Contacts of the helix formed by residues 273 - 289 (chain M) in PDB entry 5FYW
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 SER 273 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271M GLY* 2.5 25.1 - - - +
272M LYS* 1.3 89.8 + - - +
274M PRO* 1.3 72.1 - - - +
275M ILE* 3.4 17.8 - - - +
276M THR* 3.3 6.2 - - - +
277M ILE* 3.9 0.2 - - - +
187O PRO* 3.1 32.5 + - - +
188O GLU* 3.4 19.7 - - - -
191O PRO* 5.7 1.2 - - - +
52T C 5.4 0.4 - - - -
53T A 4.5 8.9 + - - -
54T C 5.6 1.0 + - - -
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Residues in contact with PRO 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235M ASN* 2.7 48.9 + - + +
238M TYR* 5.2 3.6 - - + -
271M GLY* 5.7 0.4 - - - -
273M SER* 1.3 80.8 - - - +
275M ILE* 1.3 61.1 + - - -
277M ILE* 2.8 9.0 + - + +
278M ALA 2.8 10.4 + - - -
187O PRO* 3.8 18.2 - - + -
188O GLU* 2.6 50.9 - - + +
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Residues in contact with ILE 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M THR* 4.8 10.8 - - + +
190M LYS* 4.9 20.2 - - - +
235M ASN* 5.5 0.4 - - - -
238M TYR* 5.7 2.0 - - + -
242M PHE* 3.4 38.6 - - + -
273M SER* 3.4 20.2 - - - +
274M PRO* 1.3 79.8 - - - +
276M THR* 1.3 70.6 + - - +
278M ALA* 3.2 4.4 + - + +
279M VAL* 3.0 26.8 + - + +
303M GLN 5.7 0.2 - - - +
304M VAL* 4.5 19.1 - - + -
188O GLU* 4.3 15.9 - - + +
270R MET* 4.4 13.0 - - - -
54T C 5.1 6.3 - - - +
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Residues in contact with THR 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M GLY 2.9 29.2 - - - +
272M LYS* 3.2 16.6 - - + +
273M SER* 3.3 1.8 - - - +
275M ILE* 1.3 82.6 - - - +
277M ILE* 1.3 61.8 + - + +
279M VAL* 3.1 7.1 - - - +
280M VAL* 2.9 42.7 + - - +
304M VAL* 5.3 2.0 - - - -
308M THR* 3.2 31.0 + - - +
312M GLY* 5.6 1.4 - - - -
53T A 3.9 6.5 - - - +
54T C 5.7 2.7 - - - -
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Residues in contact with ILE 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235M ASN* 4.4 5.4 - - - +
260M ALA* 5.3 8.5 - - + +
263M CYS* 4.6 17.3 - - + -
264M LYS* 5.8 1.8 - - + +
269M ILE* 6.0 3.4 - - + -
271M GLY* 3.3 42.0 - - - +
273M SER 3.9 2.9 - - - +
274M PRO* 2.8 9.4 + - + +
276M THR* 1.3 79.1 - - + +
278M ALA* 1.3 57.7 + - - +
280M VAL* 3.2 11.6 - - + +
281M SER* 2.5 48.5 + - - +
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Residues in contact with ALA 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235M ASN* 3.5 20.1 - - - +
238M TYR* 4.8 0.2 - - + -
239M ILE* 3.3 30.9 - - + +
242M PHE* 4.4 19.5 - - + -
260M ALA* 6.1 0.4 - - - -
274M PRO 2.8 5.8 + - - +
275M ILE* 3.7 9.2 - - + +
277M ILE* 1.3 77.1 - - - +
279M VAL* 1.3 62.6 + - - +
281M SER* 3.5 3.3 - - - -
282M ILE* 3.0 29.5 + - - +
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Residues in contact with VAL 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242M PHE* 5.8 1.5 - - + -
275M ILE* 3.0 17.7 + - + +
276M THR* 3.1 21.8 - - - +
278M ALA* 1.3 78.3 - - - +
280M VAL* 1.3 66.4 + - + +
282M ILE* 3.2 11.1 + - + +
283M TYR* 2.9 21.1 + - + +
298M VAL* 4.4 15.0 - - + +
302M LEU* 4.1 23.3 - - + -
304M VAL* 3.7 39.7 - - + -
309M ILE* 4.4 10.8 - - + -
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Residues in contact with VAL 280 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263M CYS* 6.4 0.2 - - - -
276M THR* 2.9 34.8 + - - +
277M ILE* 3.2 23.3 - - + +
279M VAL* 1.3 78.5 - - + +
281M SER* 1.3 70.3 + - - +
283M TYR* 2.9 9.6 + - + +
284M LEU* 2.8 24.8 + - - +
308M THR 4.3 0.2 - - - +
309M ILE* 4.0 23.3 - - - +
312M GLY* 3.9 31.4 - - - +
313M TYR* 4.8 1.3 - - - +
316M LEU* 3.8 16.2 - - + +
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Residues in contact with SER 281 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239M ILE* 5.2 2.2 - - - -
256M ALA* 4.5 7.9 - - - -
259M THR* 3.6 29.4 - - - +
