Contacts of the helix formed by residues 239 - 253 (chain A) in PDB entry 5LUQ
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 GLU 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A MSE 1.3 112.1 - - + +
240A GLU* 1.3 91.2 + - + +
241A ASP 4.6 0.6 - - - +
242A PRO* 3.1 17.3 - - - +
243A GLN* 2.9 29.2 + - - +
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Residues in contact with GLU 240 (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 ARG* 4.6 17.2 + - - +
201A LEU* 3.4 34.0 - - + +
205A LYS* 4.8 4.7 - - + +
227A LEU* 4.8 10.9 - - + +
237A SER* 5.0 4.6 + - - +
238A MSE 4.8 0.4 - - - +
239A GLU* 1.3 98.3 - - + +
241A ASP* 1.3 60.8 + - - +
242A PRO 3.5 0.2 - - - -
243A GLN* 3.6 10.9 + - - +
244A THR* 2.8 41.9 + - + +
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Residues in contact with ASP 241 (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 LEU* 3.6 14.2 - - - +
231A LEU* 3.3 22.7 - - - +
237A SER* 2.8 30.5 + - - +
240A GLU* 1.3 77.0 - - - +
242A PRO* 1.3 57.1 - - + +
244A THR* 3.3 5.2 - - - -
245A SER* 2.2 38.5 + - - -
272A LEU* 4.3 6.5 - - + -
275A PHE* 3.6 15.0 - - - -
279A ALA* 3.5 11.8 - - + +
282A PHE* 3.1 20.4 - - + -
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Residues in contact with PRO 242 (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 4.7 0.2 - - - +
239A GLU* 3.1 28.3 - - - +
241A ASP* 1.3 88.2 - - - +
243A GLN* 1.3 60.2 + - + +
245A SER* 3.5 1.3 - - - +
246A ARG* 2.5 47.0 + - + +
282A PHE* 3.2 56.9 - - + -
286A LEU* 5.0 8.3 - - + -
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Residues in contact with GLN 243 (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 LYS* 2.3 43.2 + - - +
239A GLU* 2.9 24.7 + - - +
240A GLU* 3.7 5.9 - - - +
242A PRO* 1.3 74.4 - - + +
244A THR* 1.3 69.0 + - - +
246A ARG* 4.1 16.1 - - - +
247A GLU* 2.9 37.7 + - - +
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Residues in contact with THR 244 (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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201A LEU* 6.0 5.6 - - + -
205A LYS* 4.1 28.5 - - + -
208A MSE 5.2 7.2 - - + +
224A LEU* 5.2 7.4 - - + -
227A LEU* 4.0 20.3 - - + +
240A GLU* 2.8 24.4 + - + +
241A ASP* 2.9 11.3 + - - -
243A GLN* 1.3 78.4 - - - +
245A SER* 1.3 70.5 + - - +
247A GLU* 3.3 9.8 + - - +
248A ILE* 3.0 32.6 + - - +
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Residues in contact with SER 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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241A ASP* 2.2 30.3 + - - -
242A PRO* 3.2 5.4 + - - +
244A THR* 1.3 76.9 + - - +
246A ARG* 1.3 59.9 + - - +
248A ILE* 2.6 38.5 + - - +
249A PHE* 2.9 17.9 + - - -
268A PRO* 4.3 5.8 - - - -
272A LEU* 3.5 38.2 - - - +
282A PHE* 4.3 1.2 - - - -
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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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242A PRO* 2.5 26.2 + - + +
243A GLN* 4.1 13.9 - - - +
245A SER* 1.3 75.9 + - - +
247A GLU* 1.3 91.3 + - - +
249A PHE* 3.0 26.9 + - - +
250A ASN* 3.0 35.4 + - - +
286A LEU* 4.9 8.7 - - + -
290A TYR* 3.8 39.0 + - + -
293A LEU* 4.2 22.1 - - + +
297A LEU* 4.8 0.8 - - + +
