Contacts of the helix formed by residues 282 - 304 (chain B) in PDB entry 1EZF
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 ASN 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 3.0 21.9 + - - -
192B PHE* 3.4 38.0 + - + +
193B GLU* 2.9 17.0 + - - +
281B ARG* 1.3 78.4 - - - +
283B GLN* 1.3 59.6 + - - +
284B SER* 2.6 39.8 + - - -
285B VAL* 3.0 16.4 + - + +
286B PHE* 2.8 29.4 + - - +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 5.4 0.4 + - - +
281B ARG 3.6 4.2 + - - -
282B ASN* 1.3 73.4 + - - +
284B SER* 1.3 63.5 + - - +
286B PHE* 3.3 6.8 + - - +
287B ASN* 2.8 52.9 + - - +
329B THR* 2.8 32.3 + - - +
330C ASN* 3.7 31.7 + - + +
332C PRO* 3.9 15.3 - - + -
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 5.1 2.4 - - - +
60B ALA* 3.3 28.7 - - - +
61B LEU* 3.6 8.7 - - - +
62B ASP* 2.9 33.8 + - - +
282B ASN* 2.6 20.4 + - - -
283B GLN* 1.3 78.3 - - - +
285B VAL* 1.3 63.3 + - - +
287B ASN* 3.6 2.9 + - - +
288B PHE* 3.1 23.2 + - - +
332C PRO* 3.8 16.9 - - - +
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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
----------------------------------------------------------
61B LEU* 4.0 11.7 - - + -
65B MET* 5.1 5.8 - - + -
187B PHE* 4.0 40.2 - - + -
192B PHE* 4.7 7.2 - - + -
193B GLU* 3.4 25.8 - - + +
280B LEU* 3.8 19.1 - - + -
282B ASN* 3.0 27.5 + - + +
284B SER* 1.3 78.1 - - - +
286B PHE* 1.3 67.0 + - - +
288B PHE* 3.1 3.2 + - - +
289B CYS* 2.8 23.3 + - - +
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Residues in contact with PHE 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.3 32.3 - - + -
280B LEU* 3.9 25.9 - - + +
281B ARG 5.9 0.2 - - - -
282B ASN 2.8 20.1 + - - +
283B GLN* 3.3 9.8 + - - +
285B VAL* 1.3 72.6 - - - +
287B ASN* 1.3 57.3 + - - +
289B CYS* 3.1 1.6 + - - +
290B ALA* 2.7 44.0 + - + +
328B ALA 3.7 7.9 - - - -
329B THR 3.7 16.2 - - - -
330B ASN* 3.6 13.9 - - - -
331B MET* 3.4 36.6 - - + -
334B VAL* 3.5 30.1 - - + -
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Residues in contact with ASN 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 4.2 7.4 - - + -
60B ALA* 6.5 1.3 - - + -
283B GLN* 2.8 33.6 + - - +
284B SER* 3.8 4.9 - - - +
286B PHE* 1.3 75.0 - - - +
288B PHE* 1.3 62.8 + - - +
291B ILE* 2.9 41.2 + - + +
328B ALA 4.7 3.4 - - - -
329B THR* 3.7 20.0 - - - +
330C ASN* 3.4 22.6 + - - -
332C PRO* 3.7 10.3 + - + +
333C ALA* 3.7 21.0 - - - +
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 3.2 37.9 - + - -
57B VAL* 3.4 19.7 - - + +
58B ILE* 3.5 20.2 - - + -
61B LEU* 3.8 21.1 - - + -
69B VAL* 3.7 18.4 - - + -
183B LEU* 3.9 16.4 - - + -
187B PHE* 3.8 33.0 - + - -
284B SER 3.1 12.8 + - - +
285B VAL 3.3 7.2 - - - +
287B ASN* 1.3 80.7 - - - +
289B CYS* 1.3 60.8 + - - +
292B PRO* 3.2 19.9 - - - +
992B IN0 3.2 34.0 - + + -
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Residues in contact with CYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 3.7 34.1 - - - -
207B MET* 4.0 8.2 - - + +
276B TYR* 3.8 16.2 - - - -
277B LEU* 3.8 9.2 - - + -
