Contacts of the helix formed by residues 269 - 284 (chain B) in PDB entry 5TQB
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 MSE 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B ARG* 3.6 32.5 - - + +
234B LEU* 3.3 30.7 - - + -
235B ARG* 4.4 18.2 - - - +
238B LEU* 5.5 0.4 - - - -
264B LEU* 2.8 32.1 + - + +
267B VAL* 3.1 34.5 - - + +
268B ASP* 1.3 76.2 - - - +
270B GLU* 1.3 62.8 + - - +
271B GLU* 3.2 5.2 - - - -
272B GLU* 3.2 30.5 + - - +
273B ALA* 3.1 19.1 + - - +
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Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU 4.9 0.4 - - - -
265B ILE* 4.3 15.0 - - - +
268B ASP* 3.2 26.4 - - - +
269B MSE 1.3 69.8 - - - +
271B GLU* 1.3 67.0 + - - +
273B ALA* 3.0 9.5 + - - +
274B LEU* 2.8 37.6 + - + +
297B ALA* 3.7 28.0 - - + +
300B ARG* 4.0 16.4 + - + +
301B LEU* 4.1 15.7 - - + +
304B LYS* 2.4 45.7 + - - +
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASP 4.2 3.0 - - - +
269B MSE 3.8 4.3 - - - +
270B GLU* 1.3 92.6 + - - +
272B GLU* 1.3 71.0 + - - +
274B LEU* 3.4 19.0 + - - +
275B GLU* 3.6 15.5 + - - +
301B LEU* 4.0 28.1 - - + +
304B LYS* 6.0 1.4 - - - +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ARG* 5.0 9.0 - - + +
238B LEU* 4.1 23.1 - - + -
264B LEU* 4.0 15.3 - - + -
269B MSE 3.3 40.4 - - + +
270B GLU 3.2 0.2 - - - -
271B GLU* 1.3 84.1 - - - +
273B ALA* 1.3 65.6 + - - +
275B GLU* 3.3 15.8 + - - +
276B VAL* 3.2 25.1 + - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B VAL* 4.4 8.7 - - + -
264B LEU* 3.7 24.6 - - + +
265B ILE* 4.2 17.3 - - + -
269B MSE 3.1 12.6 + - - +
270B GLU* 3.0 14.8 + - - +
272B GLU* 1.3 76.2 - - - +
274B LEU* 1.3 57.9 + - - +
276B VAL* 3.8 2.8 - - - +
277B THR* 2.9 35.4 + - - +
297B ALA* 4.2 7.4 - - + -
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLU 2.8 26.2 + - - +
271B GLU* 3.5 11.9 - - - +
272B GLU 3.2 0.4 - - - -
273B ALA* 1.3 76.8 - - - +
275B GLU* 1.3 61.9 + - + +
277B THR* 3.0 18.0 + - - -
278B GLU* 3.1 12.9 + - - +
297B ALA* 4.1 21.1 - - + +
298B ARG* 3.4 50.5 + - + +
301B LEU* 3.9 24.2 - - + -
321B THR* 5.8 1.6 - - + -
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B THR* 6.2 0.3 - - - +
271B GLU 3.8 12.8 - - - +
272B GLU* 3.3 17.1 + - - +
274B LEU* 1.3 74.5 - - + +
276B VAL* 1.3 67.8 + - + +
278B GLU* 3.3 7.1 + - - +
279B ARG* 3.2 22.3 + - - +
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B LEU* 4.2 20.0 - - + -
241B TRP* 4.4 16.2 - - + -
242B THR* 5.6 2.2 - - + -
257B ARG* 4.2 12.3 - - + +
260B LEU* 4.3 11.4 - - + -
261B VAL* 3.7 22.9 - - + -
264B LEU* 4.1 13.0 - - + -
272B GLU 3.2 16.6 + - - +
273B ALA* 3.4 5.1 + - - +
275B GLU* 1.3 78.6 - - + +
277B THR* 1.3 60.8 + - - +
279B ARG* 3.4 6.4 + - - +
280B LEU* 3.1 33.2 + - + +
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Residues in contact with THR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B VAL* 3.8 31.0 - - + -
273B ALA* 2.9 24.8 + - + +
274B LEU* 3.0 12.1 + - - -
276B VAL* 1.3 75.5 - - - +
278B GLU* 1.3 61.4 + - - +
280B LEU* 3.8 8.5 - - + +
281B ILE* 3.1 28.6 + - - +