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Residues in contact with GLU 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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205A LYS* 4.4 9.3 - - - +
208A MSE 3.7 25.3 - - - +
209A THR* 4.7 13.7 - - - +
243A GLN* 2.9 39.0 + - - +
244A THR* 3.4 6.0 - - - +
246A ARG* 1.3 97.4 + - - +
248A ILE* 1.3 63.6 + - - +
250A ASN* 2.9 12.3 + - - +
251A PHE* 2.9 50.8 + - + -
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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
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208A MSE 5.5 2.0 - - - -
220A LEU* 5.0 9.2 - - + -
224A LEU* 3.5 41.7 - - + -
244A THR* 3.0 20.7 + - - +
245A SER* 2.6 16.0 + - - +
247A GLU* 1.3 71.5 - - + +
249A PHE* 1.3 61.2 + - - +
251A PHE* 3.0 15.5 + - + +
252A VAL* 3.0 27.9 + - + +
264A ARG* 3.5 31.6 - - + +
265A TYR* 4.6 1.3 - - - -
268A PRO* 3.4 31.0 - - + -
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Residues in contact with PHE 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 SER* 2.9 41.2 + - - -
246A ARG* 3.0 14.1 + - - +
248A ILE* 1.3 76.8 - - - +
250A ASN* 1.3 63.2 + - - +
251A PHE 3.1 0.3 + - - -
252A VAL* 3.3 1.7 + - - -
253A LEU* 2.9 28.2 + - - +
265A TYR* 3.2 41.8 - + - -
268A PRO* 4.6 3.4 - - + -
269A SER* 3.8 32.5 - - - -
272A LEU* 3.4 31.9 - - + -
297A LEU* 3.3 37.0 - - + -
298A LEU* 4.9 4.0 - - + -
319A PHE* 5.1 5.2 - + - -
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Residues in contact with ASN 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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246A ARG* 3.0 37.7 + - - +
247A GLU* 2.9 13.2 + - - +
249A PHE* 1.3 74.7 - - - +
251A PHE* 1.3 68.3 + - + +
253A LEU* 3.1 37.6 + - - +
254A LYS* 4.1 10.2 - - - +
293A LEU* 4.4 22.7 - - - +
297A LEU* 4.5 1.2 - - - +
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Residues in contact with PHE 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 MSE 4.1 30.1 - - + -
215A PRO* 4.1 44.2 - - + +
220A LEU* 4.8 9.2 - - + -
247A GLU* 2.9 52.9 + - + -
248A ILE* 3.0 15.0 + - + +
250A ASN* 1.3 89.0 - - + +
252A VAL* 1.3 63.7 + - + +
253A LEU 3.7 0.2 + - - -
254A LYS* 3.8 27.3 + - - +
255A ALA 4.3 2.3 + - - -
261A ASP* 5.4 1.9 - - - +
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Residues in contact with VAL 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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248A ILE* 3.0 14.4 + - + +
249A PHE 3.8 0.2 - - - -
251A PHE* 1.3 74.9 - - + +
253A LEU* 1.3 53.9 + - - +
254A LYS 2.7 17.9 + - - -
255A ALA* 3.8 10.9 + - + +
261A ASP* 3.9 26.2 - - - +
262A LEU* 4.8 11.4 - - + -
264A ARG* 4.2 8.3 - - + -
265A TYR* 3.4 56.8 - - + +
300A TRP* 3.7 18.5 - - + -
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Residues in contact with LEU 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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249A PHE 2.9 21.7 + - - +
250A ASN* 3.1 24.9 + - - +
252A VAL* 1.3 74.5 - - - +
254A LYS* 1.3 64.1 + - - +
265A TYR* 5.1 3.1 - - + -
293A LEU* 6.0 1.8 - - + -
296A VAL* 5.0 7.9 - - + -
297A LEU* 3.5 43.3 - - + +
300A TRP* 3.5 42.4 - - + -
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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