Contacts of the helix formed by residues 321 - 343 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319C ASP* 2.7 32.4 + - + +
320C ASN* 1.3 80.0 - - - +
322C ARG* 1.3 66.4 + - - +
323C GLU* 4.2 3.6 + - - +
324C ASN* 3.3 13.3 + - - +
325C THR* 2.9 24.2 + - - -
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Residues in contact with ARG 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ASN 3.6 21.8 + - - -
321C THR* 1.3 74.1 - - - +
323C GLU* 1.3 61.2 + - - +
325C THR* 3.8 7.2 + - - -
326C LYS* 3.0 29.7 + - - +
165D ARG* 3.3 44.4 - - - +
207D GLY 5.8 0.4 - - - -
211D GLU* 3.6 32.3 + - - -
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Residues in contact with GLU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C THR* 3.2 4.1 + - - +
322C ARG* 1.3 82.8 - - - +
324C ASN* 1.3 65.1 + - - +
326C LYS* 3.4 27.2 + - - +
327C PHE* 3.2 26.1 + - + +
165D ARG* 4.8 6.8 + - - -
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Residues in contact with ASN 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ILE* 3.1 24.2 + - - +
318C ALA* 3.4 8.1 - - - -
319C ASP* 3.0 54.4 + - - +
321C THR* 3.3 8.4 + - - +
323C GLU* 1.3 79.7 - - - +
325C THR* 1.3 58.8 + - - +
327C PHE* 3.4 22.7 + - + -
328C VAL* 2.9 37.4 + - - +
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Residues in contact with THR 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ALA* 5.1 4.9 - - + -
319C ASP 2.9 28.7 - - - +
320C ASN* 3.9 12.7 + - - +
321C THR 2.9 20.1 + - - +
322C ARG* 3.8 7.1 + - - -
324C ASN* 1.3 77.2 - - - +
326C LYS* 1.3 66.7 + - - +
328C VAL* 4.3 6.1 - - + -
329C THR* 3.0 28.5 + - - -
370C GLY* 4.3 28.7 - - - -
371C ILE 4.7 4.0 - - - +
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Residues in contact with LYS 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C ARG 3.0 20.5 + - - +
323C GLU* 3.5 27.9 + - - +
324C ASN 3.2 0.4 - - - -
325C THR* 1.3 79.6 + - - +
327C PHE* 1.3 63.1 + - + +
329C THR* 3.7 5.9 - - - +
330C LYS* 3.3 49.8 + - + +
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ALA 3.6 22.7 - - - -
280C CYS 3.4 20.0 - - - -
281C THR* 4.9 0.7 - - - -
282C ASN* 3.4 47.6 + - + +
314C LEU* 4.6 1.1 - - + -
317C ILE* 3.7 14.6 - - + -
323C GLU* 3.2 16.1 + - + +
324C ASN* 3.5 34.5 - - + -
326C LYS* 1.3 77.7 - - + +
328C VAL* 1.3 66.1 + - + +
329C THR 3.2 1.6 - - - -
330C LYS* 3.7 7.9 - - - +
331C MET* 2.9 34.7 + - + +
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Residues in contact with VAL 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C LEU* 3.8 29.9 - - + +
317C ILE* 3.2 35.4 - - + -
318C ALA* 4.4 4.0 - - + -
324C ASN* 2.9 31.2 + - - +
325C THR* 4.2 5.6 - - - +
327C PHE* 1.3 85.7 - - + +
329C THR* 1.3 56.4 + - - +
331C MET* 3.9 1.0 - - - +
332C TYR* 2.9 30.7 + - - +
371C ILE* 4.0 28.3 - - + -
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Residues in contact with THR 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C THR* 3.0 20.1 + - - +
326C LYS* 3.7 7.9 - - - +
328C VAL* 1.3 74.8 - - - +
330C LYS* 1.3 71.0 + - + +
332C TYR* 3.5 2.1 + - - +
333C ASP* 3.1 30.6 + - - +
