Contacts of the helix formed by residues 321 - 343 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ASP* 2.7 33.3 + - + +
320D ASN* 1.3 79.8 - - - +
322D ARG* 1.3 60.1 + - - +
323D GLU* 4.7 1.8 + - - +
324D ASN* 3.3 12.0 + - - +
325D THR* 2.6 33.5 + - - +
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Residues in contact with ARG 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D ASN 4.1 7.5 + - - -
321D THR* 1.3 72.6 - - - +
323D GLU* 1.3 63.6 + - - +
325D THR* 3.2 8.2 + - - +
326D LYS* 2.9 32.9 + - + +
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Residues in contact with GLU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D THR* 4.7 1.4 + - - +
322D ARG* 1.3 82.6 - - - +
324D ASN* 1.3 59.8 + - - +
326D LYS* 3.2 41.2 + - - +
327D PHE* 3.2 27.3 + - + +
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Residues in contact with ASN 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ILE* 3.1 33.5 + - - +
318D ALA* 3.5 7.3 - - - -
319D ASP* 2.8 52.0 + - - +
321D THR* 3.3 10.3 + - - +
322D ARG 3.1 0.6 - - - -
323D GLU* 1.3 77.2 - - - +
325D THR* 1.3 62.1 + - - +
326D LYS 3.2 0.3 + - - -
327D PHE* 3.2 14.6 + - + -
328D VAL* 2.8 36.8 + - - +
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Residues in contact with THR 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ALA* 6.0 1.8 - - - -
319D ASP 4.3 2.0 - - - +
320D ASN* 3.7 21.1 - - - +
321D THR 2.6 37.8 + - - +
322D ARG* 4.0 7.4 + - - +
324D ASN* 1.3 79.1 + - - +
326D LYS* 1.3 56.6 + - - +
328D VAL* 4.2 6.4 - - - +
329D THR* 2.8 38.9 + - - -
370D GLY* 4.3 29.2 + - - -
371D ILE* 4.8 2.6 - - - +
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Residues in contact with LYS 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D ARG* 2.9 18.6 + - + +
323D GLU* 3.2 34.7 + - - +
325D THR* 1.3 79.4 + - - +
327D PHE* 1.3 62.8 + - - +
329D THR* 3.7 7.3 - - + +
330D LYS* 3.2 34.5 + - + +
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Residues in contact with PHE 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ALA 3.3 24.2 - - - -
280D CYS 3.6 10.3 - - - -
281D THR 4.9 0.2 - - - -
282D ASN* 3.5 50.5 + - + +
314D LEU* 4.7 0.9 - - + -
317D ILE* 3.4 30.1 - - + -
323D GLU 3.2 21.9 + - - +
324D ASN* 3.2 25.4 + - + -
326D LYS* 1.3 81.2 - - - +
328D VAL* 1.3 65.8 + - + +
329D THR 3.2 0.2 - - - -
330D LYS* 3.9 6.1 - - - +
331D MET* 2.9 33.7 + - + +
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Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D LEU* 3.7 31.2 - - + +
317D ILE* 3.2 35.0 - - + -
318D ALA* 4.2 8.7 - - + -
324D ASN* 2.8 29.9 + - - +
325D THR* 4.0 5.2 - - - +
327D PHE* 1.3 84.5 - - + +
329D THR* 1.3 56.9 + - - +
331D MET* 3.9 3.1 - - - +
332D TYR* 3.0 28.2 + - - +
371D ILE* 4.0 24.7 - - + -
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Residues in contact with THR 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D THR* 2.8 27.5 + - - -
326D LYS* 3.7 9.6 - - + +
328D VAL* 1.3 75.3 - - - +
330D LYS* 1.3 70.3 + - + +
332D TYR* 3.4 2.9 + - - +
333D ASP* 3.1 31.6 + - - +
370D GLY 4.8 1.0 + - - -
371D ILE* 4.2 11.1 - - - +
374D HIS* 3.2 46.8 + - + +
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Residues in contact with LYS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D PRO* 6.4 3.6 - - - -
326D LYS* 3.2 24.4 + - + +
327D PHE* 4.1 5.6 - - - +
329D THR* 1.3 83.9 - - + +
331D MET* 1.3 56.8 - - - +
333D ASP* 3.8 5.4 + - - +
334D LEU* 3.2 29.1 + - + +
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Residues in contact with MET 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ALA* 3.4 47.3 - - + +
282D ASN* 3.7 15.3 - - - +
283D GLN 3.5 26.2 - - - +
284D PRO* 3.8 18.4 - - + -
287D VAL* 4.0 15.3 - - + -
314D LEU* 4.1 8.3 - - + -
327D PHE* 2.9 20.5 + - + +
328D VAL 3.9 3.1 - - - +
330D LYS* 1.3 76.0 - - - +
332D TYR* 1.3 65.1 + - - +
334D LEU* 3.3 19.4 + - - +
335D LEU* 3.1 33.1 + - + +
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Residues in contact with TYR 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D LEU* 3.5 45.7 - - + +
314D LEU* 3.8 14.5 - - + +
315D VAL* 4.8 2.0 - - + -
328D VAL 3.0 20.7 + - - +
329D THR 3.5 6.1 - - - +
331D MET* 1.3 75.0 - - - +
333D ASP* 1.3 68.6 + - - +
335D LEU* 3.3 5.4 + - - +
