Contacts of the helix formed by residues 266 - 283 (chain A) in PDB entry 3IE7
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 PRO 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ASN 3.7 4.7 - - - +
265A MSE 1.3 88.2 - - - +
267A ILE* 1.3 68.0 + - + +
268A THR* 4.5 11.2 - - - +
269A GLU* 3.1 24.9 + - + +
270A THR* 3.0 16.1 + - - -
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Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 4.0 19.1 - - + -
227A CYS* 4.2 9.6 - - - -
229A HIS* 4.0 30.1 - - + +
234A TYR* 3.5 31.6 - - + +
257A PHE* 3.9 32.3 - - + -
261A LEU* 5.0 2.2 - - + -
265A MSE 3.5 1.2 + - - -
266A PRO* 1.3 71.0 - - - +
268A THR* 1.3 67.3 + - + +
270A THR* 3.3 8.0 + - + -
271A LEU* 3.0 34.2 + - + +
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR* 3.7 35.0 - - + +
266A PRO* 4.5 8.0 - - - +
267A ILE* 1.3 78.8 - - + +
269A GLU* 1.3 58.9 + - - +
271A LEU* 3.3 2.1 + - - -
272A LYS* 3.0 36.6 + - - +
304A ILE* 3.3 30.2 - - + +
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Residues in contact with GLU 269 (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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265A MSE 3.6 28.3 - - - +
266A PRO* 3.1 31.2 + - + +
268A THR* 1.3 79.6 + - - +
270A THR* 1.3 60.3 + - - +
272A LYS* 3.1 11.3 + - - +
273A VAL* 2.9 28.2 + - - +
299A LYS* 3.0 30.4 + - - +
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Residues in contact with THR 270 (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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256A ALA 4.9 0.2 - - - +
257A PHE* 3.3 51.3 - - + +
260A GLY* 3.6 11.4 - - - -
261A LEU* 4.0 9.5 + - + +
265A MSE 3.2 34.9 + - - +
266A PRO 3.0 4.5 + - - -
267A ILE* 3.6 12.1 - - - -
269A GLU* 1.3 76.7 - - - +
271A LEU* 1.3 56.7 + - - +
273A VAL* 3.3 6.6 + - - +
274A ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 271 (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 VAL* 4.6 0.7 - - + -
225A SER* 4.8 1.1 - - - +
227A CYS* 3.8 31.2 - - + -
234A TYR* 4.2 15.0 - - + -
236A VAL* 3.9 22.7 - - + -
253A PHE* 4.2 17.0 - - + -
257A PHE* 3.8 21.3 - - + -
267A ILE* 3.0 36.5 + - + +
268A THR* 3.6 4.3 - - - +
270A THR* 1.3 74.6 - - - +
272A LYS* 1.3 60.2 + - - +
274A ALA* 3.4 3.7 + - - +
275A THR* 2.8 35.3 + - - -
304A ILE* 3.6 14.6 - - + -
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Residues in contact with LYS 272 (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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268A THR* 3.0 26.5 + - - +
269A GLU* 3.1 10.7 + - - +
271A LEU* 1.3 75.8 - - - +
273A VAL* 1.3 58.9 + - - +
275A THR* 3.3 1.9 + - - -
276A GLY* 2.8 27.2 + - - -
299A LYS* 3.7 36.7 - - + +
300A ASN* 6.1 0.2 - - - -
302A VAL* 4.0 31.9 - - + +
304A ILE* 3.6 28.5 - - + +
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Residues in contact with VAL 273 (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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50A PHE* 4.0 32.1 - - + -
256A ALA* 4.3 10.3 - - + +
260A GLY* 5.7 1.1 - - - +
265A MSE 3.9 22.2 - - + -
269A GLU 2.9 19.9 + - - +
270A THR* 3.7 6.5 - - - +
272A LYS* 1.3 76.6 - - - +
274A ALA* 1.3 61.8 + - - +
276A GLY* 3.3 0.7 + - - -
277A CYS* 3.0 27.9 + - - -
299A LYS* 3.5 37.4 - - + +
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Residues in contact with ALA 274 (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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253A PHE* 3.5 49.6 - - + +
256A ALA* 3.6 12.1 - - - +
257A PHE* 3.9 10.8 - - + +
270A THR 2.9 17.4 + - - +
271A LEU 3.8 2.5 - - - +
272A LYS 3.3 0.2 - - - -
273A VAL* 1.3 76.8 - - - +
275A THR* 1.3 57.5 + - - +
277A CYS* 3.5 1.6 + - - +
278A SER* 2.9 31.2 + - - -
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Residues in contact with THR 275 (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 GLY* 5.6 0.4 - - - -
225A SER* 4.7 0.3 + - - -
236A VAL* 3.3 18.0 - - + +
238A PRO* 3.5 34.3 - - + -
253A PHE* 3.8 12.1 - - - -
271A LEU 2.8 21.9 + - - -
272A LYS 3.8 3.1 - - - -
274A ALA* 1.3 74.9 - - - +
