Contacts of the helix formed by residues 301 - 320 (chain B) in PDB entry 1JFZ
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 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LYS* 3.9 32.6 + - + +
300B ILE* 1.3 100.8 + - - +
302B GLU* 1.3 59.8 + - - +
303B THR* 3.2 15.5 + - - +
304B ILE* 2.7 52.1 - - - +
305B ILE* 3.5 15.6 - - - +
460C PRO 5.3 5.4 - - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU* 2.8 48.6 - - - +
278B GLU* 5.1 5.9 - - - +
281B ASN* 3.2 36.1 + - - +
301B ASN* 1.3 76.5 - - - +
303B THR* 1.3 57.8 + - - +
305B ILE* 4.2 2.2 - - - -
306B GLY 3.7 5.7 + - - -
460C PRO* 5.8 5.8 - - + +
461C ASN* 5.5 5.4 - - + +
463C ARG* 5.3 3.5 + - - -
548C HIS* 5.7 2.6 + - - -
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU* 3.1 19.9 + - - +
301B ASN* 3.2 13.9 + - - +
302B GLU* 1.3 79.5 + - - +
304B ILE* 1.3 61.8 + - - +
305B ILE 3.3 0.2 - - - -
307B ASP* 3.0 43.9 + - - +
460C PRO 5.4 4.0 + - - -
461C ASN* 6.0 1.9 - - - +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B HIS* 3.6 18.4 - - + +
236B TYR* 2.8 28.7 - - + +
293B ILE* 3.4 29.8 - - + -
295B ILE* 3.3 23.1 - - + -
300B ILE* 2.7 34.3 - - + +
301B ASN* 2.7 26.1 - - - +
303B THR* 1.3 73.4 - - - +
305B ILE* 1.3 57.0 + - - +
307B ASP* 3.1 4.0 - - - +
308B VAL* 2.6 42.4 + - + +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ASN* 3.1 30.3 - - - +
284B ALA* 4.1 19.5 - - + -
285B GLN* 5.0 6.3 - - - +
289B LEU* 3.8 3.9 - - + +
290B HIS* 3.9 34.8 - - + +
293B ILE* 3.7 23.6 - - + -
300B ILE* 3.7 8.1 - - + -
301B ASN 3.5 18.6 - - - +
302B GLU 4.2 1.8 - - - +
303B THR 3.3 0.2 - - - -
304B ILE* 1.3 77.4 - - - +
306B GLY* 1.3 58.8 + - - +
307B ASP 3.0 1.1 - - - -
308B VAL* 2.9 2.8 + - - +
309B PHE* 2.5 34.3 + - - +
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Residues in contact with GLY 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU* 5.0 4.3 - - - -
280B PHE* 3.9 24.0 - - - -
281B ASN* 4.5 3.1 - - - -
302B GLU 3.7 11.8 + - - -
305B ILE* 1.3 83.8 - - - +
307B ASP* 1.3 53.3 + - - +
309B PHE* 3.2 11.8 - - - +
310B GLU* 2.9 35.8 + - - +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TYR* 3.6 18.5 + - + -
240B GLU* 3.1 26.7 - - - +
303B THR* 3.0 34.1 + - - +
304B ILE 3.1 5.8 - - - +
306B GLY* 1.3 75.3 - - - +
308B VAL* 1.3 54.9 + - - +
309B PHE 3.1 0.2 - - - -
310B GLU* 3.1 6.4 + - - +
311B ALA* 2.7 30.7 + - - +
762B MN 2.3 35.6 + - - -
633D LYS* 4.3 7.8 + - - -
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA 3.6 16.2 - - - +
225B LEU* 3.8 25.4 - - + -
236B TYR* 3.5 31.2 - - + -
289B LEU* 3.7 15.7 - - + -
293B ILE* 4.2 14.8 - - + -
304B ILE* 2.6 35.0 + - + +
305B ILE* 2.9 6.5 + - - +
307B ASP* 1.3 70.7 - - - +
309B PHE* 1.3 56.8 + - - +
311B ALA* 4.2 2.0 - - - +
312B LEU* 2.7 33.5 + - + +
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Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 4.9 4.3 - - + -
280B PHE* 4.1 28.7 - + - +
283B LEU* 3.5 39.0 - - + -
284B ALA* 3.9 17.9 - - + -
