Contacts of the helix formed by residues 299 - 321 (chain B) in PDB entry 4J15
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 TYR 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 2.9 25.6 + - - +
295B PHE* 3.4 16.5 - - + -
298B HIS* 1.3 86.5 + + - +
300B HIS* 1.3 79.2 + + - +
301B GLU 3.1 0.4 - - - -
302B VAL* 2.9 15.7 + - - +
303B MET* 3.0 11.0 + - + -
392B ASP* 2.7 28.8 + - - -
393B LYS* 2.9 26.0 + - - +
414B ASN* 3.4 42.4 - - + -
416B TYR* 3.6 31.6 - + - -
430B GLN* 3.7 20.4 - - + -
467B ALA* 4.2 6.6 - - + +
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Residues in contact with HIS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 2.9 27.4 + - - +
604A GOL 3.6 22.8 - - - -
298B HIS* 3.0 29.2 + + + +
299B TYR* 1.3 99.1 + + - +
301B GLU* 1.3 57.0 + - - +
302B VAL 3.1 0.2 - - - -
303B MET* 3.6 21.9 - - + +
304B GLU* 2.8 44.9 + - - +
345B ARG* 3.7 15.3 + - - -
392B ASP* 2.7 25.9 + - - -
393B LYS* 5.2 3.4 - - - -
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 6.1 0.3 - - - -
293B MET* 4.6 6.4 - - + +
295B PHE* 3.4 9.8 - - + +
296B ASN* 2.7 41.1 + - - +
297B TYR* 2.9 25.8 + - - +
298B HIS* 2.9 26.5 + - + +
300B HIS* 1.3 76.3 - - - +
302B VAL* 1.3 60.7 + - + +
304B GLU* 4.0 8.9 - - - +
305B GLU* 3.4 27.3 + - - +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 5.2 1.6 - - + -
293B MET* 3.5 52.5 - - + +
295B PHE* 3.7 26.9 - - + -
299B TYR 2.9 7.4 + - - +
301B GLU* 1.3 73.0 - - - +
303B MET* 1.3 65.2 + - - +
304B GLU 3.1 1.6 - - - -
305B GLU* 2.9 3.3 + - - +
306B ILE* 2.8 40.4 + - + +
416B TYR* 4.3 0.7 - - - +
467B ALA* 3.6 31.0 - - + +
468B GLY* 4.3 0.7 - - - -
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Residues in contact with MET 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B TYR 3.0 13.9 + - - +
300B HIS* 3.6 31.4 - - + +
302B VAL* 1.3 75.1 - - - +
304B GLU* 1.3 67.0 + - + +
306B ILE* 3.3 6.4 + - - +
307B ALA* 2.9 30.8 + - - +
345B ARG* 3.3 27.6 - - + -
390B ILE* 3.8 30.1 - - + -
392B ASP* 4.1 13.0 - - - +
416B TYR* 4.0 30.8 + - + -
418B MET* 3.7 17.7 - - + +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 4.8 6.2 + - - -
300B HIS* 2.8 33.8 + - - +
301B GLU* 4.0 7.9 - - - +
303B MET* 1.3 88.3 - - + +
305B GLU* 1.3 57.9 + - + +
307B ALA* 3.8 5.3 - - - +
308B ASP* 2.9 32.5 + - - +
390B ILE* 5.9 0.4 - - + -
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 5.9 1.1 - - + -
213B LYS* 2.8 54.8 + - + +
215B PHE* 5.2 5.7 - - + -
264B LYS* 5.1 3.3 + - - -
291B ILE* 5.9 0.2 - - - -
293B MET* 4.0 30.0 - - + +
301B GLU 3.4 15.6 + - - +
302B VAL 2.9 8.3 + - - +
304B GLU* 1.3 79.6 - - + +
306B ILE* 1.3 55.6 + - + +
308B ASP* 3.8 4.2 - - - +
309B THR* 2.7 36.7 + - - -
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 4.1 26.5 - - + -
302B VAL* 2.8 30.0 + - + +
303B MET 3.6 6.1 - - - +
305B GLU* 1.3 74.5 - - + +
307B ALA* 1.3 65.7 + - - +
309B THR* 3.2 8.8 + - - -
310B MET* 3.1 26.2 + - + +
