Contacts of the helix formed by residues 244 - 259 (chain A) in PDB entry 3L0I
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 ILE 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A VAL* 6.4 1.1 - - + -
239A SER 5.1 0.7 - - - +
240A VAL* 3.6 16.2 + - + +
242A THR 3.6 0.6 - - - -
243A HIS* 1.3 90.4 - - + +
245A MSE 1.3 67.8 - - - +
246A ARG 3.3 1.1 - - - -
247A PRO* 3.2 11.7 - - - +
248A ILE* 3.1 22.5 + - + +
295A VAL* 3.9 27.6 - - + -
299A ALA* 4.0 16.8 - - + -
317A MSE 3.6 30.5 - - + -
325A MSE 4.1 22.4 - - + -
326A LEU* 4.5 13.2 - - + -
329A VAL* 4.1 15.5 - - + -
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Residues in contact with MSE 245 (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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240A VAL* 3.1 17.6 + - - +
241A LYS* 4.2 9.6 - - + +
244A ILE* 1.3 78.4 - - - +
246A ARG* 1.3 57.1 + - - +
248A ILE* 3.3 6.9 + - - +
249A ASP* 2.9 45.3 + - - +
296A TYR* 4.7 20.4 - - + +
299A ALA* 3.7 35.7 - - + +
300A MSE 4.6 8.7 - - - +
303A ARG* 4.1 40.8 - - - +
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Residues in contact with ARG 246 (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 PHE* 4.5 11.2 - - + -
241A LYS* 3.0 25.7 + - + +
242A THR* 4.4 6.3 - - - +
245A MSE 1.3 73.4 - - - +
247A PRO* 1.4 72.8 - - + +
249A ASP* 3.2 7.7 + - - +
250A PHE* 3.1 37.8 + - + -
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Residues in contact with PRO 247 (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 ALA* 3.6 30.0 - - + +
228A PHE* 3.7 25.3 - - + +
242A THR 3.6 11.2 - - - +
243A HIS 3.3 22.7 - - - +
244A ILE* 3.2 13.2 - - - +
246A ARG* 1.4 94.5 - - + +
248A ILE* 1.3 57.0 + - + +
250A PHE* 3.3 1.6 + - + +
251A MSE 2.7 36.7 + - - +
329A VAL* 5.3 6.1 - - + -
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 3.1 28.6 + - + +
245A MSE 3.7 7.4 - - - +
246A ARG 3.2 0.2 - - - -
247A PRO* 1.3 81.1 - - + +
249A ASP* 1.3 57.9 + - - +
251A MSE 3.2 4.5 + - + +
252A LEU* 2.8 34.8 + - + +
292A ILE* 4.2 20.6 - - + +
295A VAL* 4.7 10.3 - - + -
296A TYR* 3.7 36.8 - - + -
329A VAL* 5.2 5.8 - - + -
332A ILE* 4.0 39.7 - - + -
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Residues in contact with ASP 249 (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 MSE 2.9 35.1 + - - +
246A ARG* 3.7 6.9 + - - +
248A ILE* 1.3 75.9 - - - +
250A PHE* 1.3 58.1 + - + +
252A LEU* 3.6 11.3 + - - +
253A MSE 3.3 40.7 + - + +
271A ALA* 5.3 1.0 - - - +
296A TYR* 3.4 30.3 + - - -
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Residues in contact with PHE 250 (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 PHE* 3.6 55.2 - + - +
223A LYS* 4.6 32.1 - - + -
224A ALA* 4.4 3.8 - - + +
228A PHE* 4.9 12.1 - + - -
246A ARG* 3.1 36.1 + - + -
247A PRO* 3.7 7.2 - - + +
249A ASP* 1.3 74.8 - - + +
251A MSE 1.3 61.1 + - - +
252A LEU 3.2 0.2 - - - -
253A MSE 3.2 21.1 + - + -
254A GLY* 2.8 25.3 + - - -
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Residues in contact with MSE 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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221A TYR* 3.7 30.0 - - + +
224A ALA* 4.0 17.4 - - - +
247A PRO 2.7 21.7 + - - +
248A ILE* 3.2 13.0 + - + +
250A PHE* 1.3 73.4 - - - +
252A LEU* 1.3 55.8 + - - +
254A GLY 4.5 0.2 - - - +
255A LEU* 3.2 41.1 + - + +
292A ILE* 4.9 6.1 - - + -
332A ILE* 3.4 43.1 - - + +
333A ARG* 5.8 0.7 - - - -
335A LEU* 3.8 23.3 - - + +
336A GLY* 3.6 24.2 - - - +
339A ARG* 5.5 0.4 - - + -
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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
----------------------------------------------------------
