Contacts of the helix formed by residues 288 - 309 (chain m) in PDB entry 5M32
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 PHE 288 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282m MET 5.1 6.7 - - - +
283m LYS 6.1 0.2 - - - +
285m ASP 3.7 11.7 - - - +
286m TRP* 3.0 15.2 + - - +
287m LEU* 1.3 73.9 - - - +
289m ALA* 1.3 67.2 + - + +
290m PRO* 3.8 0.6 - - - +
291m HIS* 3.3 8.2 + - - +
292m TYR* 2.9 31.5 + - - +
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Residues in contact with ALA 289 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288m PHE* 1.3 81.5 - - + +
290m PRO* 1.4 71.5 - - + +
292m TYR* 3.3 3.7 + - - +
293m ARG* 3.1 27.4 + - - +
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Residues in contact with PRO 290 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192m ARG* 2.9 19.4 + - - +
289m ALA* 1.4 89.7 - - + +
291m HIS* 1.3 55.3 + - + +
293m ARG* 4.4 7.4 - - + +
294m TYR* 2.7 39.9 + - + +
38s VAL* 4.6 17.3 - - + -
42s ASN* 4.3 19.7 - - + -
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Residues in contact with HIS 291 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189m VAL 5.0 6.7 - - - +
190m ALA* 6.3 0.4 - - - -
192m ARG* 3.5 16.0 + - - +
194m PHE* 4.6 13.2 - - + -
287m LEU* 4.0 15.5 - - + +
288m PHE 3.4 13.9 - - - +
289m ALA 3.1 0.2 - - - -
290m PRO* 1.3 84.1 - - + +
292m TYR* 1.3 49.8 + - - +
294m TYR* 4.5 0.3 - - - +
295m TYR* 2.6 37.8 + - - +
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Residues in contact with TYR 292 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279m GLU* 6.0 1.6 - - + -
282m MET* 3.6 31.4 - - + +
288m PHE 2.9 15.5 + - - +
289m ALA* 4.3 2.5 - - - +
291m HIS* 1.3 75.6 - - - +
293m ARG* 1.3 63.0 + - - +
295m TYR* 3.6 5.6 - - - +
296m VAL* 2.9 30.3 + - - +
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Residues in contact with ARG 293 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289m ALA 3.1 16.8 + - - +
290m PRO* 4.4 4.7 - - + -
292m TYR* 1.3 78.0 - - - +
294m TYR* 1.3 57.5 + - - +
296m VAL* 4.0 3.1 - - - +
297m ARG* 3.0 27.2 + - - +
42s ASN* 6.3 2.2 - - + -
44s ASP* 5.6 12.8 - - + -
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Residues in contact with TYR 294 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192m ARG* 3.4 23.6 - - - +
194m PHE* 5.6 1.6 - - + -
290m PRO* 2.7 24.0 + - + +
293m ARG* 1.3 75.5 - - - +
295m TYR* 1.3 57.8 + - - +
297m ARG* 3.3 9.1 + - - +
298m GLU* 2.9 30.1 + - - +
42s ASN* 5.5 8.0 - - + +
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Residues in contact with TYR 295 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192m ARG* 5.1 0.2 - - - +
194m PHE* 5.3 7.0 - - + -
229m ILE* 4.2 16.8 - - + +
291m HIS 2.6 26.0 + - - +
292m TYR* 3.7 7.2 - - - +
293m ARG 3.2 0.4 - - - -
294m TYR* 1.3 74.9 - - - +
296m VAL* 1.3 60.0 + - - +
298m GLU* 3.3 0.7 + - - -
299m MET* 2.9 31.5 + - - +
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Residues in contact with VAL 296 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275m LEU 6.2 0.2 - - - +
279m GLU* 5.4 11.0 - - + -
292m TYR 2.9 17.8 + - - +
293m ARG* 4.2 3.8 - - - +
295m TYR* 1.3 73.6 - - - +
297m ARG* 1.3 60.2 + - - +
299m MET* 4.0 5.3 - - - +
300m ARG* 2.9 32.7 + - - +
50s ASP* 5.8 6.7 - - + -
51s ASP* 5.2 14.8 - - + -
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Residues in contact with ARG 297 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293m ARG 3.0 19.5 + - - +
294m TYR* 3.3 10.8 - - - +
295m TYR 3.2 0.2 - - - -
296m VAL* 1.3 78.9 - - - +
298m GLU* 1.3 57.2 + - + +
300m ARG* 3.5 4.4 - - - +
301m ILE* 2.9 29.6 + - - +
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Residues in contact with GLU 298 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228m MET 5.2 0.7 - - - +
229m ILE* 3.6 29.3 - - + +
294m TYR 2.9 16.3 + - - +
297m ARG* 1.3 74.7 - - - +
299m MET* 1.3 61.9 + - - +
301m ILE* 4.3 5.6 - - - +
302m HIS* 2.9 32.8 + - - +
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Residues in contact with MET 299 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228m MET 6.0 1.8 - - - -