287B LEU* 3.9 12.3 - - + -
289B LEU* 3.5 9.1 - - + +
305B ILE 2.5 17.8 + - - +
306B GLY* 3.2 14.4 - - - +
308B VAL* 1.3 75.6 - - - +
310B GLU* 1.3 62.2 - - - +
312B LEU* 3.3 8.1 + - + +
313B TRP* 3.4 47.1 + + - -
331B PHE* 4.1 13.5 - + - -
335B PHE* 3.7 23.1 - + - -
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Residues in contact with GLU 310 (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* 3.1 10.2 - - - +
243B GLY* 3.1 39.1 - - - +
244B ASP* 3.4 29.0 - - - +
247B VAL* 5.1 5.8 - - + -
275B ILE 5.4 0.2 - - - +
280B PHE* 3.4 31.9 - - + -
306B GLY 2.9 13.6 + - - +
307B ASP* 3.3 9.3 - - - +
309B PHE* 1.3 75.2 - - + +
311B ALA* 1.3 65.0 + - - +
312B LEU 3.3 0.5 + - - -
313B TRP* 3.5 3.5 + - - +
314B ALA 3.5 7.1 + - - -
762B MN 2.2 37.1 + - - -
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 3.5 14.6 - - + +
236B TYR* 3.5 30.3 - - + +
239B LEU* 3.7 8.2 - - + +
240B GLU* 3.3 30.2 - - - +
307B ASP 2.7 16.4 + - - +
308B VAL 4.1 0.9 - - - +
310B GLU* 1.3 73.4 - - - +
312B LEU* 1.3 58.1 + - - +
314B ALA* 3.5 2.5 + - - +
315B ALA* 3.0 22.5 + - - +
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Residues in contact with LEU 312 (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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207B LEU* 4.4 6.1 - - + -
211B LEU* 3.8 33.4 - - + -
215B PHE* 4.5 1.6 - - + -
221B LEU* 4.0 25.1 - - + -
224B ALA* 4.0 10.7 - - + +
225B LEU* 5.2 1.6 - - + -
287B LEU* 3.8 29.8 - - + -
289B LEU* 4.2 18.6 - - + -
308B VAL* 2.7 21.7 + - + +
309B PHE* 3.6 5.4 - - + +
310B GLU 3.1 0.4 - - - -
311B ALA* 1.3 77.5 - - - +
313B TRP* 1.3 72.2 + - + +
315B ALA* 3.2 9.5 + - - +
316B VAL* 3.3 13.6 + - + +
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Residues in contact with TRP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.8 21.1 - - + -
246B LEU* 3.0 27.3 - - + +
247B VAL* 4.0 13.7 - - + -
287B LEU* 4.5 0.6 - - - +
309B PHE* 3.4 52.3 + + - +
310B GLU 3.5 1.5 + - - +
311B ALA 3.4 0.2 - - - -
312B LEU* 1.3 86.4 - - + +
314B ALA* 1.3 57.2 + - - +
315B ALA 3.4 0.2 - - - -
316B VAL* 3.8 18.6 - - + +
317B TYR* 3.3 18.2 + - - +
327B THR* 3.8 22.8 - - + +
330B LEU* 3.6 16.2 - - + -
331B PHE* 3.5 43.1 - + + -
334B LEU* 3.4 35.0 - - + -
335B PHE* 3.7 9.3 - + - -
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Residues in contact with ALA 314 (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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239B LEU* 3.2 35.0 - - + +
242B LEU* 4.0 11.4 - - + -
243B GLY* 3.4 17.9 - - - +
246B LEU* 3.8 7.5 - - + +
310B GLU 3.5 3.2 + - - +
311B ALA 3.7 6.7 - - - +
312B LEU 3.2 0.4 - - - -
313B TRP* 1.3 76.8 - - - +
315B ALA* 1.3 63.5 + - - +
316B VAL 3.3 0.4 - - - -
317B TYR* 3.3 4.6 - - - +
318B ILE* 3.2 30.0 + - - +
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Residues in contact with ALA 315 (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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215B PHE* 3.8 13.7 - - + -
