Contacts of the helix formed by residues 287 - 304 (chain N) in PDB entry 5A31
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 ARG 287 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283N ARG 5.9 2.0 - - - +
285N PHE 4.8 2.9 - - - +
286N LEU* 1.3 76.2 - - + +
288N GLU* 1.3 56.6 + - + +
289N PHE 2.6 19.8 - - - +
290N HIS* 3.9 8.6 + - - +
291N LYS* 3.5 51.3 + - - +
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Residues in contact with GLU 288 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272N ARG* 4.5 8.2 + - - +
276N ARG* 2.8 39.6 + - - -
283N ARG* 3.3 41.1 + - + +
285N PHE* 3.2 41.7 - - + +
286N LEU 2.3 9.5 + - - -
287N ARG* 1.3 69.7 - - + +
289N PHE* 1.3 69.1 + - + +
291N LYS* 3.9 2.9 - - - +
292N TRP* 2.8 26.9 + - - +
295N ARG* 4.7 1.9 + - - -
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Residues in contact with PHE 289 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269N THR 5.1 1.8 - - - -
272N ARG* 4.2 25.6 - - + -
273N MET* 3.9 31.6 - - + -
276N ARG* 4.8 9.4 - - + -
277N CYS* 5.1 3.6 - - - -
285N PHE* 2.7 43.5 - + + -
286N LEU 2.6 11.5 + - - +
287N ARG 2.6 11.0 - - - +
288N GLU* 1.3 75.4 - - + +
290N HIS* 1.3 53.6 - - - +
291N LYS 2.1 26.4 + - - -
292N TRP* 3.5 31.2 - + + -
293N ILE* 3.8 6.3 - - + +
332N PHE* 3.1 48.0 - + + -
336N TYR* 5.7 0.9 - + - -
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Residues in contact with HIS 290 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286N LEU* 3.8 36.1 - - + -
287N ARG* 3.9 7.5 + - - +
289N PHE* 1.3 69.9 - - - +
291N LYS* 1.3 58.7 + - + +
292N TRP 3.4 0.4 - - - -
293N ILE* 3.5 22.0 - - + +
294N GLU* 2.7 32.7 + - - +
325N ARG* 5.0 4.0 + - - -
329N GLN* 4.1 20.2 - - + +
332N PHE* 5.7 1.6 - + - -
333N TYR* 3.1 30.5 + + - -
363N TYR* 3.9 17.8 + + - -
367N ARG* 4.0 2.3 + - - -
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Residues in contact with LYS 291 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287N ARG* 3.5 56.2 - - - +
288N GLU* 4.0 1.8 - - - +
289N PHE 2.1 16.4 + - - -
290N HIS* 1.3 71.9 - - + +
292N TRP* 1.3 58.5 + - - +
293N ILE 3.2 0.2 - - - -
294N GLU* 3.4 6.2 + - - +
295N ARG* 3.0 53.1 + - - +
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Residues in contact with TRP 292 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181N LEU* 5.6 0.7 - - + -
185N MET* 3.9 32.9 - - + +
268N VAL* 4.7 12.6 - - + -
269N THR* 3.4 48.9 - - + -
272N ARG* 3.4 50.0 - - + +
288N GLU 2.8 23.2 + - - +
289N PHE* 3.1 26.7 + + + -
291N LYS* 1.3 75.0 - - - +
293N ILE* 1.3 68.7 + - + +
295N ARG* 3.7 9.9 - - - +
296N VAL* 2.9 61.3 + - + +
328N VAL* 5.5 1.8 - - + -
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Residues in contact with ILE 293 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289N PHE* 4.2 6.1 - - + -
290N HIS* 3.4 28.0 + - + +
291N LYS 3.2 0.6 - - - -
292N TRP* 1.3 85.2 - - + +
294N GLU* 1.3 59.1 + - - +
296N VAL* 3.1 6.5 + - - +
297N VAL* 2.8 35.4 + - + +
325N ARG* 4.5 10.3 - - + +
328N VAL* 4.0 25.6 - - + +
329N GLN* 4.1 28.0 - - + +
332N PHE* 3.7 42.0 - - + -
333N TYR* 5.9 0.2 - - + -
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Residues in contact with GLU 294 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290N HIS 2.7 19.3 + - - +
291N LYS* 3.4 7.6 + - - +
293N ILE* 1.3 71.1 - - - +
295N ARG* 1.3 58.3 + - + +
297N VAL* 3.2 9.9 + - - +
298N GLY* 2.9 25.3 + - - -
325N ARG* 4.0 24.9 - - - +
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Residues in contact with ARG 295 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184N TYR* 3.8 10.6 - - - -
185N MET* 3.6 33.1 - - + +
188N LYS* 4.1 40.6 + - + +
288N GLU 4.7 2.0 + - - -
291N LYS* 3.0 56.0 + - - +
292N TRP* 3.7 7.3 - - - +
294N GLU* 1.3 75.7 - - + +
296N VAL* 1.3 62.4 + - - +
298N GLY* 3.3 3.0 + - - +
