Contacts of the helix formed by residues 321 - 343 (chain B) in PDB entry 3JXI
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 THR 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ASP* 2.8 32.1 + - + +
320B ASN* 1.3 81.0 - - - +
322B ARG* 1.3 65.6 + - - +
323B GLU* 3.1 3.5 + - - +
324B ASN* 3.3 12.0 + - - +
325B THR* 2.9 23.6 + - - -
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Residues in contact with ARG 322 (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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320B ASN 3.9 1.8 + - - -
321B THR* 1.3 72.4 - - - +
323B GLU* 1.3 80.7 + - - +
325B THR* 3.6 5.4 + - - +
326B LYS* 3.1 30.6 + - + +
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B THR* 3.1 4.2 + - - +
322B ARG* 1.3 105.3 + - + +
324B ASN* 1.3 67.0 + - - +
326B LYS* 3.0 34.9 - - - +
327B PHE* 3.3 25.1 + - - +
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Residues in contact with ASN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 3.3 17.8 + - - +
318B ALA* 3.1 9.2 - - - +
319B ASP* 2.9 54.9 + - - +
321B THR* 3.2 8.5 + - - +
323B GLU* 1.3 77.7 - - - +
325B THR* 1.3 60.0 + - - +
327B PHE* 3.3 27.1 + - - -
328B VAL* 2.9 40.5 + - - +
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ASP 3.8 12.5 + - - -
320B ASN 4.1 7.3 + - - -
321B THR 2.9 18.7 + - - -
322B ARG* 3.9 6.1 - - - +
324B ASN* 1.3 77.7 - - - +
326B LYS* 1.3 65.1 + - - +
328B VAL* 4.1 3.8 - - - +
329B THR* 2.9 36.9 + - - +
370B GLY* 4.1 36.3 - - - +
371B ILE* 4.7 1.6 + - - +
374B HIS* 5.8 0.4 - - + -
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ARG* 3.1 18.3 + - + +
323B GLU* 3.0 39.5 - - - +
325B THR* 1.3 77.5 - - - +
327B PHE* 1.3 59.2 + - + +
329B THR* 3.6 6.2 - - - +
330B LYS* 3.0 52.0 + - + +
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ALA 3.7 15.0 - - - -
280B CYS 3.3 26.2 - - - -
281B THR 5.1 0.2 - - - -
282B ASN* 3.5 47.4 + - + +
314B LEU* 4.5 1.1 - - + -
317B ILE* 3.4 20.6 - - + -
323B GLU 3.3 16.0 + - - +
324B ASN* 3.6 30.5 - - - -
326B LYS* 1.3 77.9 - - + +
328B VAL* 1.3 71.1 + - + +
330B LYS* 3.8 11.4 - - + +
331B MET* 3.0 29.6 + - + +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 3.5 37.6 - - + +
317B ILE* 3.7 31.0 - - + -
318B ALA* 4.4 3.6 - - + -
324B ASN* 2.9 35.1 + - - +
325B THR* 4.1 3.8 - - - +
327B PHE* 1.3 81.7 - - + +
329B THR* 1.3 53.0 + - - +
331B MET* 3.6 1.2 - - - +
332B TYR* 2.8 37.1 + - - +
371B ILE* 3.9 25.4 - - + -
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Residues in contact with THR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B THR* 2.9 27.6 + - - +
326B LYS* 3.7 8.1 - - - +
328B VAL* 1.3 75.4 - - - +
330B LYS* 1.3 72.4 + - + +
332B TYR* 3.8 0.3 - - - +
333B ASP* 3.2 28.8 + - - +
370B GLY 4.6 0.2 + - - -
371B ILE* 4.0 13.7 - - - +
374B HIS* 3.2 49.4 - - + +
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Residues in contact with LYS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASN* 6.2 0.2 - - - +
326B LYS* 3.0 43.9 + - + +
327B PHE* 3.4 10.5 + - + +
329B THR* 1.3 86.6 - - + +
331B MET* 1.3 58.6 + - - +
333B ASP* 3.9 4.7 - - - +
334B LEU* 3.0 27.5 + - - +
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Residues in contact with MET 331 (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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279B ALA* 3.6 39.5 - - + +
282B ASN* 3.7 15.9 - - - +
283B GLN 3.7 7.4 - - - +
284B PRO* 3.7 37.5 - - + -
287B VAL* 4.0 23.1 - - - -
314B LEU* 4.0 9.0 - - + -
327B PHE* 3.0 18.6 + - + +
328B VAL 3.6 2.7 - - - +
330B LYS* 1.3 76.6 - - + +
332B TYR* 1.3 65.4 + - - +
334B LEU* 3.3 13.8 + - - +
335B LEU* 3.1 33.2 + - + +
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Residues in contact with TYR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU* 3.6 49.9 - - + +
314B LEU* 3.6 16.2 - - + +
315B VAL* 4.6 1.3 - - + -
328B VAL 2.8 21.3 + - - +
329B THR 3.8 4.7 - - - +
331B MET* 1.3 73.9 - - - +
333B ASP* 1.3 68.4 - - - +
335B LEU 3.4 0.2 + - - -
336B LEU* 3.0 32.5 + - + +
349B GLU* 2.4 43.2 + - + +
359B PRO* 3.5 18.3 - - + +
360B LEU 4.5 1.0 + - - -
371B ILE* 3.8 20.9 - - + -
374B HIS* 5.4 0.2 - + - -
375B ILE* 3.5 33.4 - - + +
378B ARG* 4.1 5.6 - - - -