248A ILE* 2.8 31.4 + - + +
249A ASP* 3.9 14.4 - - - +
251A MSE 1.3 76.1 - - - +
253A MSE 1.3 59.9 + - - +
254A GLY 3.2 0.4 - - - -
255A LEU* 3.4 14.9 + - + +
256A ARG* 2.9 40.6 + - - +
271A ALA* 3.7 33.0 - - + +
274A THR* 3.8 26.2 - - + +
275A ILE* 4.4 19.7 - - + -
278A LEU* 5.1 2.0 - - + -
292A ILE* 4.5 12.3 - - + -
296A TYR* 4.9 3.4 - - + -
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Residues in contact with MSE 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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220A PHE* 4.0 26.5 - - + -
249A ASP* 3.3 28.8 + - + +
250A PHE* 3.2 34.6 + - + +
252A LEU* 1.3 75.9 - - - +
254A GLY* 1.3 60.5 + - - +
256A ARG* 3.4 28.3 - - - +
257A GLU* 3.0 30.8 + - - +
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Residues in contact with GLY 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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217A ALA* 3.9 9.7 - - - +
220A PHE* 3.9 13.7 - - - +
221A TYR* 3.2 27.6 + - - -
250A PHE 2.8 16.0 + - - -
252A LEU 3.2 0.2 - - - -
253A MSE 1.3 73.3 - - - +
255A LEU* 1.3 54.6 + - - +
256A ARG 3.0 4.0 - - - -
257A GLU 3.3 1.2 + - - -
258A GLU* 2.9 27.9 + - - +
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Residues in contact with LEU 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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221A TYR* 3.1 22.0 + - + +
251A MSE 3.2 26.1 + - + +
252A LEU* 3.7 14.4 - - + +
254A GLY* 1.3 74.6 - - - +
256A ARG* 1.3 59.0 + - - +
258A GLU* 4.2 1.8 - - - +
259A PHE* 3.2 49.4 + - + -
261A LEU* 3.3 11.7 - - + +
274A THR* 5.2 1.1 - - + -
278A LEU* 4.1 27.6 - - + -
284A LEU* 3.8 22.4 - - + -
292A ILE* 4.1 24.0 - - + -
335A LEU* 5.3 3.6 - - + -
339A ARG* 5.0 3.8 - - - +
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Residues in contact with ARG 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 LEU* 2.9 24.7 + - - +
253A MSE 3.4 30.2 - - - +
254A GLY 3.0 0.2 - - - -
255A LEU* 1.3 79.1 - - - +
257A GLU* 1.3 61.5 + - + +
260A ASN* 3.2 7.4 + - - -
261A LEU* 3.0 50.6 + - + +
268A HIS* 3.7 24.4 - - - +
269A LEU* 3.8 28.6 + - - +
270A SER 3.9 9.3 + - - -
271A ALA* 4.8 1.8 - - - +
274A THR* 2.8 33.7 + - - +
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Residues in contact with GLU 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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212A SER* 3.5 34.1 - - - +
213A ASN* 3.2 27.2 + - - +
214A MSE 4.3 1.4 - - - +
216A SER* 3.7 12.2 - - - -
217A ALA* 3.9 19.0 - - + +
220A PHE* 3.1 27.8 - - + -
253A MSE 3.0 18.0 + - - +
254A GLY 3.3 0.2 + - - -
256A ARG* 1.3 77.1 - - + +
258A GLU* 1.3 64.2 + - - +
259A PHE 3.5 0.2 - - - -
260A ASN* 4.0 2.8 + - - +
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Residues in contact with GLU 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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210A SER 5.5 4.5 + - - -
214A MSE 4.3 30.5 - - + +
217A ALA* 3.7 10.5 - - + +
221A TYR* 3.1 18.8 + - + +
254A GLY 2.9 16.3 + - - +
257A GLU* 1.3 78.9 - - - +
259A PHE* 1.3 78.4 + - + +
260A ASN* 3.7 0.7 + - - +
339A ARG* 2.9 51.3 + - - +
342A ARG* 4.2 18.2 + - - +
343A ILE* 4.8 6.1 - - + +
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Residues in contact with PHE 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 LEU* 3.2 49.6 + - + +
258A GLU* 1.3 94.0 - - + +
260A ASN* 1.3 70.7 + - - +
261A LEU* 3.1 7.0 + - + +
278A LEU* 4.1 7.0 - - + -
283A LEU* 3.5 65.3 - - + +
284A LEU* 4.6 1.1 - - + -
339A ARG* 3.5 27.8 - - - -
342A ARG* 6.2 0.7 - - - -
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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