290B VAL* 3.9 7.8 - - + +
293B LEU* 4.4 3.1 - - + +
294B GLY* 3.9 26.0 - - - +
297B ALA* 5.4 0.4 - - + -
298B ARG* 3.2 18.2 + - - -
328B TRP* 3.9 6.1 - - - -
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A HIS* 4.8 12.3 + - - +
204A ARG* 4.5 28.0 + - - +
274B LEU 3.1 16.3 + - - +
275B GLU* 3.7 7.5 - - - +
276B VAL 3.2 0.2 - - - -
277B THR* 1.3 76.8 + - - +
279B ARG* 1.3 64.3 + - - +
281B ILE* 3.4 1.3 + - - -
282B ALA* 3.1 18.6 + - - +
298B ARG* 3.9 14.3 + - - +
328B TRP* 4.2 8.7 - - + -
402B EDO 3.3 28.6 + - - +
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Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.7 27.5 - - - +
241B TRP* 4.0 26.2 + - + -
242B THR* 3.8 21.0 + - - +
244B LEU 4.2 10.5 + - - -
246B PRO* 4.0 24.5 - - - +
251B VAL* 4.3 12.1 - - - +
257B ARG* 3.5 19.3 - - - +
275B GLU 3.2 12.7 + - - +
276B VAL* 3.7 9.2 - - - +
278B GLU* 1.3 77.6 - - - +
280B LEU* 1.3 62.4 + - - +
282B ALA* 3.0 17.6 + - - +
283B GLU* 3.3 20.6 + - - +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B PHE* 3.4 43.9 - - + +
257B ARG* 3.4 55.4 - - + +
258B VAL* 4.5 2.9 - - + +
261B VAL* 4.2 9.2 - - + -
276B VAL* 3.1 35.8 + - + +
277B THR* 3.8 7.6 - - - +
278B GLU 3.3 0.2 - - - -
279B ARG* 1.3 77.0 - - - +
281B ILE* 1.3 57.8 + - - +
283B GLU* 3.0 3.6 + - - -
284B ASP 3.0 23.7 + - - +
290B VAL* 3.9 23.6 - - + -
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ARG* 4.5 1.3 - - - +
248A GLY* 3.6 3.6 - - - -
277B THR 3.1 18.5 + - - +
278B GLU 3.9 3.6 - - - +
279B ARG 3.3 0.2 - - - -
280B LEU* 1.3 71.0 - - - +
282B ALA* 1.3 61.0 + - - +
283B GLU 3.0 6.1 + - - -
284B ASP 3.9 13.2 - - - +
285B ASP* 3.5 18.8 + - + +
287B SER 4.4 0.4 - - - +
290B VAL* 3.6 21.8 - - + -
291B TRP* 3.6 58.8 - - + +
328B TRP* 3.5 21.5 - - + -
402B EDO 3.5 24.5 + - - +
403B EDO 4.9 0.2 - - - +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ARG* 5.6 7.9 - - - +
243A LEU* 4.1 28.5 - - + +
246A ALA 4.1 3.8 - - - +
247A PRO* 4.0 4.1 - - + +
248A GLY 3.0 19.0 + - - +
249A GLY 4.0 0.5 + - - -
278B GLU 3.1 12.5 + - - +
279B ARG* 3.0 15.3 + - - +
281B ILE* 1.3 76.8 - - - +
283B GLU* 1.3 57.1 + - - +
402B EDO 3.5 22.6 - - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.8 3.9 - - - +
40A HIS* 3.3 50.1 + - + +
243A LEU* 3.4 25.4 - - + +
246A ALA 5.5 0.4 - - - -
249A GLY* 3.3 21.4 - - - +
246B PRO* 4.5 11.1 - - - +
251B VAL* 5.5 0.2 - - - +
254B PHE* 3.7 7.8 - - + -
257B ARG* 3.0 39.2 + - - -
279B ARG* 3.5 19.6 + - - +
280B LEU 3.0 7.0 + - - +
282B ALA* 1.3 78.9 - - - +
284B ASP* 1.3 61.6 + - - +
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LYS* 3.8 33.4 - - + +
40A HIS* 4.6 11.8 - - + +
41A THR* 5.7 1.4 - - - -
51A TYR* 4.2 6.8 + - - -
248A GLY 3.5 5.3 - - - +
249A GLY* 4.8 0.7 - - - -
254B PHE* 4.0 17.5 - - + -
280B LEU 3.0 11.2 + - - +
281B ILE* 3.6 8.3 + - - +
283B GLU* 1.3 80.0 - - - +
285B ASP* 1.3 59.1 + - - +
286B LEU* 2.9 27.0 + - - +
287B SER* 3.5 27.5 + - - -
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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