280B LEU* 3.7 19.7 - - + -
285B VAL* 2.8 21.9 + - - +
288B PHE* 1.3 77.9 - - - +
290B ALA* 1.3 62.6 + - - +
292B PRO* 3.4 10.0 - - - +
293B GLN* 3.4 18.4 + - - +
992B IN0 3.9 15.6 - - - -
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.7 22.8 - - + +
286B PHE* 2.7 46.4 + - + +
289B CYS* 1.3 71.6 - - - +
291B ILE* 1.3 65.2 + - - +
293B GLN* 3.0 5.0 + - - +
294B VAL* 3.0 26.3 + - - +
328B ALA* 3.8 11.4 - - + +
334B VAL* 4.2 7.2 - - + -
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 5.1 6.7 - - + -
57B VAL* 5.0 16.6 - - + -
287B ASN* 2.9 30.7 + - + +
290B ALA* 1.3 74.8 - - - +
292B PRO* 1.3 71.6 - - + +
294B VAL* 3.4 2.5 + - - +
295B MET* 3.0 42.7 + - + +
328B ALA* 3.9 33.2 - - + +
329B THR* 5.5 3.8 - - + -
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Residues in contact with PRO 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 3.4 31.2 - - + -
211B LEU* 3.5 27.2 - - + +
288B PHE 3.2 19.5 - - - +
289B CYS 3.4 8.1 - - - +
291B ILE* 1.3 94.3 - - + +
293B GLN* 1.3 55.8 + - - +
295B MET* 3.2 10.4 + - + +
296B ALA* 2.9 30.8 + - - +
992B IN0 3.9 16.4 - - + +
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Residues in contact with GLN 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B MET* 3.1 56.6 + - + +
210B PHE* 3.1 27.5 - - - -
211B LEU* 3.5 22.2 - - - +
273B VAL* 3.3 28.3 - - + +
277B LEU* 4.5 7.2 - - + -
289B CYS 3.4 15.5 + - - +
290B ALA 3.0 9.0 + - - +
292B PRO* 1.3 76.6 - - - +
294B VAL* 1.3 59.6 + - + +
296B ALA* 3.2 3.5 + - - +
297B ILE* 2.9 37.3 + - + +
338B ILE* 5.8 0.2 - - + -
992B IN0 4.9 1.0 - - - -
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA 3.0 13.9 + - - +
291B ILE* 4.0 3.1 - - - +
293B GLN* 1.3 77.0 - - + +
295B MET* 1.3 59.1 + - + +
297B ILE* 3.3 7.7 + - - +
298B ALA* 2.9 28.3 + - + +
328B ALA* 4.1 21.5 - - + -
334B VAL* 4.1 25.6 - - + -
337B ILE* 3.6 29.8 - - + -
338B ILE* 4.5 11.2 - - + -
341B TYR* 4.5 7.9 - - + -
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Residues in contact with MET 295 (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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53B SER* 5.3 5.6 - - - +
291B ILE* 3.0 40.1 + - + +
292B PRO* 3.6 8.5 - - + +
294B VAL* 1.3 77.2 - - + +
296B ALA* 1.3 57.5 + - - +
298B ALA* 3.4 7.6 + - - +
299B THR* 3.0 35.8 + - + +
992B IN0 4.0 24.2 - - - +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE* 3.7 14.4 - - + -
211B LEU* 3.6 19.7 - - + -
214B THR* 3.9 16.8 + - + +
292B PRO 2.9 16.4 + - - +
293B GLN 3.5 5.4 - - - +
294B VAL 3.2 0.2 - - - -
295B MET* 1.3 74.7 - - - +
297B ILE* 1.3 64.3 + - - +
298B ALA 3.1 0.2 - - - -
299B THR* 2.6 22.5 + - - -
300B LEU* 2.9 15.1 + - - +
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Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE* 3.4 24.5 - - + -
267B LEU* 5.9 1.8 - - + -
270B ILE* 3.4 22.4 - - + -
273B VAL* 5.3 2.0 - - + -
293B GLN* 2.9 27.2 + - + +
294B VAL* 3.8 5.4 - - - +
296B ALA* 1.3 75.5 - - - +
298B ALA* 1.3 62.4 + - - +
300B LEU* 3.5 4.3 + - + +
301B ALA* 3.1 23.1 + - + +
