Contacts of the helix formed by residues 250 - 267 (chain A) in PDB entry 3IKH
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A LEU* 3.5 12.6 - - - -
215A GLN* 5.5 0.2 - - - -
245A ARG* 2.8 44.8 + - - -
247A VAL* 3.9 7.2 - - + +
248A ALA 3.8 9.1 - - - +
249A PRO* 1.3 74.4 - - - +
251A ALA* 1.3 66.1 + - - +
252A LEU* 3.9 8.1 - - - +
253A ALA* 2.9 16.4 + - - +
254A LEU* 3.2 15.2 + - - +
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Residues in contact with ALA 251 (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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208A LEU* 3.7 9.3 - - - +
215A GLN* 3.6 29.9 + - + +
217A CYS* 4.7 4.3 - - + +
250A ASP* 1.3 76.4 - - - +
252A LEU* 1.3 62.4 + - - +
254A LEU* 3.2 9.8 + - - +
255A ALA* 3.1 21.2 + - - +
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Residues in contact with LEU 252 (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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245A ARG* 3.7 37.2 - - - +
250A ASP* 3.3 5.8 + - - +
251A ALA* 1.3 76.4 - - - +
253A ALA* 1.3 66.6 + - - +
255A ALA* 3.2 10.8 + - + -
256A HIS* 2.9 54.3 + - + +
259A ARG* 5.9 2.2 - - - +
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Residues in contact with ALA 253 (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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238A MSE 3.6 34.4 - - + +
241A SER* 3.6 7.4 - - - +
242A ALA 4.4 1.3 - - - +
245A ARG* 3.3 12.3 - - - +
249A PRO* 4.3 3.6 - - + -
250A ASP* 2.9 33.5 + - - +
252A LEU* 1.3 77.5 - - - +
254A LEU* 1.3 58.5 + - - +
256A HIS* 3.4 2.8 + - - +
257A ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 254 (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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198A VAL* 4.4 7.4 - - + -
206A ALA* 4.3 13.7 - - + +
207A TRP 4.1 7.4 - - - +
208A LEU* 3.8 39.5 - - + +
215A GLN 5.1 0.7 - - - +
217A CYS* 3.7 25.4 - - + -
234A PHE* 3.8 15.2 - - + -
238A MSE 4.0 22.7 - - + -
249A PRO* 5.1 0.4 - - + -
250A ASP 3.2 20.3 + - - +
251A ALA* 3.7 8.1 - - - +
253A ALA* 1.3 78.4 - - + +
255A ALA* 1.3 54.8 + - - +
257A ALA* 3.3 6.6 + - - +
258A SER* 2.7 37.2 + - - -
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Residues in contact with ALA 255 (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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217A CYS* 3.6 14.5 - - - -
220A VAL* 5.0 1.7 - - - +
251A ALA 3.1 12.8 + - - +
252A LEU* 3.2 20.6 + - + +
254A LEU* 1.3 75.4 - - - +
256A HIS* 1.3 66.1 + - - +
258A SER* 3.3 4.2 + - - -
259A ARG* 3.1 33.0 + - - +
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Residues in contact with HIS 256 (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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237A VAL* 3.9 4.5 - - + -
241A SER* 2.8 29.2 - - - +
245A ARG* 4.4 2.4 + - - -
252A LEU* 2.9 47.6 + - + +
253A ALA 3.7 4.5 - - - +
255A ALA* 1.3 76.2 - - - +
257A ALA* 1.3 57.4 + - - +
259A ARG* 3.2 17.1 + - - +
260A ALA* 3.0 24.4 + - - +
283A LEU* 3.2 44.5 + - + +
284A LEU* 3.4 33.7 + - + -
285A THR 5.0 4.7 - - - -
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Residues in contact with ALA 257 (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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234A PHE* 3.2 45.1 - - + +
237A VAL* 3.9 13.0 - - - +
238A MSE 3.7 10.3 - - + +
253A ALA 3.0 18.4 + - - +
254A LEU 3.5 4.7 - - - +
256A HIS* 1.3 74.8 - - - +
258A SER* 1.3 60.1 + - - +
260A ALA* 3.2 1.9 + - - +
261A ALA* 2.8 31.2 + - - +
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Residues in contact with SER 258 (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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205A GLY* 6.0 0.3 - - - -
217A CYS* 3.6 13.7 + - - -
218A PRO 3.7 17.0 + - - -
219A ALA* 4.6 0.3 - - - -
220A VAL* 3.8 17.4 + - - +
234A PHE* 3.5 11.4 - - - -
254A LEU 2.7 21.6 + - - -
255A ALA* 3.7 7.2 - - - -
257A ALA* 1.3 75.9 - - - +
259A ARG* 1.3 56.8 - - - +
261A ALA* 3.5 1.6 + - - +
262A ALA* 3.0 28.6 + - - +
900A ATP 3.9 19.5 + - - -