220B LEU* 3.4 29.9 - - + +
221B LEU* 4.6 0.4 - - - -
224B ALA* 4.0 9.2 - - + -
239B LEU* 3.9 12.5 - - + +
311B ALA 3.0 17.3 + - - +
312B LEU* 3.2 6.0 + - - +
314B ALA* 1.3 78.6 - - - +
316B VAL* 1.3 55.4 + - - +
318B ILE* 3.8 2.7 - - - +
319B ASP* 2.8 32.9 + - - +
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Residues in contact with VAL 316 (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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211B LEU* 4.1 17.7 - - + -
213B TYR* 4.2 14.6 - - + -
215B PHE* 3.6 25.8 - - + -
312B LEU* 3.4 13.7 - - + +
313B TRP* 3.8 23.3 - - + +
314B ALA 3.3 0.2 - - - -
315B ALA* 1.3 73.3 - - - +
317B TYR* 1.3 68.3 + - - +
319B ASP* 3.8 2.0 - - - +
320B SER* 2.9 28.9 + - - -
327B THR* 3.9 18.2 - - + +
330B LEU* 4.2 22.7 - - + -
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Residues in contact with TYR 317 (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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49A PHE* 3.2 20.1 - + - -
53A ASP* 2.4 39.7 + - - -
128A ARG* 2.8 20.4 + - - -
242B LEU* 3.8 21.3 - - + -
246B LEU* 4.2 12.1 - - + -
313B TRP 3.3 12.5 + - - +
314B ALA* 3.3 11.0 - - - +
316B VAL* 1.3 78.3 - - - +
318B ILE* 1.3 60.6 - - + +
320B SER* 2.3 25.3 + - - -
322B ARG* 2.9 48.8 + - + +
323B ASP 4.1 0.9 - - - -
324B ALA* 3.6 27.6 - - + -
327B THR* 3.4 14.1 - - - +
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Residues in contact with ILE 318 (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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56A VAL* 5.2 6.3 - - + -
220B LEU* 3.7 20.9 - - + -
239B LEU* 3.5 30.3 - - + -
242B LEU* 4.0 24.2 - - + -
314B ALA 3.2 12.0 + - - +
315B ALA 3.9 2.5 - - - +
317B TYR* 1.3 81.2 - - + +
319B ASP* 1.3 66.4 + - - +
320B SER 3.0 1.6 - - - -
321B GLY* 2.9 15.1 + - - -
322B ARG* 3.7 31.3 + - - +
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Residues in contact with ASP 319 (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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213B TYR* 2.6 24.8 + - + +
215B PHE* 3.1 22.1 - - + -
216B LYS* 2.7 37.6 + - - +
217B ASP* 3.0 33.8 + - - +
220B LEU* 3.8 10.9 - - + +
315B ALA 2.8 22.3 + - - +
316B VAL 3.9 2.2 - - - +
318B ILE* 1.3 74.1 - - - +
320B SER* 1.3 57.6 + - - +
321B GLY* 3.0 6.1 + - - -
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Residues in contact with SER 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 3.6 12.8 + - - -
216B LYS* 5.2 4.3 - - - +
316B VAL* 2.9 15.9 + - - -
317B TYR 2.3 23.7 + - - -
318B ILE 3.0 0.8 - - - -
319B ASP* 1.3 75.4 - - - +
321B GLY* 1.3 58.4 + - - +
323B ASP* 2.8 32.4 + - - +
326B PHE* 4.5 14.8 - - - -
327B THR* 3.7 8.3 + - - -
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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
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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