299N TRP* 3.1 17.8 + - - +
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Residues in contact with VAL 296 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181N LEU* 4.8 8.5 - - + -
185N MET* 4.4 9.4 - - - -
265N LEU* 3.9 29.2 - - + -
292N TRP* 2.9 70.9 + - + +
293N ILE* 3.4 7.4 - - - +
295N ARG* 1.3 74.6 - - - +
297N VAL* 1.3 65.6 + - - +
299N TRP* 3.1 27.1 - - + +
300N LEU* 3.5 4.6 + - + +
328N VAL* 4.6 13.5 - - + -
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Residues in contact with VAL 297 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293N ILE* 2.8 28.5 + - + +
294N GLU* 3.2 10.1 + - - +
296N VAL* 1.3 69.2 - - - +
298N GLY* 1.3 66.6 + - - +
300N LEU* 3.0 24.5 + - + +
301N GLY* 3.0 10.6 + - - -
321N LEU* 4.6 12.6 - - + +
324N TRP* 4.4 13.7 - - + +
325N ARG* 3.6 45.1 - - + +
328N VAL* 5.1 4.3 - - + -
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Residues in contact with GLY 298 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184N TYR* 4.2 13.2 + - - -
188N LYS* 5.5 2.2 - - - -
294N GLU 2.9 13.6 + - - -
295N ARG* 3.6 6.1 - - - -
296N VAL 3.3 0.4 - - - -
297N VAL* 1.3 77.8 - - - +
299N TRP* 1.3 59.2 + - - +
301N GLY* 3.4 3.1 + - - -
302N LYS* 3.1 23.7 + - - +
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Residues in contact with TRP 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177N TYR* 4.0 19.3 - + + -
180N PHE* 2.1 73.6 - + + -
181N LEU* 3.1 48.5 - - + +
184N TYR* 3.8 28.5 - + + -
261N VAL* 5.2 6.7 + - + +
264N THR* 5.9 1.1 - - - -
265N LEU* 5.0 3.7 - - + +
295N ARG 3.1 9.7 + - - +
296N VAL* 3.1 16.6 - - - +
298N GLY* 1.3 74.6 - - - +
300N LEU* 1.3 98.0 + - + +
302N LYS* 3.2 8.2 - - - +
303N VAL* 3.1 36.3 + - + +
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Residues in contact with LEU 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261N VAL* 4.9 13.9 - - + -
265N LEU* 4.1 23.3 - - + -
296N VAL 3.8 5.2 - - - +
297N VAL* 3.0 18.5 + - + +
299N TRP* 1.3 104.6 - - + +
301N GLY* 1.3 57.1 + - - +
303N VAL* 2.8 23.5 + - + +
304N PHE* 3.1 28.4 - - + -
324N TRP* 3.6 44.2 - - + -
328N VAL* 4.8 9.6 - - + -
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Residues in contact with GLY 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297N VAL* 3.0 12.5 + - - -
298N GLY* 3.4 5.6 + - - -
300N LEU* 1.3 74.8 - - - +
302N LYS* 1.3 59.6 + - - +
304N PHE* 3.5 19.5 + - - -
321N LEU* 5.4 5.2 - - - -
324N TRP* 4.1 10.8 - - - -
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Residues in contact with LYS 302 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N PHE* 4.1 28.5 - - + -
184N TYR* 4.0 27.7 - - + +
237N LEU* 3.7 32.5 + - - +
240N PHE* 5.1 0.8 - - - +
241N HIS* 3.0 52.4 + - + +
244N SER* 4.9 4.2 + - - -
298N GLY 3.1 13.0 + - - +
299N TRP* 3.2 11.7 - - - +
301N GLY* 1.3 74.6 - - - +
303N VAL* 1.3 62.0 + - - +
304N PHE* 3.6 1.7 + - - -
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Residues in contact with VAL 303 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177N TYR* 4.3 16.6 - - + +
180N PHE* 3.8 23.8 - - + -
244N SER* 3.5 30.4 + - - +
253N LEU* 3.9 24.4 - - + +
261N VAL* 4.9 4.7 - - + -
299N TRP* 3.1 34.7 + - + +
300N LEU* 2.8 15.8 + - + +
302N LYS* 1.3 73.0 - - - +
304N PHE* 1.3 78.0 + - + +
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Residues in contact with PHE 304 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248N HIS* 5.6 8.1 + - - +
253N LEU* 3.5 34.5 - - + +
254N ALA* 5.2 6.7 - - + -
258N ALA* 5.0 15.3 - - + -
261N VAL* 4.4 20.0 - - + -
300N LEU* 3.1 35.9 + - + +
301N GLY* 3.6 14.8 - - - +
302N LYS 3.5 1.6 - - - +
303N VAL* 1.3 93.3 - - + +
321N LEU* 5.9 1.6 - - + -
324N TRP* 3.0 42.8 - + + -
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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