229m ILE* 4.4 4.3 - - + +
259m TYR* 4.2 19.1 - - - +
275m LEU* 5.3 10.3 - - + -
295m TYR 2.9 17.7 + - - +
296m VAL* 4.0 7.2 - - - +
298m GLU* 1.3 77.6 - - - +
300m ARG* 1.3 56.7 + - - +
302m HIS* 3.9 3.3 - - - +
303m ALA* 2.9 31.2 + - - +
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Residues in contact with ARG 300 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296m VAL 2.9 21.7 + - - +
297m ARG* 3.5 6.7 - - - +
299m MET* 1.3 75.6 - - - +
301m ILE* 1.3 57.7 + - - +
303m ALA* 3.0 7.9 + - - +
304m TYR* 3.0 27.3 + - - +
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Residues in contact with ILE 301 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297m ARG 2.9 20.5 + - - +
298m GLU* 4.4 4.9 - - - +
300m ARG* 1.3 72.2 - - - +
302m HIS* 1.3 58.0 + - - +
304m TYR* 3.3 5.5 + - - +
305m SER* 2.9 32.5 + - - -
337m PHE* 5.7 9.6 - - + -
342m ARG* 5.9 7.2 - - + -
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Residues in contact with HIS 302 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228m MET* 4.5 15.7 - - + +
229m ILE 5.9 0.7 - - - +
263m LEU* 6.3 4.0 - - + -
298m GLU 2.9 21.4 + - - +
299m MET* 4.2 3.1 - - - +
301m ILE* 1.3 75.9 - - - +
303m ALA* 1.3 61.6 + - - +
305m SER* 4.3 5.1 - - - -
306m GLN* 3.1 25.1 + - - +
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Residues in contact with ALA 303 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263m LEU* 6.1 5.4 - - + -
299m MET 2.9 19.9 + - - +
300m ARG* 3.0 7.4 + - - +
302m HIS* 1.3 78.1 - - - +
304m TYR* 1.3 62.2 + - - +
306m GLN* 3.6 5.5 + - - +
307m LEU* 3.5 18.5 + - - +
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Residues in contact with TYR 304 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300m ARG 3.0 13.9 + - - +
301m ILE* 4.1 4.9 - - - +
303m ALA* 1.3 74.4 - - - +
305m SER* 1.3 66.3 + - - +
307m LEU* 3.1 15.2 + - - +
308m LEU* 3.3 16.3 + - - +
334m LEU* 6.5 0.9 - - + -
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Residues in contact with SER 305 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301m ILE 2.9 18.8 + - - -
302m HIS* 4.3 4.9 - - - -
304m TYR* 1.3 76.9 - - - +
306m GLN* 1.3 61.4 + - - +
307m LEU 3.5 0.3 + - - -
308m LEU* 4.9 1.8 - - - +
309m GLU* 3.3 26.6 + - - +
342m ARG 5.8 1.6 - - - -
343m LEU* 4.9 20.4 - - - +
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Residues in contact with GLN 306 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233m ARG* 4.9 20.6 - - + +
302m HIS 3.1 20.9 + - - +
303m ALA* 3.7 7.4 - - - +
304m TYR 3.2 0.2 - - - -
305m SER* 1.3 79.2 - - - +
307m LEU* 1.3 62.4 + - - +
309m GLU* 4.2 6.7 + - - +
310m SER* 4.7 4.3 + - - -
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Residues in contact with LEU 307 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303m ALA 3.5 9.0 + - - +
304m TYR* 3.1 11.9 + - - +
306m GLN* 1.3 83.3 - - - +
308m LEU* 1.3 62.7 + - + +
309m GLU 3.4 1.2 + - - -
310m SER* 3.8 11.6 + - - -
311m TYR* 4.7 3.1 + - - +
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Residues in contact with LEU 308 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304m TYR 3.3 12.1 + - - +
305m SER* 5.6 0.9 - - - -
307m LEU* 1.3 76.6 - - + +
309m GLU* 1.3 58.9 + - - +
310m SER 3.3 1.3 - - - -
311m TYR* 3.1 30.6 + - - +
314m LEU* 4.6 19.0 - - + +
344m HIS 6.0 0.2 - - - +
345m CYS* 5.3 11.4 - - + -
354m VAL* 6.3 0.7 - - + -
356m THR* 3.8 15.9 - - - -
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Residues in contact with GLU 309 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376l GLY 4.8 1.9 - - - +
377l ILE* 4.5 8.5 - - - +
305m SER 3.3 20.2 + - - +
306m GLN* 4.5 4.9 - - - +
307m LEU 3.3 1.6 - - - -
308m LEU* 1.3 78.9 - - - +
310m SER* 1.3 60.1 + - - +
311m TYR 3.4 3.1 + - - +
356m THR* 5.5 2.4 - - - -
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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
------------------------------------------------------------
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