416B TYR* 4.1 12.1 - - + +
418B MET* 3.8 14.6 - - + -
426B LEU* 3.6 25.8 - - + -
468B GLY* 3.8 32.3 - - - +
469B GLY* 4.0 9.2 - - - +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET 2.9 20.7 + - - +
304B GLU* 3.9 5.6 - - - +
306B ILE* 1.3 72.7 - - - +
308B ASP* 1.3 58.3 + - - +
310B MET* 3.2 6.2 + - - +
311B VAL* 3.0 27.9 + - - +
343B THR* 3.5 23.3 - - + +
388B PHE* 3.8 12.9 - - + -
390B ILE* 3.8 22.0 - - + -
418B MET* 4.0 5.4 - - + +
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Residues in contact with ASP 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LYS* 2.8 28.8 + - - +
304B GLU 2.9 19.5 + - - +
305B GLU* 3.8 6.5 - - - +
307B ALA* 1.3 74.2 - - - +
309B THR* 1.3 60.4 + - - +
311B VAL* 3.2 11.8 + - - +
312B GLN* 2.9 48.9 + - - +
341B GLU* 5.6 0.5 - - - +
343B THR* 5.3 0.2 - - - -
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 4.2 26.7 - - + +
209B THR* 4.2 17.9 - - + -
210B LEU* 3.6 36.1 - - + +
213B LYS* 3.9 6.9 - - - -
291B ILE* 5.0 3.4 - - + -
305B GLU 2.7 20.6 + - - -
306B ILE* 3.2 10.6 + - - -
308B ASP* 1.3 76.7 + - - +
310B MET* 1.3 58.1 + - - +
312B GLN* 3.3 3.8 + - - +
313B ILE* 3.0 31.0 + - + +
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Residues in contact with MET 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 5.6 2.2 - - - -
306B ILE* 3.1 21.9 + - + +
307B ALA 3.5 6.7 - - - +
309B THR* 1.3 76.3 - - - +
311B VAL* 1.3 59.9 + - - +
313B ILE* 3.1 25.7 + - + +
314B PHE* 2.9 60.4 + - + -
388B PHE* 3.7 25.4 - - + -
418B MET* 5.1 1.8 - - - -
420B MET* 4.4 0.2 - - - -
425B ILE* 4.1 17.3 - - + -
426B LEU* 6.0 0.4 - - + -
471B ILE* 4.0 27.6 - - + -
476B VAL* 4.1 17.5 - - + -
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA 3.0 19.1 + - - +
308B ASP* 3.2 15.0 + - - +
310B MET* 1.3 74.6 - - - +
312B GLN* 1.3 69.8 + - - +
314B PHE* 3.3 8.4 + - + +
315B LYS* 3.0 43.7 + - + +
339B PHE* 4.2 10.3 - - + -
340B LEU 4.2 12.6 - - - +
341B GLU* 3.8 23.6 - - + +
342B PRO* 5.7 0.9 - - + -
343B THR* 3.6 19.3 - - - +
388B PHE* 4.5 8.1 - - + -
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Residues in contact with GLN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.2 7.4 - - + +
209B THR* 3.5 35.9 - - + +
308B ASP* 2.9 41.1 + - - +
309B THR 3.6 4.9 - - - +
310B MET 3.3 0.2 - - - -
311B VAL* 1.3 86.0 - - - +
313B ILE* 1.3 61.0 + - - +
315B LYS* 3.9 21.2 - - - +
316B GLY* 3.0 21.0 + - - -
341B GLU* 4.7 2.8 - - - +
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 4.3 27.6 - - + +
205B LEU* 3.6 12.5 - - + +
206B PHE* 4.0 45.3 - - + +
309B THR 3.0 21.1 + - - +
310B MET* 3.1 33.6 + - + +
312B GLN* 1.3 75.9 - - - +
314B PHE* 1.3 71.7 + - + +
316B GLY 3.2 1.6 + - - -
317B LEU* 2.9 42.1 + - + +
471B ILE* 5.0 2.5 - - + -
476B VAL* 5.6 1.3 - - + -
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B MET* 2.9 52.6 + - + +
311B VAL* 3.8 5.4 - - - +
313B ILE* 1.3 80.7 - - + +
315B LYS* 1.3 63.2 + - - +
317B LEU* 3.4 2.7 + - - +