276A GLY* 1.3 60.1 + - - +
278A SER* 3.1 7.3 + - - -
279A ALA* 2.9 29.1 + - - +
302A VAL* 3.7 22.0 - - + -
900A ATP 3.9 10.9 + - - +
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PRO* 6.0 0.2 - - - -
272A LYS 2.8 16.8 + - - -
273A VAL 3.3 0.9 + - - -
275A THR* 1.3 77.5 - - - +
277A CYS* 1.3 61.4 + - - +
279A ALA* 3.4 3.5 + - - +
280A SER* 3.1 22.2 + - - -
295A ALA* 3.7 13.7 - - - +
298A LEU* 3.8 9.6 - - - +
299A LYS* 3.9 22.7 - - - -
302A VAL* 4.3 1.7 - - - +
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Residues in contact with CYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.8 25.8 - - - -
252A VAL* 3.5 23.6 - - + +
256A ALA* 3.9 10.5 - - + -
273A VAL* 3.0 23.5 + - - +
274A ALA 3.9 0.4 - - - +
276A GLY* 1.3 73.5 - - - +
278A SER* 1.3 59.5 - - - +
280A SER* 3.2 4.9 + - - -
281A LYS* 3.0 22.3 + - - +
290A PHE* 3.6 26.3 - - + +
292A LEU* 4.8 2.2 - - - -
295A ALA* 3.7 17.0 - - - -
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Residues in contact with SER 278 (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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249A ALA 3.4 17.3 - - - -
252A VAL* 3.7 8.9 - - - +
253A PHE* 3.9 5.9 - - - -
274A ALA 2.9 19.8 + - - -
275A THR* 3.1 8.5 + - - -
277A CYS* 1.3 73.8 - - - +
279A ALA* 1.3 65.0 + - - +
281A LYS* 3.2 4.9 + - - +
282A VAL* 3.1 27.4 + - - +
900A ATP 3.0 40.4 + - - -
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Residues in contact with ALA 279 (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 PRO* 4.9 7.4 - - + -
239A PRO* 4.9 4.5 - - + -
241A VAL* 3.8 11.3 - - + +
275A THR 2.9 19.2 + - - +
276A GLY* 3.6 5.8 - - - +
277A CYS 3.2 0.2 - - - -
278A SER* 1.3 76.3 + - - +
280A SER* 1.3 64.5 + - - +
282A VAL* 3.3 11.6 + - - +
283A MSE 3.5 16.1 + - - +
298A LEU* 3.9 15.7 - - + -
900A ATP 4.0 25.8 - - + +
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Residues in contact with SER 280 (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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276A GLY 3.1 13.4 + - - -
277A CYS 3.5 8.7 - - - -
279A ALA* 1.3 77.9 - - - +
281A LYS* 1.3 62.2 + - - +
283A MSE 3.1 16.1 + - - +
284A GLN* 3.1 22.2 + - - -
290A PHE* 4.1 1.3 - - - -
291A ASP* 2.8 49.1 + - - +
294A ALA* 4.0 3.4 - - - +
295A ALA* 4.2 4.9 - - - -
298A LEU* 3.8 15.0 - - - +
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Residues in contact with LYS 281 (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 ASN 2.9 21.6 + - - -
247A THR 2.8 25.4 + - - -
248A GLY* 4.4 0.4 - - - -
249A ALA* 3.9 17.0 - - + +
252A VAL* 3.9 19.7 - - + -
277A CYS 3.0 13.5 + - - +
278A SER* 3.2 10.7 + - - +
280A SER* 1.3 77.2 - - - +
282A VAL* 1.3 58.4 + - - +
284A GLN* 2.9 21.0 + - - +
286A ASP* 2.8 21.7 + - - -
287A SER 3.2 1.8 - - - -
288A SER* 3.0 35.7 - - - +
289A SER 2.8 30.5 - - - +
290A PHE* 3.7 2.4 - - + +
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Residues in contact with VAL 282 (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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241A VAL* 4.8 2.5 - - + -
243A GLU* 3.2 43.5 - - + +
244A ARG 2.7 31.9 + - - -
245A ASN 3.2 14.2 + - - -
246A ASP* 4.0 9.4 - - + -
249A ALA* 3.8 17.7 - - + -
278A SER 3.1 15.6 + - - +
279A ALA 3.7 7.2 - - - +
280A SER 3.3 0.2 - - - -
281A LYS* 1.3 75.2 - - - +
283A MSE 1.3 52.0 + - - +
284A GLN 3.2 0.9 - - - -
900A ATP 3.6 36.1 - - + +
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Residues in contact with MSE 283 (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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241A VAL* 3.8 30.7 - - + -
242A GLN* 3.6 27.5 - - + +
244A ARG* 3.1 27.5 + - - -
279A ALA 3.5 13.5 - - - +
280A SER* 3.1 12.3 + - - +
281A LYS 3.0 0.8 - - - -
282A VAL* 1.3 78.1 - - - +
284A GLN* 1.3 67.8 + - - +
294A ALA* 5.4 8.7 - - + -
298A LEU* 4.2 15.0 - - - -
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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
------------------------------------------------------------
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