338B ILE* 3.4 46.2 - - + +
341B TYR* 3.7 26.0 - - + -
342B MET* 5.0 11.0 - - + -
345B ILE* 5.4 1.4 - - + +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B VAL* 2.9 18.4 + - + +
295B MET* 3.5 10.1 - - - +
297B ILE* 1.3 78.3 - - - +
299B THR* 1.3 57.3 + - + +
301B ALA* 3.4 3.8 + - - +
302B ALA* 3.0 27.0 + - - +
341B TYR* 3.5 38.7 - - + +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR* 3.4 12.6 + - - -
218B ARG* 5.1 22.6 + - + +
295B MET* 3.0 20.3 + - + +
296B ALA* 2.6 25.7 + - - -
298B ALA* 1.3 75.9 - - + +
300B LEU* 1.3 52.9 + - - +
302B ALA* 3.1 7.0 + - - +
303B CYS* 2.7 47.8 + - - -
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Residues in contact with LEU 300 (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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210B PHE* 3.7 33.2 - - + -
214B THR* 3.5 28.7 - - + +
217B ILE* 4.0 22.7 - - + -
263B ILE* 4.1 21.4 - - + +
266B ALA* 3.8 12.8 - - + -
267B LEU* 3.8 18.6 - - + -
296B ALA 2.9 17.4 + - - +
297B ILE* 3.8 5.4 - - - +
299B THR* 1.3 75.1 + - - +
301B ALA* 1.3 53.5 + - - +
303B CYS* 3.1 5.0 + - + +
304B TYR* 2.7 36.0 + - - +
345B ILE* 4.4 7.4 - - + -
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE 3.1 14.5 + - - +
298B ALA 3.7 4.9 - - - +
300B LEU* 1.3 79.6 - - - +
302B ALA* 1.3 50.9 + - - +
304B TYR* 3.7 3.8 + - - +
341B TYR* 3.7 29.8 - - + +
344B GLU* 4.3 15.8 - - + +
345B ILE* 3.7 24.8 - - + +
348B ARG* 2.7 34.3 + - - -
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Residues in contact with ALA 302 (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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298B ALA 3.0 17.3 + - - +
299B THR* 3.1 7.8 + - - +
301B ALA* 1.3 78.1 - - - +
303B CYS* 1.3 58.7 + - - +
306B ASN* 3.0 25.5 + - - -
314B VAL* 4.4 17.8 - - + +
344B GLU* 5.7 1.3 - - - -
348B ARG* 3.0 15.2 + - - +
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Residues in contact with CYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 4.7 4.5 - - + -
218B ARG* 4.3 32.5 - - - -
259B LEU* 3.2 14.9 - - + +
263B ILE* 3.9 9.9 - - + -
299B THR* 2.7 30.7 + - - +
300B LEU* 3.7 5.6 - - - +
302B ALA* 1.3 74.9 - - - +
304B TYR* 1.3 64.2 + - - +
306B ASN* 3.0 20.4 + - - +
309B VAL* 3.7 20.7 - - + +
314B VAL* 4.6 13.5 - - - -
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Residues in contact with TYR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ASN* 3.3 34.3 - - + +
263B ILE* 3.4 25.1 - - + +
300B LEU 2.7 19.7 + - - +
301B ALA 3.8 8.5 - - - +
302B ALA 3.4 1.0 - - - -
303B CYS* 1.3 70.3 - - - +
305B ASN* 1.3 72.9 + - + +
306B ASN 3.0 0.7 + - - -
345B ILE* 3.6 40.2 - - + -
348B ARG* 2.5 66.9 + - + -
349B ILE* 3.3 27.1 - - + +
350B PRO* 3.6 8.2 - - + +
353B ASP* 4.8 3.1 + - - -
356B SER* 5.3 0.2 - - - -
359B THR* 4.2 14.4 + - + +
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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) + - + + + + + -
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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