Contacts of the helix formed by residues 217 - 236 (chain A) in PDB entry 2DW1
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 ASP 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ASN* 3.0 17.4 + - - +
215A ASN* 3.2 4.5 + - + +
216A GLY* 1.3 72.0 - - - +
218A LEU* 1.3 65.3 + - - +
219A ASP* 3.5 11.6 + - - +
220A LYS* 3.0 53.5 + - + +
221A ILE* 3.0 17.0 + - - +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL* 4.2 20.4 - - + -
216A GLY* 2.7 25.1 + - - +
217A ASP* 1.3 71.9 + - - +
219A ASP* 1.3 62.3 + - - +
221A ILE* 3.6 6.8 - - + +
222A LYS* 3.0 45.8 + - - +
250A ILE* 4.3 35.0 - - + -
252A SER* 4.4 13.9 - - - +
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP* 3.1 10.1 + - - +
218A LEU* 1.3 77.6 - - - +
220A LYS* 1.3 59.0 + - - +
222A LYS* 3.3 10.2 + - - +
223A THR* 2.9 44.9 + - - -
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ASN* 3.6 29.4 + - + +
217A ASP* 3.0 37.3 + - + +
219A ASP* 1.3 79.0 - - - +
221A ILE* 1.3 66.1 + - - +
223A THR* 4.0 5.1 - - - -
224A ARG* 3.1 26.8 + - + +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL* 3.8 32.5 - - + -
210A MET* 4.0 18.8 - - + +
211A VAL* 4.7 6.5 - - + -
214A ASN* 3.0 45.1 - - + +
217A ASP 3.0 15.1 + - - +
218A LEU* 3.6 17.9 - - + +
219A ASP 3.3 0.2 - - - -
220A LYS* 1.3 74.4 - - - +
222A LYS* 1.3 59.8 + - - +
224A ARG* 3.1 11.2 + - - +
225A MET* 3.0 36.3 + - + +
250A ILE* 4.0 14.8 - - + -
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Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU* 3.0 44.4 + - - +
219A ASP* 3.7 9.0 - - - +
221A ILE* 1.3 75.6 - - + +
223A THR* 1.3 66.3 + - - +
225A MET* 3.0 11.4 + - - -
226A TYR* 3.0 45.4 + - + +
248A LEU* 3.8 24.7 - - + -
250A ILE* 4.9 10.5 - - + -
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Residues in contact with THR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASP* 2.9 36.8 + - - -
220A LYS* 4.0 6.1 - - - -
222A LYS* 1.3 72.2 - - - +
224A ARG* 1.3 63.8 + - - +
226A TYR* 3.5 16.3 + - + +
227A GLU* 3.1 34.1 + - + +
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Residues in contact with ARG 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A MET* 5.0 7.3 - - - +
214A ASN* 5.4 7.9 + - - +
220A LYS* 3.1 23.0 + - + +
221A ILE* 3.3 9.4 - - - +
222A LYS 3.0 0.6 - - - -
223A THR* 1.3 77.7 - - - +
225A MET* 1.3 62.1 + - - +
227A GLU* 3.3 7.0 + - - +
228A ILE* 3.0 43.3 + - + +
290A LEU* 6.5 0.4 - - - -
319A ASP* 2.9 27.3 + - - -
321A SER 2.5 28.7 + - - -
322A GLU* 3.4 39.3 + - - +
323A ILE 4.4 0.4 + - - -
324A ASN* 2.8 29.0 + - - +
327A VAL* 3.4 17.4 - - - +
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Residues in contact with MET 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 3.0 42.8 - - + -
206A VAL* 4.0 15.3 - - + -
210A MET* 4.8 2.2 - - - -
221A ILE* 3.0 29.2 + - + +
222A LYS 3.0 5.1 + - - +
224A ARG* 1.3 76.8 - - - +
226A TYR* 1.3 67.7 + - - +
228A ILE* 3.2 8.6 + - - +
229A VAL* 2.9 30.0 + - - +
245A LEU* 4.6 4.7 - - + -
248A LEU* 4.0 24.9 - - + -
290A LEU* 3.2 43.3 - - + -
331A MET* 4.9 0.9 - - + -
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Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 3.0 42.8 + - + +
223A THR* 3.6 16.2 - - + +
225A MET* 1.3 75.0 - - + +
227A GLU* 1.3 67.7 + - - +
229A VAL* 4.0 2.4 - - - +
230A ASN* 3.0 24.3 + - - +
245A LEU* 3.8 26.7 - - + -
248A LEU* 4.4 10.7 - - + +
399A ILE* 4.0 19.1 + - + +
400A SER* 3.9 20.4 - - - -
401A PRO* 3.5 36.6 - - + -
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A THR* 3.1 26.2 + - + +
224A ARG* 3.4 8.5 - - - +
225A MET 3.2 0.2 - - - -
226A TYR* 1.3 82.3 - - - +