260M ALA* 4.3 8.8 - - - -
263M CYS* 4.4 4.0 - - - -
277M ILE* 2.5 37.4 + - - +
278M ALA* 3.5 6.7 - - - -
280M VAL* 1.3 78.5 - - - +
282M ILE* 1.3 60.0 + - - +
284M LEU* 3.4 2.1 + - - +
285M ASN* 2.3 35.4 + - - -
316M LEU* 4.2 4.9 - - - -
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Residues in contact with ILE 282 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239M ILE* 4.2 14.1 - - + +
242M PHE* 3.5 33.9 - - + -
243M CYS* 4.5 10.5 - - - +
246M LEU* 4.4 20.4 - - + -
248M LEU* 4.4 12.6 - - + -
252M VAL* 5.7 2.9 - - + -
256M ALA* 4.3 16.1 - - + +
278M ALA 3.0 19.8 + - - +
279M VAL* 3.4 10.5 - - - +
280M VAL 3.1 0.2 - - - -
281M SER* 1.3 75.0 - - - +
283M TYR* 1.3 58.6 + - - +
285M ASN* 2.6 30.5 + - - +
286M ILE* 2.8 19.2 + - + +
298M VAL* 5.5 4.9 - - + -
302M LEU* 4.8 5.6 - - + -
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Residues in contact with TYR 283 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279M VAL* 2.9 17.1 + - + +
280M VAL* 2.9 13.0 + - - +
282M ILE* 1.3 73.3 - - - +
284M LEU* 1.3 62.9 + - - +
286M ILE* 3.0 14.2 - - + +
287M LEU* 2.9 61.5 + - + +
294M THR 3.3 25.3 + - - -
295M ALA* 4.0 15.6 - - + +
298M VAL* 4.4 17.3 - - + -
309M ILE* 4.7 20.9 - - + -
310M LYS* 3.9 21.5 + - + -
313M TYR* 4.0 34.3 - + + -
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Residues in contact with LEU 284 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259M THR* 4.2 15.7 - - + +
280M VAL 2.8 9.3 + - - -
281M SER 3.5 6.5 - - - +
283M TYR* 1.3 75.1 - - - +
285M ASN* 1.3 68.1 + - - +
287M LEU* 2.8 17.0 + - + +
288M LEU* 2.9 17.0 + - + +
313M TYR* 4.5 20.6 - - + -
316M LEU* 3.5 41.1 - - + +
317M TYR* 5.6 5.6 - - + -
320M ARG* 5.5 13.2 - - + -
323M LEU* 4.1 20.9 - - + -
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Residues in contact with ASN 285 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252M VAL* 4.5 14.8 - - + +
255M SER* 2.2 34.5 + - - +
256M ALA* 3.3 19.0 - - + +
259M THR* 3.0 29.5 + - - +
281M SER 2.3 36.0 + - - -
282M ILE* 2.6 13.0 + - - +
284M LEU* 1.3 79.3 - - - +
286M ILE* 1.3 62.0 + - - +
288M LEU* 3.1 14.8 - - - +
289M PHE* 2.9 24.3 - - + -
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Residues in contact with ILE 286 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248M LEU* 4.8 3.6 - - + -
252M VAL* 4.9 8.1 - - + +
282M ILE* 2.8 25.9 + - + +
283M TYR* 3.0 34.1 - - + +
285M ASN* 1.3 71.5 - - - +
287M LEU* 1.3 57.3 + - + +
289M PHE* 2.5 39.8 + - - +
291M ILE* 3.1 47.9 - - + +
293M ILE* 3.5 44.6 - - + +
294M THR 5.9 1.1 - - - +
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Residues in contact with LEU 287 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283M TYR* 2.9 65.3 + - + +
284M LEU* 2.8 10.6 + - + +
286M ILE* 1.3 77.1 - - + +
288M LEU* 1.3 67.9 + - - +
289M PHE 3.1 7.8 - - - +
291M ILE 5.8 1.8 - - - +
292M PRO* 6.5 1.1 - - + -
293M ILE 6.3 0.9 - - - +
294M THR* 5.1 8.7 - - - +
313M TYR* 4.1 21.8 - - + +
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Residues in contact with LEU 288 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255M SER* 4.8 8.5 - - - +
284M LEU* 2.9 16.8 + - + +
285M ASN* 3.1 13.0 - - - +
287M LEU* 1.3 78.9 - - - +
289M PHE* 1.3 85.8 + - + +
324M VAL* 6.5 0.7 - - + -
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Residues in contact with PHE 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251M GLN* 4.4 28.3 - - + -
252M VAL* 4.3 20.6 - - + -
255M SER* 4.4 20.6 - - - -
285M ASN 2.9 27.1 - - - -
286M ILE* 2.5 23.6 + - - +
287M LEU* 3.1 10.4 - - - +
288M LEU* 1.3 99.8 - - + +
290M GLN* 1.3 64.5 + - + +
291M ILE* 4.2 16.1 - - + +
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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) + - + + + + + -
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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