Contacts of the helix formed by residues 251 - 264 (chain A) in PDB entry 3MIZ
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 ASN 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A LEU* 3.4 28.8 - - + +
195A ARG* 4.1 7.2 - - - +
219A MSE 5.7 0.4 - - - +
249A SER* 2.7 29.0 + - - -
250A GLY* 1.3 77.2 - - - +
252A ASP* 1.3 64.7 + - - +
253A GLU* 3.3 17.3 + - - +
254A MSE 2.9 29.7 + - - +
255A ALA 3.4 0.2 + - - -
278A PHE 3.3 20.2 - - - +
279A ASP* 3.6 15.6 + - - +
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Residues in contact with ASP 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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251A ASN* 1.3 70.2 - - - +
253A GLU* 1.3 66.8 + - - +
255A ALA* 2.9 19.2 + - - +
277A GLY* 3.3 5.7 - - - -
278A PHE 2.7 39.7 + - - +
279A ASP* 4.7 0.6 + - - +
280A ASP* 2.5 32.9 + - - -
281A PHE* 2.8 23.1 + - + -
284A VAL* 3.4 15.8 - - + +
285A THR* 3.2 17.2 - - + +
292A LEU* 3.4 12.5 - - + +
294A THR* 2.8 7.7 + - - -
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Residues in contact with GLU 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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74A TYR* 3.4 42.0 + - - -
228A ASN* 5.9 0.5 + - - -
251A ASN* 3.3 17.4 + - - +
252A ASP* 1.3 79.2 - - - +
254A MSE 1.3 64.0 + - + +
256A ILE* 3.2 28.3 + - + +
257A GLN* 4.4 2.4 + - - +
279A ASP* 5.7 0.2 + - - -
281A PHE* 4.6 15.5 - - + -
284A VAL* 4.3 11.6 - - + +
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Residues in contact with MSE 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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183A ILE* 3.4 34.1 - - + +
184A ARG 3.3 21.1 - - - +
185A LEU* 3.8 18.4 - - - -
218A GLY* 4.2 1.1 - - - -
219A MSE 3.6 23.8 - - + -
228A ASN* 5.6 0.2 - - - +
230A VAL* 3.6 29.3 - - + +
249A SER* 3.2 13.9 - - - +
250A GLY* 3.6 24.7 - - - +
251A ASN* 2.9 21.6 + - - +
253A GLU* 1.3 74.9 - - + +
255A ALA* 1.3 63.0 + - - +
257A GLN* 3.1 17.1 + - - +
258A ILE* 3.4 13.4 + - - +
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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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249A SER* 3.2 22.1 + - - +
251A ASN 4.1 1.3 - - - +
252A ASP 2.9 15.9 + - - +
254A MSE 1.3 74.1 - - - +
256A ILE* 1.3 64.5 + - - +
258A ILE* 3.1 6.6 + - - -
259A TYR* 2.8 32.0 + - + -
275A ILE* 4.7 2.2 - - + -
288A LEU* 4.0 7.2 - - + -
292A LEU* 3.8 30.5 - - + -
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Residues in contact with ILE 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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252A ASP 3.7 0.2 + - - -
253A GLU* 3.5 20.2 - - + +
254A MSE 3.1 0.6 - - - -
255A ALA* 1.3 80.3 - - - +
257A GLN* 1.3 66.7 + - + +
259A TYR* 3.4 2.8 + - - +
260A ILE* 3.2 36.7 + - + +
284A VAL* 3.7 37.5 - - + -
288A LEU* 4.0 19.7 - - + +
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Residues in contact with GLN 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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228A ASN* 3.0 36.7 + - - +
229A TYR* 4.6 0.7 - - - -
230A VAL* 3.6 13.4 + - + +
231A PHE* 2.9 50.6 + - + +
253A GLU 5.3 1.9 + - - +
254A MSE 3.1 13.8 + - - +
256A ILE* 1.3 82.8 - - + +