228A ILE* 1.3 62.7 + - - +
230A ASN* 3.1 20.0 + - - +
231A THR* 3.2 17.3 + - - -
324A ASN* 4.1 26.8 + - + +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ARG* 3.0 38.9 + - + +
225A MET* 3.7 18.2 - - - +
227A GLU* 1.3 75.0 - - - +
229A VAL* 1.3 62.3 + - + +
231A THR* 3.2 6.0 + - - -
232A VAL* 3.0 20.6 + - - +
290A LEU* 4.7 3.8 - - + -
324A ASN* 3.9 19.3 - - + +
327A VAL* 3.5 26.2 - - + -
328A ALA* 3.6 30.2 - - - +
331A MET* 3.8 25.4 - - + -
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 4.3 8.3 - - + -
204A LEU* 3.7 26.9 - - + -
225A MET 2.9 25.7 + - - +
226A TYR* 4.1 3.6 - - - +
228A ILE* 1.3 72.9 - - - +
230A ASN* 1.3 57.5 + - - +
232A VAL* 3.2 7.4 + - - +
233A ASN* 2.9 27.5 + - - +
243A VAL* 4.1 25.1 - - + +
244A ALA* 4.8 0.2 - - - -
245A LEU* 4.0 39.5 - - + +
331A MET* 4.5 4.0 - - + -
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Residues in contact with ASN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TYR 3.0 14.6 + - - +
227A GLU* 3.1 17.0 + - - +
229A VAL* 1.3 77.0 - - - +
231A THR* 1.3 61.9 + - - +
233A ASN* 3.3 7.9 + - - +
234A GLU* 3.1 39.2 + - - +
403A VAL* 5.1 17.7 - - - +
406A ASN* 4.4 21.6 - - - +
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Residues in contact with THR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLU 3.2 11.8 + - - -
228A ILE* 3.2 7.8 + - - -
230A ASN* 1.3 75.6 + - - +
232A VAL* 1.3 55.7 + - - +
234A GLU* 3.1 17.4 + - + +
235A ILE* 2.7 46.2 + - + +
324A ASN* 5.1 4.3 + - - +
325A LEU* 4.3 18.1 - - + -
328A ALA* 3.7 22.1 - - + +
367A THR* 4.9 3.8 - - + -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ILE 3.0 20.0 + - - +
229A VAL* 3.2 9.2 + - - +
231A THR* 1.3 75.5 - - - +
233A ASN* 1.3 58.8 + - - +
235A ILE* 3.0 11.5 + - - +
236A TYR* 2.9 50.0 + - + -
243A VAL* 3.9 21.3 - - + -
328A ALA* 3.7 22.9 - - - +
331A MET* 3.8 26.7 - - + -
332A ALA* 4.3 3.4 - - - +
335A MET* 4.4 9.9 - - - -
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Residues in contact with ASN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A VAL 2.9 13.1 + - - +
230A ASN* 3.4 14.5 + - - +
232A VAL* 1.3 77.5 - - - +
234A GLU* 1.3 66.9 + - - +
236A TYR* 3.2 11.0 + - - +
237A ARG* 3.5 12.8 + - - +
241A ILE 4.5 1.2 - - - +
242A HIS* 3.4 18.5 + - - -
243A VAL* 3.1 43.0 + - - +
406A ASN* 3.1 38.8 + - - +
408A LEU* 3.7 8.9 - - - +
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ASN* 3.1 41.3 + - - +
231A THR* 3.4 18.1 + - + +
233A ASN* 1.3 80.3 - - - +
235A ILE* 1.3 63.6 + - + +
236A TYR 3.2 0.7 + - - -
237A ARG* 3.3 25.9 + - - +
238A TYR 5.0 0.2 + - - -
406A ASN* 6.3 2.0 - - - -
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A THR* 2.7 36.3 + - + +
232A VAL* 3.0 10.3 + - - +
234A GLU* 1.3 74.2 - - + +
236A TYR* 1.3 60.4 + - + +
237A ARG 3.6 0.5 + - - -
238A TYR* 4.4 9.2 + - - +
325A LEU* 5.3 0.2 - - + -
328A ALA* 4.1 23.1 - - + +
329A VAL* 4.8 7.2 - - + -
332A ALA* 3.9 12.3 - - + -
356A ILE* 3.4 31.9 - - + -
367A THR* 3.9 40.0 - - + +
369A PHE* 3.6 22.6 - - + -
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Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A VAL* 2.9 37.1 + - + +
233A ASN 3.2 3.8 + - - +
234A GLU 3.1 0.8 - - - -
235A ILE* 1.3 78.1 - - + +
237A ARG* 1.3 65.4 + - - +
238A TYR 3.3 2.2 - - - -
239A MET* 3.2 36.6 + - + -
241A ILE* 2.9 42.2 + - + +
243A VAL* 4.1 13.9 - - + -
332A ALA* 2.8 42.3 + - + -
335A MET* 3.5 10.0 - - + -
336A GLY* 3.1 20.8 + - - -
339A LEU* 3.5 22.8 - - + +
369A PHE* 3.4 20.8 - + - -
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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