Contacts of the helix formed by residues 271 - 292 (chain B) 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 PRO 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU 4.6 0.4 - - - +
270B PRO* 1.3 89.3 - - + +
272B THR* 1.3 57.3 + - - +
274B ALA* 3.6 7.7 - - + +
275B TYR* 2.9 31.5 + - - +
370B VAL* 4.1 23.2 - - + +
374B LEU* 4.3 17.0 - - + +
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Residues in contact with THR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B PRO* 3.2 5.7 - - - -
271B PRO* 1.3 83.7 - - - +
273B ASP* 1.3 57.0 + - - +
275B TYR* 3.9 2.7 - - - +
276B TYR* 2.9 32.1 + - - +
366B GLN* 5.2 15.3 - - - -
370B VAL* 5.2 2.4 - - - +
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Residues in contact with ASP 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU* 5.8 9.0 - - + -
269B LEU* 5.1 5.6 - - + +
270B PRO* 3.3 30.3 + - + +
272B THR* 1.3 77.4 - - - +
274B ALA* 1.3 52.8 + - - +
276B TYR* 4.4 5.6 - - - -
277B LYS* 2.7 39.3 + - + +
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 5.3 9.6 - - + -
269B LEU* 4.9 12.3 - - + +
270B PRO 2.8 17.4 + - - +
271B PRO* 3.6 9.4 - - + +
272B THR 3.2 0.2 - - - -
273B ASP* 1.3 75.9 - - - +
275B TYR* 1.3 61.2 + - - +
277B LYS* 4.1 1.7 - - - +
278B LEU* 2.9 32.7 + - - +
374B LEU* 5.7 5.2 - - + -
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Residues in contact with TYR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO 2.9 17.1 + - - +
272B THR* 4.3 2.5 - - - +
274B ALA* 1.3 76.2 - - - +
276B TYR* 1.3 57.5 + - - +
278B LEU* 4.4 3.1 - - - +
279B ARG* 2.8 30.7 + - - +
367B ARG* 5.3 9.2 - - + -
369B PHE* 5.4 7.2 - - + -
370B VAL* 4.8 17.7 - - + +
374B LEU* 6.3 1.1 - - + -
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Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASN* 5.0 17.4 - - + +
360A SER* 6.0 7.4 - - - -
272B THR 2.9 19.8 + - - +
273B ASP* 4.4 4.0 - - - -
275B TYR* 1.3 77.6 - - - +
277B LYS* 1.3 59.6 + - - +
279B ARG* 3.5 5.5 + - - +
280B HIS* 2.9 27.7 + - - +
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASP* 2.7 23.6 + - + +
274B ALA* 4.1 2.7 - - - +
276B TYR* 1.3 75.8 - - - +
278B LEU* 1.3 59.1 + - - +
280B HIS* 3.1 8.9 + - - +
281B ILE* 2.9 26.9 + - - +
865B GLY* 5.3 13.7 - - - -
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ALA 2.9 19.7 + - - +
275B TYR* 4.4 3.4 - - - +
277B LYS* 1.3 76.0 - - - +
279B ARG* 1.3 57.3 + - - +
281B ILE* 3.2 7.7 + - - +
282B VAL* 2.9 29.5 + - - +
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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
----------------------------------------------------------
275B TYR 2.8 21.9 + - - +
276B TYR* 3.7 7.2 - - - +
277B LYS 3.2 0.2 - - - -
278B LEU* 1.3 76.5 - - - +
280B HIS* 1.3 56.6 + - - +
282B VAL* 3.8 6.4 - - - +
283B ASP* 2.9 27.5 + - - +
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Residues in contact with HIS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASN* 6.0 0.2 - - + -
358A PRO* 4.3 27.6 - - + -
276B TYR 2.9 18.1 + - - +
277B LYS* 3.1 8.3 + - - +
279B ARG* 1.3 76.9 - - - +
281B ILE* 1.3 59.5 + - - +
283B ASP* 3.2 7.9 + - - +
284B GLU* 2.9 27.7 + - - +
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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
----------------------------------------------------------
234B GLY* 5.3 13.9 - - - -
277B LYS 2.9 12.5 + - - +
278B LEU* 3.2 11.2 + - - +
280B HIS* 1.3 75.7 - - - +
282B VAL* 1.3 57.5 + - - +
284B GLU* 3.2 7.2 + - - +
285B VAL* 2.9 27.4 + - - +