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Residues in contact with ARG 259 (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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220A VAL* 3.8 20.3 - - + +
252A LEU* 5.9 1.6 - - - +
255A ALA* 3.1 22.3 + - - +
256A HIS* 3.4 23.3 + - - +
258A SER* 1.3 77.6 - - - +
260A ALA* 1.3 61.1 + - - +
262A ALA* 3.4 14.3 + - + +
263A ILE* 3.5 13.8 + - + +
282A ALA 5.3 0.2 + - - -
283A LEU* 3.7 46.0 + - + +
285A THR 6.1 0.6 - - - -
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Residues in contact with ALA 260 (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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233A THR* 3.6 13.3 - - + +
237A VAL* 3.4 33.7 - - + -
256A HIS 3.0 13.7 + - - +
257A ALA 3.2 2.9 + - - +
259A ARG* 1.3 75.2 - - - +
261A ALA* 1.3 65.2 + - - +
263A ILE* 3.0 18.2 + - - +
264A THR* 3.3 8.8 + - - -
275A PRO* 4.1 7.9 - - + +
280A LEU* 4.3 0.4 - - + -
283A LEU* 3.9 18.4 - - + +
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Residues in contact with ALA 261 (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 ALA* 3.8 13.9 - - - +
233A THR* 3.7 11.8 - - - +
234A PHE* 4.3 5.4 - - + +
257A ALA 2.8 18.4 + - - +
258A SER 3.9 3.1 - - - +
260A ALA* 1.3 75.8 - - - +
262A ALA* 1.3 63.1 + - - +
264A THR* 3.2 3.2 + - - -
265A VAL* 3.0 29.0 + - - +
900A ATP 3.4 34.8 - - - +
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Residues in contact with ALA 262 (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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220A VAL* 3.8 33.2 - - + +
221A PRO 4.8 0.4 - - - +
222A ALA* 3.8 18.9 - - + +
223A GLU* 4.8 0.5 - - - +
258A SER 3.0 13.9 + - - +
259A ARG* 3.4 11.2 - - + +
260A ALA 3.1 0.2 - - - -
261A ALA* 1.3 78.1 - - - +
263A ILE* 1.3 61.6 + - + +
265A VAL* 3.6 1.0 + - - -
266A SER* 3.3 21.1 + - - -
900A ATP 4.5 7.1 + - + -
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Residues in contact with ILE 263 (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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259A ARG* 3.6 16.4 - - + +
260A ALA 3.0 7.7 + - - +
262A ALA* 1.3 75.4 - - + +
264A THR* 1.3 65.6 + - - +
266A SER* 2.6 25.8 + - - +
267A ARG* 3.3 45.3 + - - +
273A ALA 4.1 3.6 - - - +
275A PRO* 4.0 25.1 - - + -
279A GLU* 4.3 14.8 - - + +
283A LEU* 4.2 15.5 - - + -
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Residues in contact with THR 264 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ASP 3.1 4.7 - - - +
228A THR 3.1 26.7 - - - +
229A GLY 3.9 7.2 - - - -
230A ALA* 3.9 4.3 - - + +
233A THR* 2.8 28.0 + - - +
260A ALA 3.3 2.1 + - - -
261A ALA 3.2 8.4 + - - -
263A ILE* 1.3 80.0 - - - +
265A VAL* 1.3 58.3 + - - +
267A ARG* 2.9 26.5 + - - +
273A ALA* 4.1 13.1 - - + +
274A PHE* 3.5 18.8 - - + -
275A PRO* 3.4 17.7 - - - +
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Residues in contact with VAL 265 (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 ALA* 4.8 1.8 - - + -
223A GLU 3.8 3.4 - - - +
224A ALA* 3.2 28.7 - - + +
225A LEU 3.0 8.3 + - - -
226A ASP 3.0 34.2 + - - -
227A THR* 3.9 11.9 - - + +
230A ALA* 3.8 20.4 - - + -
261A ALA 3.0 17.3 + - - +
262A ALA* 3.9 6.5 - - - +
264A THR* 1.3 75.9 - - - +
266A SER* 1.3 58.8 + - - +
900A ATP 3.7 42.8 - - + +
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Residues in contact with SER 266 (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 GLU* 3.4 42.2 - - - +
225A LEU* 3.4 19.9 - - - +
262A ALA 3.3 8.1 + - - -
263A ILE* 2.6 26.2 + - - +
265A VAL* 1.3 79.7 - - - +
267A ARG* 1.3 66.2 + - - +
153B SER* 6.2 0.2 - - - -
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Residues in contact with ARG 267 (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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225A LEU* 4.5 2.0 - - - -
226A ASP* 3.4 14.4 - - - +
263A ILE* 3.3 21.5 + - - +
264A THR 2.9 16.5 + - - +
266A SER* 1.3 91.8 + - - +
268A ARG* 1.3 65.3 + - - +
269A GLY 4.0 0.9 + - - +
272A SER 4.4 4.7 - - - +
273A ALA* 3.0 43.9 + - + +
274A PHE 3.4 8.1 + - - -
279A GLU* 2.5 43.4 + - - -
150B TYR* 6.3 0.2 - - - -
153B SER* 3.8 28.1 + - - +
154B ARG* 3.6 39.3 + - - +
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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