318B GLN* 3.1 28.4 + - - +
337B PHE* 3.5 28.7 - + - -
339B PHE* 3.5 33.9 - + + -
388B PHE* 3.5 30.5 - + - -
420B MET* 3.8 25.4 - - + -
476B VAL* 5.1 1.8 - - + -
480B PHE* 3.9 25.2 - + + -
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Residues in contact with LYS 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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311B VAL* 3.0 38.3 + - + +
312B GLN* 3.9 22.7 - - - +
314B PHE* 1.3 78.6 - - - +
316B GLY* 1.3 56.6 + - - +
318B GLN* 3.1 6.8 + - - +
319B GLU* 2.8 50.5 + - - +
339B PHE* 3.6 20.4 - - + -
341B GLU* 3.4 24.8 + - - +
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Residues in contact with GLY 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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205B LEU* 3.9 22.7 - - - -
312B GLN 3.0 16.0 + - - -
313B ILE 3.7 2.7 - - - -
315B LYS* 1.3 74.9 - - - +
317B LEU* 1.3 59.3 + - - +
319B GLU* 4.4 8.1 - - - -
320B ARG* 2.9 41.5 + - - +
321B PHE* 4.0 0.9 - - - -
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Residues in contact with LEU 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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198B LEU* 4.0 19.5 - - + +
202B ILE* 3.7 37.0 - - + +
205B LEU* 3.8 16.6 - - + -
313B ILE* 2.9 26.6 + - + +
314B PHE 3.7 4.0 - - - +
315B LYS 3.3 0.2 - - - -
316B GLY* 1.3 75.8 - - - +
318B GLN* 1.3 59.4 + - - +
321B PHE* 2.8 49.4 + - + +
325B ILE* 3.4 9.5 - - + +
480B PHE* 3.8 42.0 - - + -
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Residues in contact with GLN 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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314B PHE 3.1 15.4 + - - +
315B LYS* 3.7 4.8 - - - +
317B LEU* 1.3 75.7 - - - +
319B GLU* 1.3 59.3 - - - +
321B PHE 4.8 0.2 - - - -
322B GLN* 3.2 29.1 - - - +
325B ILE* 4.2 6.1 - - + -
336B PRO* 4.7 5.0 - - - +
337B PHE* 3.0 37.6 + - - +
339B PHE* 3.5 27.8 - - - -
480B PHE* 3.9 14.8 - - + -
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LYS* 2.8 42.2 + - - +
316B GLY* 3.9 6.9 - - - +
318B GLN* 1.3 79.3 - - - +
320B ARG* 1.3 70.6 + - + +
321B PHE 3.8 0.2 - - - -
322B GLN* 5.0 4.5 + - - +
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B HIS* 3.8 29.5 + - - -
205B LEU* 3.6 20.4 - - - +
208B GLU* 3.4 22.2 + - - -
316B GLY* 2.9 19.0 + - - +
319B GLU* 1.3 87.7 + - + +
321B PHE* 1.3 81.7 + - + +
322B GLN* 3.5 2.8 + - - -
324B GLU* 4.0 5.0 - - - +
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ARG* 3.5 21.8 - - + -
198B LEU* 3.9 20.6 - - + -
201B GLY* 3.5 28.0 - - - -
204B HIS* 6.3 2.0 - + - -
205B LEU* 4.8 4.7 - - + -
316B GLY 4.0 5.6 - - - -
317B LEU* 2.8 31.2 + - + +
320B ARG* 1.3 103.5 - - + +
322B GLN* 1.3 59.1 + - - +
323B THR 3.4 2.5 - - - -
324B GLU* 3.4 35.5 - - + +
325B ILE* 2.9 28.6 + - - +
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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