336D LEU* 3.1 42.1 + - + +
349D GLU* 2.7 33.8 + - - +
359D PRO* 3.5 18.5 - - + +
360D LEU 4.9 0.2 + - - -
371D ILE* 4.2 19.3 - - + -
374D HIS* 5.0 0.9 - + - -
375D ILE* 3.4 34.1 - - + +
378D ARG* 4.3 2.5 - - - -
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Residues in contact with ASP 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D THR* 3.1 12.9 + - - +
330D LYS* 4.2 5.1 - - - +
332D TYR* 1.3 79.8 - - - +
334D LEU* 1.3 65.3 + - - +
336D LEU* 3.8 6.1 - - - +
337D ILE* 3.1 38.5 + - + +
374D HIS* 2.6 44.3 + - - -
378D ARG* 3.6 21.4 - - - +
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D PRO* 5.0 7.4 - - + +
287D VAL* 3.4 34.3 - - + -
288D HIS* 3.3 35.4 - - + +
330D LYS* 3.2 19.9 + - + +
331D MET* 3.3 23.5 + - - +
333D ASP* 1.3 76.2 - - - +
335D LEU* 1.3 60.3 - - + +
337D ILE* 3.8 6.7 - - - +
338D LYS* 3.1 39.3 + - + +
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Residues in contact with LEU 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D LEU* 4.4 15.0 - - + -
279D ALA* 4.3 0.4 - - + -
287D VAL* 4.0 25.4 - - + -
291D THR* 5.7 0.9 - - + -
300D LEU* 3.1 40.6 - - + +
310D VAL* 3.5 42.2 - - + -
311D LEU* 4.5 4.9 - - + -
314D LEU* 3.7 17.3 - - + -
331D MET* 3.1 27.7 + - + +
332D TYR* 3.3 4.5 + - - +
334D LEU* 1.3 82.3 - - + +
336D LEU* 1.3 57.5 + - - +
338D LYS* 4.0 3.1 - - + -
339D CYS* 3.3 12.1 + - - +
348D LEU* 4.3 5.8 - - + +
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D LEU* 4.4 10.3 - - + -
332D TYR* 3.1 34.0 + - + +
333D ASP* 3.9 6.1 - - - +
334D LEU 3.2 0.2 - - - -
335D LEU* 1.3 75.6 - - - +
337D ILE* 1.3 65.6 + - + +
338D LYS 3.1 1.3 - - - -
339D CYS* 3.2 4.5 + - + +
340D ALA* 3.0 22.7 + - - +
347D ASN* 5.2 2.9 - - - +
348D LEU* 4.4 14.1 - - + +
349D GLU* 3.5 39.7 - - + +
378D ARG* 3.6 30.5 - - - +
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Residues in contact with ILE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D ASP* 3.1 27.9 + - + +
334D LEU* 3.8 6.3 - - - +
336D LEU* 1.3 77.5 - - + +
338D LYS* 1.3 60.5 + - + +
340D ALA* 3.4 8.6 + - + +
341D LYS* 3.2 41.8 + - + +
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Residues in contact with LYS 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D VAL* 6.2 1.3 - - - -
288D HIS* 4.9 7.0 - - + +
291D THR* 3.2 30.8 + - - -
292D GLU* 3.0 43.6 + - - +
300D LEU* 3.5 20.2 - - + -
334D LEU* 3.1 34.6 + - + +
335D LEU* 4.5 2.2 - - + -
336D LEU 3.1 0.2 - - - -
337D ILE* 1.3 76.0 - - + +
339D CYS* 1.3 52.8 + - - +
341D LYS* 3.2 27.3 + - + +
342D LEU* 2.8 51.5 + - + +
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Residues in contact with CYS 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D LEU* 4.0 8.7 - - + +
301D ARG* 4.1 20.0 - - - -
335D LEU 3.3 13.9 + - - +
336D LEU* 3.2 8.8 + - + +
338D LYS* 1.3 77.1 - - - +
340D ALA* 1.3 59.8 + - - +
342D LEU* 4.7 1.6 - - - -
343D PHE* 3.0 51.0 + - - +
344D PRO* 4.1 0.2 - - - +
346D THR* 4.7 9.3 - - - +
348D LEU* 3.8 39.9 - - + +
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Residues in contact with ALA 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D LEU 3.0 11.9 + - - +
337D ILE* 3.5 14.4 - - + +
339D CYS* 1.3 77.1 - - - +
341D LYS* 1.3 60.6 + - + +
344D PRO* 3.5 24.9 - - - +
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Residues in contact with LYS 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D ILE* 3.2 35.0 + - + +
338D LYS* 3.2 29.4 + - + +
340D ALA* 1.3 78.5 - - + +
342D LEU* 1.3 69.1 + - + +
344D PRO* 3.8 7.3 - - - +
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Residues in contact with LEU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D THR* 5.0 8.5 - - - +
297D GLN* 5.1 10.1 - - - +
300D LEU* 4.2 20.0 - - + -
338D LYS* 2.8 39.7 + - + +
341D LYS* 1.3 78.0 - - + +
343D PHE* 1.3 102.5 + - + +
344D PRO* 3.4 6.7 - - - +
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Residues in contact with PHE 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D ASP* 3.4 22.4 - - - -
300D LEU* 4.7 9.9 - - + -
301D ARG* 3.5 44.6 - - + +
339D CYS* 3.0 26.2 + - - +
342D LEU* 1.3 120.9 - - + +
344D PRO* 1.3 60.9 - - - +
345D ASP 3.3 2.9 - - - -
346D THR* 3.1 40.1 + - + +
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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