Contacts of the helix formed by residues 218 - 230 (chain P) in PDB entry 2IMW
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 GLY 218 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214P LYS* 2.7 23.4 + - - +
215P GLY 4.7 0.2 - - - -
216P MET 3.7 1.0 - - - -
217P ILE* 1.3 74.8 - - - +
219P GLU* 1.3 65.5 + - - -
220P ALA 3.3 0.7 - - - -
221P LYS 3.6 0.2 + - - -
222P ALA* 3.2 24.1 + - - +
1807S A 3.2 26.2 - - - -
1808S G 5.1 4.7 - - - -
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Residues in contact with GLU 219 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P PHE* 4.5 5.3 - - + -
214P LYS* 3.7 47.1 + - + +
218P GLY* 1.3 73.2 - - - -
220P ALA* 1.3 57.6 + - - +
222P ALA* 3.5 3.2 + - - +
223P LYS* 3.0 65.2 + - + +
503P EDO 4.9 4.6 + - - +
1807S A 2.9 9.5 + - - +
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Residues in contact with ALA 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219P GLU* 1.3 73.8 - - - +
221P LYS* 1.3 58.4 + - + +
224P TYR* 3.0 17.3 + - - +
503P EDO 2.7 46.6 + - - +
1806S A 3.1 46.2 - - - +
1807S A 2.7 11.3 + - - +
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Residues in contact with LYS 221 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185P GLY* 2.8 31.6 - - - +
186P ILE* 4.2 7.9 - - + -
190P THR* 3.9 26.8 + - + +
217P ILE* 3.8 30.5 - - + +
218P GLY 3.6 2.6 + - - -
220P ALA* 1.3 77.6 - - + +
222P ALA* 1.3 65.5 + - - +
224P TYR* 3.5 12.2 - - + +
225P LEU* 3.0 30.3 + - - +
1806S A 5.7 8.3 - - - -
1807S A 4.2 0.4 + - - -
1915T C 4.8 11.1 + - - -
1916T C 4.0 16.2 + - - -
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Residues in contact with ALA 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P PHE* 3.7 22.2 - - + -
213P LEU* 3.9 22.0 - - + -
214P LYS* 4.1 10.3 - - - +
217P ILE* 3.6 10.8 - - + +
218P GLY 3.2 19.5 + - - +
219P GLU 3.7 4.3 - - - +
220P ALA 3.2 0.2 - - - -
221P LYS* 1.3 76.7 - - - +
223P LYS* 1.3 62.8 + - - +
225P LEU* 3.3 1.6 + - - +
226P ILE* 3.0 28.1 + - - +
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Residues in contact with LYS 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P PHE* 4.0 20.6 - - + -
219P GLU* 3.0 52.7 + - + +
220P ALA 3.7 4.0 - - - +
222P ALA* 1.3 75.8 - - - +
224P TYR* 1.3 56.6 + - - +
226P ILE* 3.5 4.4 + - - +
227P SER* 2.9 32.4 + - - -
503P EDO 3.7 24.0 + - - +
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Residues in contact with TYR 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149P VAL* 3.5 19.5 - - + +
183P VAL* 3.8 12.5 - - + +
184P PRO* 2.7 33.9 + - - +
185P GLY* 5.0 2.9 - - - -
186P ILE* 4.9 3.6 - - + -
220P ALA 3.0 17.6 + - - +
221P LYS* 3.5 16.6 - - + +
223P LYS* 1.3 76.2 - - - +
225P LEU* 1.3 74.2 + - + +
227P SER* 2.8 22.2 + - - -
228P LEU* 3.1 29.5 + - + +
233P TYR* 3.7 31.0 - + - -
503P EDO 3.6 8.9 + - - +
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Residues in contact with LEU 225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P ILE* 4.1 18.8 - - + -
183P VAL* 4.1 5.6 - - + -
186P ILE* 3.8 35.4 - - + -
194P LEU* 4.2 9.6 - - + -
202P LEU* 3.6 23.2 - - + +
205P THR* 4.0 18.2 - - + -
213P LEU* 5.3 0.7 - - + -
217P ILE* 3.7 22.2 - - + -
221P LYS 3.0 21.2 + - - +
222P ALA* 3.9 2.9 - - - +
224P TYR* 1.3 90.4 - - + +
226P ILE* 1.3 58.2 + - - +
228P LEU* 3.3 5.8 + - + +
229P ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205P THR* 3.8 36.6 - - - +
206P LEU* 3.8 9.2 - - + -
210P PHE* 3.5 37.2 - - + -
213P LEU* 4.1 6.7 - - + -
222P ALA 3.0 18.8 + - - +
223P LYS* 3.9 4.0 - - - +
225P LEU* 1.3 73.7 - - - +
227P SER* 1.3 60.3 + - - +
229P ALA* 3.2 1.1 + - - +
230P ARG* 2.8 69.1 + - - +
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Residues in contact with SER 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223P LYS 2.9 16.2 + - - -
224P TYR* 2.8 18.7 + - - -
226P ILE* 1.3 77.0 - - - +
228P LEU* 1.3 59.1 + - - +
230P ARG* 3.5 7.5 + - - +
231P ASP 3.3 1.9 + - - -
232P GLU* 2.8 37.0 + - - -
233P TYR* 3.1 28.9 + - - -
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Residues in contact with LEU 228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147P ASN* 4.5 1.1 - - - +
149P VAL* 3.8 23.1 - - + -
150P PHE* 4.1 19.6 - - + -
175P ILE* 3.4 13.4 - - - +
183P VAL* 3.8 18.8 - - + -
202P LEU* 4.1 19.5 - - + -
224P TYR* 3.1 44.7 + - + +
225P LEU* 3.4 7.6 - - - +
227P SER* 1.3 79.1 + - - +
229P ALA* 1.3 60.3 + - - +
231P ASP* 2.8 18.7 + - - -
233P TYR* 3.6 31.2 - - + -
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Residues in contact with ALA 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175P ILE* 3.6 25.9 - - - +
202P LEU* 3.2 37.6 - - + +
203P VAL* 4.1 1.6 - - - +
205P THR* 3.5 12.3 - - - +
206P LEU* 3.7 23.2 - - + +
225P LEU 2.9 13.0 + - - +
226P ILE 3.8 3.4 - - - +
228P LEU* 1.3 73.4 - - - +
230P ARG* 1.3 58.4 + - - +
231P ASP* 3.2 0.7 + - - +
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Residues in contact with ARG 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206P LEU* 3.5 19.8 - - + +
226P ILE* 2.8 43.3 + - - +
227P SER* 3.8 7.3 - - - +
229P ALA* 1.3 75.4 - - - +
231P ASP* 1.3 71.9 + - - +
232P GLU* 3.3 37.0 + - + +
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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