - + -
218B LEU 2.9 15.9 + - - +
219B LYS* 3.9 6.7 - - + +
220B ASP 3.3 0.4 - - - -
221B GLU* 1.3 76.4 - - - +
223B GLY* 1.3 56.6 + - - +
225B LEU* 3.2 5.4 + - + +
226B ARG* 2.8 32.9 + - - +
351B PHE* 3.8 24.8 - - + -
355B LEU* 4.6 1.6 - - - -
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Residues in contact with GLY 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 LYS 3.8 5.0 + - - -
220B ASP* 3.2 8.4 + - - -
222B MSE 1.3 76.0 - - - +
224B ASN* 1.3 64.3 + - - +
226B ARG* 3.4 10.1 + - - +
227B LYS* 3.0 34.2 + - - +
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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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220B ASP* 3.1 17.8 + - - +
221B GLU* 3.0 39.5 + - - +
223B GLY* 1.3 76.0 - - - +
225B LEU* 1.3 63.0 + - - +
227B LYS* 3.4 14.8 + - - +
228B LEU* 3.1 23.3 + - - +
385B LYS* 4.0 12.2 - - - +
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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 PHE* 4.1 7.2 - - + -
192B MSE 4.2 18.2 - - + -
221B GLU 2.8 19.1 + - - +
222B MSE 3.5 5.6 - - - +
224B ASN* 1.3 71.8 - - - +
226B ARG* 1.3 65.6 + - - +
228B LEU* 3.2 12.3 + - + +
229B LEU* 3.0 41.4 + - + +
347B LEU* 4.0 26.0 - - + -
348B ALA* 4.1 14.1 - - + +
351B PHE* 3.8 34.8 - - + -
381B TYR* 3.7 15.7 + - + +
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Residues in contact with ARG 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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189B PHE* 3.5 54.4 - - + +
193B GLU* 2.4 39.5 + - - +
222B MSE 2.8 21.9 + - - +
223B GLY* 3.7 10.4 - - - +
224B ASN 3.3 0.2 - - - -
225B LEU* 1.3 75.8 - - - +
227B LYS* 1.3 55.5 + - + +
229B LEU* 3.2 1.7 + - - +
230B GLU* 2.7 59.7 + - + +
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Residues in contact with LYS 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 GLY 3.0 22.7 + - - +
224B ASN* 3.6 15.3 - - - +
225B LEU 3.2 0.2 - - - -
226B ARG* 1.3 80.3 - - + +
228B LEU* 1.3 62.5 + - - +
230B GLU* 3.5 15.4 + - - +
231B SER* 3.5 18.5 + - - -
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Residues in contact with LEU 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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224B ASN 3.1 13.8 + - - +
225B LEU* 3.6 16.8 - - + +
227B LYS* 1.3 77.9 - - - +
229B LEU* 1.3 56.0 + - + +
231B SER* 3.1 18.1 + - - +
232B THR* 2.7 26.7 + - - +
344B ARG* 4.0 44.2 - - + +
347B LEU* 3.7 29.6 - - + -
381B TYR* 6.1 0.4 - - - +
385B LYS* 6.1 3.6 - - + -
388B LEU* 4.5 6.1 - - + -
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Residues in contact with LEU 229 (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 LEU* 4.2 2.2 - - + -
189B PHE* 4.0 26.2 - - + -
225B LEU* 3.0 27.7 + - + +
226B ARG 4.0 2.2 - - - +
228B LEU* 1.3 75.3 - - + +
230B GLU* 1.3 67.1 + - - +
231B SER 3.1 2.0 - - - -
232B THR* 3.0 24.3 + - - +
272B TYR* 6.2 1.1 - - + -
344B ARG* 3.6 40.6 - - + +
345B TYR* 3.5 35.8 + - + +
348B ALA* 3.9 25.8 - - + -
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Residues in contact with GLU 230 (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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226B ARG* 2.7 48.9 + - + +
227B LYS* 3.7 15.7 - - - +
229B LEU* 1.3 73.4 - - - +
231B SER* 1.3 58.0 + - - +
232B THR 3.6 1.6 + - - -
233B PRO* 5.2 2.1 - - - +
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Residues in contact with SER 231 (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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227B LYS 3.5 8.9 + - - -
228B LEU* 3.1 18.2 + - - +
229B LEU 3.1 1.2 - - - -
230B GLU* 1.3 76.7 - - - +
232B THR* 1.3 57.1 + - - +
233B PRO* 3.4 11.3 - - - +
344B ARG* 3.9 14.0 + - - -
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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