Contacts of the helix formed by residues 243 - 291 (chain U) in PDB entry 5MQF
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 THR 243 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242U VAL* 3.8 28.9 - - - +
244U MSE 3.8 27.8 - - - +
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Residues in contact with MSE 244 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243U THR* 3.8 26.0 - - - +
245U ASP* 3.8 28.7 - - - +
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Residues in contact with ASP 245 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244U MSE 3.8 28.9 - - - +
246U LYS* 3.8 26.2 - - - +
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Residues in contact with LYS 246 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245U ASP* 3.8 26.0 - - - +
247U VAL* 3.8 29.2 - - - +
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Residues in contact with VAL 247 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246U LYS* 3.8 27.1 - - - +
248U HIS* 3.8 28.9 - - - +
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Residues in contact with HIS 248 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247U VAL* 3.8 29.2 - - - +
249U TYR* 3.8 26.2 - - - +
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Residues in contact with TYR 249 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248U HIS* 3.8 25.4 - - - +
250U CYS* 3.8 28.9 - - - +
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Residues in contact with CYS 250 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249U TYR* 3.8 29.2 - - - +
251U GLU* 3.8 26.0 - - - +
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Residues in contact with GLU 251 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250U CYS* 3.8 29.2 - - - +
252U ARG* 3.8 26.7 - - - +
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Residues in contact with ARG 252 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251U GLU* 3.8 25.4 - - - +
253U PHE* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with PHE 253 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252U ARG* 3.8 29.2 - - - +
254U ILE* 3.8 27.1 - - - +
----------------------------------------------------------
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Residues in contact with ILE 254 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253U PHE* 3.8 28.9 - - - +
255U GLU* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with GLU 255 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254U ILE* 3.8 29.4 - - - +
256U LEU* 3.8 25.1 - - - +
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Residues in contact with LEU 256 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255U GLU* 3.8 28.0 - - - +
257U MSE 3.8 27.1 - - - +
----------------------------------------------------------
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Residues in contact with MSE 257 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256U LEU* 3.8 29.8 - - - +
258U ILE* 3.8 26.0 - - - +
----------------------------------------------------------
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Residues in contact with ILE 258 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257U MSE 3.8 26.9 - - - +
259U ASP* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with ASP 259 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258U ILE* 3.8 29.4 - - - +
260U LEU* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 260 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259U ASP* 3.8 25.4 - - - +
261U GLU* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 261 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260U LEU* 3.8 28.9 - - - +
262U ALA* 3.8 26.9 - - - +
267U ARG* 4.7 17.7 - - - +
----------------------------------------------------------
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Residues in contact with ALA 262 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261U GLU* 3.8 27.4 - - - +
263U LEU* 3.8 28.5 - - - +
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Residues in contact with LEU 263 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262U ALA* 3.8 28.7 - - - +
264U LEU* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 264 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263U LEU* 3.8 28.9 - - - +
265U PRO* 3.8 27.1 - - - -
----------------------------------------------------------
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Residues in contact with PRO 265 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264U LEU* 3.8 26.0 - - - -
266U THR* 3.8 29.2 - - - -
----------------------------------------------------------
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Residues in contact with THR 266 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265U PRO* 3.8 26.2 - - - -
267U ARG* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 267 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261U GLU* 4.7 19.5 - - - +
266U THR* 3.8 28.7 - - - +
268U ARG* 3.8 27.6 - - - +
----------------------------------------------------------
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Residues in contact with ARG 268 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267U ARG* 3.8 26.9 - - - +
269U TRP* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with TRP 269 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268U ARG* 3.8 27.6 - - - +
270U PHE* 3.8 28.5 - - - +
----------------------------------------------------------
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Residues in contact with PHE 270 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269U TRP* 3.8 29.2 - - - +
271U ASN* 3.8 26.2 - - - +
----------------------------------------------------------
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Residues in contact with ASN 271 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270U PHE* 3.8 25.6 - - - +
272U THR* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with THR 272 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271U ASN* 3.8 28.5 - - - +
273U ILE* 3.8 26.0 - - - +
----------------------------------------------------------
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Residues in contact with ILE 273 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272U THR* 3.8 26.2 - - - +
274U LEU* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 274 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273U ILE* 3.8 26.0 - - - +
275U ASP* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with ASP 275 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274U LEU* 3.8 29.4 - - - +
276U ASP* 3.8 26.0 - - - +
----------------------------------------------------------
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Residues in contact with ASP 276 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275U ASP* 3.8 25.6 - - - +
277U SER* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with SER 277 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276U ASP* 3.8 28.5 - - - +
278U HIS* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with HIS 278 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277U SER* 3.8 25.4 - - - +
279U LEU* 3.8 28.5 - - - +
----------------------------------------------------------
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Residues in contact with LEU 279 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278U HIS* 3.8 26.0 - - - +
280U LEU* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 280 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279U LEU* 3.8 29.8 - - - +
281U VAL* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL 281 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280U LEU* 3.8 26.0 - - - +
282U HIS* 3.8 28.3 - - - +
----------------------------------------------------------
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Residues in contact with HIS 282 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281U VAL* 3.8 25.8 - - - +
283U CYS* 3.8 28.5 - - - +
----------------------------------------------------------
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Residues in contact with CYS 283 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282U HIS* 3.8 28.9 - - - +
284U TYR* 3.8 27.1 - - - +
----------------------------------------------------------
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Residues in contact with TYR 284 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283U CYS* 3.8 27.1 - - - +
285U LEU* 3.8 28.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 285 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284U TYR* 3.8 26.2 - - - +
286U SER* 3.8 28.7 - - - +
----------------------------------------------------------
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Residues in contact with SER 286 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285U LEU* 3.8 28.9 - - - +
287U ASN* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with ASN 287 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286U SER* 3.8 28.9 - - - +
288U LEU* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 288 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287U ASN* 3.8 29.2 - - - +
289U VAL* 3.8 27.8 - - - +
----------------------------------------------------------
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Residues in contact with VAL 289 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288U LEU* 3.8 25.4 - - - +
290U ARG* 3.8 29.2 - - - +
----------------------------------------------------------
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Residues in contact with ARG 290 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289U VAL* 3.8 29.4 - - - +
291U ARG* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with ARG 291 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290U ARG* 3.8 27.1 - - - +
292U GLU* 3.8 28.9 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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