258A ILE* 1.3 58.7 + - - +
260A ILE* 3.5 6.6 + - + -
261A ALA* 2.9 28.2 + - - +
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Residues in contact with ILE 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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183A ILE* 3.8 24.7 - - + -
230A VAL* 3.9 14.1 - - + -
234A ALA* 4.1 10.5 - - + -
238A LEU* 4.7 2.2 - - + +
247A ILE* 4.2 27.6 - - + -
249A SER* 3.5 39.9 - - - +
254A MSE 3.5 10.1 - - + +
255A ALA* 3.1 7.7 + - - +
257A GLN* 1.3 73.6 - - - +
259A TYR* 1.3 66.5 + - - +
261A ALA* 3.7 5.6 - - - +
262A ALA* 3.0 23.2 + - - +
275A ILE* 3.9 21.7 - - + +
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Residues in contact with TYR 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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255A ALA* 2.8 25.2 + - + +
256A ILE 3.6 5.8 - - - +
258A ILE* 1.3 75.9 - - - +
260A ILE* 1.3 60.0 + - + +
262A ALA* 3.3 1.7 + - - +
263A MSE 3.0 43.4 + - - +
269A ILE* 4.1 15.7 - - + -
275A ILE* 3.8 28.7 - - + -
288A LEU* 3.6 33.4 - - + -
289A LYS 3.6 19.5 - - - -
290A PRO* 2.8 33.9 + - + -
292A LEU* 3.6 25.2 - - + +
335A SER* 3.2 22.1 - - - -
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Residues in contact with ILE 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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231A PHE* 3.9 15.9 - - + -
256A ILE* 3.2 32.2 + - + +
257A GLN* 3.8 6.7 - - + +
259A TYR* 1.3 77.0 - - + +
261A ALA* 1.3 60.4 + - - +
263A MSE 4.7 7.0 - - - -
264A ALA* 2.9 37.4 + - + +
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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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231A PHE* 3.4 17.8 - - + -
234A ALA* 3.8 22.9 - - + -
235A THR* 3.7 21.9 + - - +
238A LEU* 4.3 4.0 - - + -
257A GLN 2.9 18.4 + - - +
258A ILE 3.7 4.5 - - - +
259A TYR 3.3 0.2 - - - -
260A ILE* 1.3 78.1 - - - +
262A ALA* 1.3 64.4 + - - +
264A ALA* 3.5 6.1 + - - +
265A LEU* 3.5 21.4 + - - +
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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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238A LEU* 3.7 19.7 - - + +
258A ILE 3.0 18.7 + - - +
259A TYR 3.7 3.1 - - - +
261A ALA* 1.3 77.3 - - - +
263A MSE 1.3 62.9 + - - +
265A LEU* 3.0 12.7 + - - +
266A GLY 3.5 0.2 + - - -
267A LEU* 3.0 28.4 + - + +
269A ILE* 4.3 10.8 - - + -
273A VAL* 4.1 23.1 - - + -
275A ILE* 4.7 2.2 - - + -
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Residues in contact with MSE 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 TYR* 3.0 33.8 + - - +
260A ILE* 4.1 6.5 - - - +
262A ALA* 1.3 70.1 - - - +
264A ALA* 1.3 58.4 + - - +
265A LEU 3.0 5.4 - - - -
266A GLY* 2.9 19.1 + - - -
267A LEU 3.6 14.8 - - - +
268A ARG* 5.9 0.4 - - - -
269A ILE* 4.3 18.6 - - + +
289A LYS 5.1 7.4 - - - +
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Residues in contact with ALA 264 (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 PHE* 4.7 13.0 - - + -
260A ILE* 2.9 23.4 + - + +
261A ALA* 3.7 8.1 - - - +
262A ALA 3.2 0.4 - - - -
263A MSE 1.3 76.0 - - - +
265A LEU* 1.3 62.3 + - + +
266A GLY 3.4 1.1 + - - -
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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