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Residues in contact with ASP 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B THR* 3.2 10.1 + - - +
330B LYS* 3.9 5.3 - - - +
332B TYR* 1.3 83.3 - - - +
334B LEU* 1.3 66.8 + - - +
336B LEU* 4.3 6.5 - - - -
337B ILE* 3.0 41.9 + - + +
374B HIS* 2.7 41.3 + - - -
378B ARG* 4.0 23.8 + - - +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 5.1 4.3 - - + +
287B VAL* 4.0 24.9 - - + -
288B HIS* 3.5 39.9 - - + +
330B LYS 3.0 17.9 + - - +
331B MET* 3.4 20.2 - - - +
333B ASP* 1.3 74.6 - - - +
335B LEU* 1.3 58.2 + - + +
337B ILE* 3.8 4.8 - - + +
338B LYS* 3.0 38.4 + - + +
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 4.3 10.3 - - + -
279B ALA* 4.1 3.6 - - + -
287B VAL* 3.7 27.8 - - + -
291B THR* 5.0 1.6 - - + -
300B LEU* 3.2 35.0 - - + +
310B VAL* 3.6 36.8 - - + -
311B LEU* 4.2 8.1 - - + -
314B LEU* 4.2 6.5 - - + -
331B MET* 3.1 34.2 + - + +
332B TYR 3.8 2.7 - - - +
334B LEU* 1.3 79.5 - - + +
336B LEU* 1.3 60.6 + - - +
338B LYS* 3.5 4.4 + - + -
339B CYS* 2.9 26.7 + - - +
348B LEU* 4.4 2.2 - - + -
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Residues in contact with LEU 336 (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 LEU* 4.7 2.7 - - + -
332B TYR* 3.0 23.6 + - + +
333B ASP* 3.9 6.1 - - - +
335B LEU* 1.3 74.7 - - - +
337B ILE* 1.3 66.1 + - + +
339B CYS* 3.2 7.5 + - + +
340B ALA* 3.0 29.4 + - + +
347B ASN* 3.8 15.7 - - - +
348B LEU* 4.2 14.1 - - + +
349B GLU* 3.8 32.8 - - + +
378B ARG* 3.6 43.5 - - - +
382B ASP* 4.9 2.2 - - - +
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Residues in contact with ILE 337 (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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333B ASP* 3.0 34.9 + - + +
334B LEU* 3.8 4.5 - - + +
336B LEU* 1.3 83.3 - - + +
338B LYS* 1.3 63.8 + - - +
340B ALA* 3.2 7.8 + - - +
341B LYS* 3.0 22.7 + - + +
378B ARG* 5.7 5.4 - - - -
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 5.5 1.1 - - - -
288B HIS* 4.4 11.7 - - - +
291B THR* 3.3 26.3 + - + +
292B GLU* 2.8 38.9 + - - +
300B LEU* 3.5 26.9 - - + -
334B LEU* 3.0 27.6 + - + +
335B LEU* 3.6 9.0 - - + +
337B ILE* 1.3 77.3 - - - +
339B CYS* 1.3 55.7 + - - +
341B LYS* 3.3 28.1 + - - +
342B LEU* 3.0 31.7 + - + +
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Residues in contact with CYS 339 (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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300B LEU* 4.0 14.3 - - + +
301B ARG* 4.0 18.6 - - - -
335B LEU 2.9 15.5 + - - +
336B LEU 3.2 8.7 + - - +
338B LYS* 1.3 76.7 - - - +
340B ALA* 1.3 54.3 + - - +
343B PHE* 2.7 56.5 + - - +
346B THR* 4.1 12.1 - - - +
348B LEU* 3.9 32.1 - - + +
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Residues in contact with ALA 340 (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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336B LEU* 3.0 15.2 + - + +
337B ILE* 3.2 10.5 + - - +
339B CYS* 1.3 76.5 - - - +
341B LYS* 1.3 64.3 + - - +
343B PHE 3.9 7.0 - - - -
344B PRO* 3.3 25.7 - - + +
346B THR 4.4 7.4 + - - +
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Residues in contact with LYS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ILE* 3.0 13.9 + - + +
338B LYS* 3.3 37.9 + - - +
340B ALA* 1.3 79.5 - - - +
342B LEU* 1.3 92.3 + - + +
344B PRO* 3.8 9.2 - - - +
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Residues in contact with LEU 342 (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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291B THR* 5.2 9.4 - - - +
297B GLN* 5.9 3.6 - - - +
300B LEU* 3.5 30.1 - - + -
338B LYS* 3.0 21.9 + - + +
341B LYS* 1.3 102.0 - - - +
343B PHE* 1.3 91.4 + - + +
344B PRO* 3.5 6.8 - - - +
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Residues in contact with PHE 343 (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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299B ASP* 4.6 4.9 - - - -
300B LEU* 5.0 4.3 - - + -
301B ARG* 3.5 55.0 - - + -
339B CYS* 2.7 30.0 + - - +
340B ALA 3.6 1.3 - - - +
342B LEU* 1.3 104.5 - - + +
344B PRO* 1.4 59.2 - - - +
345B ASP* 3.1 10.5 - - - +
346B THR* 3.0 46.2 + - + +
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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