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU 2.9 16.3 + - - +
279B ARG* 4.0 6.7 - - - +
281B ILE* 1.3 76.9 - - - +
283B ASP* 1.3 58.2 + - - +
285B VAL* 3.8 7.5 - - - +
286B ASN* 2.9 32.4 + - - +
300B LEU* 5.1 6.3 - - + +
301B SER* 5.7 2.2 - - - +
302B PRO* 5.3 13.7 - - + -
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A SER* 5.7 9.6 - - - -
279B ARG 2.9 20.2 + - - +
280B HIS* 3.5 9.9 - - - +
281B ILE 3.2 0.2 - - - -
282B VAL* 1.3 78.8 - - - +
284B GLU* 1.3 56.8 + - - +
286B ASN* 5.0 2.5 - - - -
287B GLY* 2.9 24.6 + - - -
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Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 5.7 9.6 - - + -
280B HIS 2.9 13.0 + - - +
281B ILE* 3.2 9.8 + - - +
283B ASP* 1.3 76.6 - - - +
285B VAL* 1.3 58.6 + - - +
287B GLY* 4.7 0.9 - - - -
288B LEU* 2.9 30.5 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B VAL* 5.2 14.4 - - + -
281B ILE 2.9 16.1 + - - +
282B VAL* 3.3 7.6 + - - +
284B GLU* 1.3 77.2 - - - +
286B ASN* 1.3 58.1 + - - +
288B LEU* 3.3 4.5 + - - +
289B ILE* 2.9 29.2 + - - +
300B LEU* 5.1 7.4 - - + -
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Residues in contact with ASN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B VAL 2.9 16.3 + - - +
283B ASP* 4.6 2.9 - - - +
285B VAL* 1.3 76.9 - - - +
287B GLY* 1.3 58.1 + - - +
289B ILE* 3.9 6.6 - - - +
290B SER* 2.9 32.9 + - - -
300B LEU* 3.9 33.1 - - + +
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ASP 2.9 22.9 + - - -
284B GLU* 3.8 1.8 - - - -
285B VAL 3.2 0.4 - - - -
286B ASN* 1.3 78.1 - - - +
288B LEU* 1.3 47.8 + - - +
290B SER* 4.6 1.7 - - - -
291B MET* 2.5 39.9 + - - +
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Residues in contact with LEU 288 (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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240B GLU* 6.5 0.9 - - - -
243B ILE* 5.2 14.9 - - + +
284B GLU 2.9 18.5 + - - +
285B VAL* 3.9 4.3 - - - +
287B GLY* 1.3 74.6 - - - +
289B ILE* 1.3 61.2 + - - +
291B MET* 3.5 5.6 - - - -
292B TYR* 2.9 29.8 + - - +
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ILE* 6.1 2.2 - - - +
285B VAL 2.9 18.1 + - - +
286B ASN* 3.9 7.2 - - - +
288B LEU* 1.3 77.4 - - - +
290B SER* 1.3 62.7 + - - +
292B TYR* 3.2 18.6 + - - +
293B SER 4.1 7.4 + - - +
295B ASP 5.0 2.6 - - - +
298B LEU* 4.8 19.1 - - + -
300B LEU* 5.6 4.5 - - + -
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Residues in contact with SER 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASN 2.9 17.2 + - - -
287B GLY* 4.6 2.0 - - - -
289B ILE* 1.3 76.9 - - - +
291B MET* 1.3 60.2 + - - +
292B TYR 3.2 1.5 + - - -
293B SER* 4.4 6.8 + - - +
294B THR 5.7 0.9 - - - +
295B ASP 5.3 1.6 - - - -
296B GLU* 4.6 26.6 - - - +
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Residues in contact with MET 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLY 2.5 25.4 + - - +
288B LEU* 3.5 7.6 - - - +
289B ILE 3.2 0.4 - - - -
290B SER* 1.3 74.7 - - - +
292B TYR* 1.3 64.7 + - - +
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Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ILE 5.2 1.8 - - - +
244B LYS* 5.9 2.2 - - - -
247B VAL* 3.8 28.3 - - + -
288B LEU 2.9 15.8 + - - +
289B ILE* 3.4 10.3 - - - +
290B SER 3.2 1.2 - - - -
291B MET* 1.3 82.0 - - - +
293B SER* 1.3 68.5 + - - +
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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
------------------------------------------------------------
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