370C GLY 4.4 5.0 + - - -
371C ILE* 3.8 14.2 - - - +
374C HIS* 3.3 46.7 + - + +
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Residues in contact with LYS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C ASN* 6.1 1.1 - - - +
326C LYS* 3.3 45.7 + - + +
327C PHE* 3.7 10.1 - - - +
329C THR* 1.3 85.1 - - + +
331C MET* 1.3 52.8 + - - +
333C ASP* 3.2 9.0 + - - +
334C LEU* 2.8 34.3 + - - +
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Residues in contact with MET 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C ALA* 3.5 48.2 - - + +
282C ASN* 3.6 16.2 - - - +
283C GLN 3.5 25.8 - - - +
284C PRO* 3.7 14.6 - - + -
287C VAL* 4.1 7.6 - - - -
314C LEU* 4.1 12.1 - - + -
327C PHE* 2.9 20.1 + - + +
328C VAL 3.9 3.6 - - - +
330C LYS* 1.3 77.2 - - - +
332C TYR* 1.3 57.4 + - - +
334C LEU* 3.3 29.1 + - - +
335C LEU* 3.0 36.7 + - + +
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Residues in contact with TYR 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C LEU* 3.9 44.3 - - + +
314C LEU* 4.0 14.7 - - + +
315C VAL* 4.6 0.9 - - + -
328C VAL 2.9 19.7 + - - +
329C THR 3.5 5.8 - - - +
331C MET* 1.3 76.3 - - - +
333C ASP* 1.3 67.3 + - - +
335C LEU* 3.4 4.2 + - - +
336C LEU* 3.1 38.7 + - + +
349C GLU* 2.9 31.8 + - - +
359C PRO* 3.4 17.5 - - + +
360C LEU 4.6 0.7 + - - -
371C ILE* 4.0 21.5 - - + -
374C HIS* 5.1 1.6 - + - -
375C ILE* 3.4 35.8 - - + +
378C ARG* 4.3 3.4 - - - -
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Residues in contact with ASP 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C THR* 3.1 11.5 + - - +
330C LYS* 3.5 9.2 - - - +
332C TYR* 1.3 76.3 - - - +
334C LEU* 1.3 66.9 + - - +
336C LEU* 3.4 7.6 + - - +
337C ILE* 3.2 33.5 + - + +
374C HIS* 2.9 37.1 + - - -
378C ARG* 4.1 16.7 - - - +
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Residues in contact with LEU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C PRO* 4.2 19.3 - - + -
287C VAL* 4.0 19.1 - - + -
288C HIS* 3.6 32.8 - - + +
330C LYS 2.8 17.7 + - - +
331C MET* 3.3 32.7 + - - +
333C ASP* 1.3 71.5 - - - +
335C LEU* 1.3 58.0 + - - +
337C ILE* 3.2 13.2 + - + +
338C LYS* 3.0 32.2 + - + +
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Residues in contact with LEU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C LEU* 4.9 10.8 - - + -
279C ALA* 4.2 0.2 - - + -
287C VAL* 3.6 34.5 - - + -
300C LEU* 4.2 13.0 - - + +
310C VAL* 3.5 44.9 - - + -
311C LEU* 4.3 11.0 - - + -
314C LEU* 3.5 18.2 - - + -
331C MET* 3.0 26.0 + - + +
332C TYR 3.9 3.1 - - - +
333C ASP 3.3 0.2 - - - -
334C LEU* 1.3 76.2 - - + +
336C LEU* 1.3 58.0 + - - +
338C LYS* 3.9 5.6 - - + +
339C CYS* 3.0 29.3 + - - +
348C LEU* 4.4 4.9 - - + +
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Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C LEU* 3.7 24.5 - - + -
332C TYR* 3.1 40.9 + - + +
333C ASP* 3.9 6.5 - - - +
334C LEU 3.3 0.2 - - - -
335C LEU* 1.3 76.9 - - - +
337C ILE* 1.3 58.7 + - + +
339C CYS* 3.4 4.7 + - + +
340C ALA* 3.0 27.7 + - - +
347C ASN* 5.5 1.1 - - - +
348C LEU* 4.0 15.3 - - + +
349C GLU* 3.9 15.0 - - + +
378C ARG* 3.5 40.4 - - - +
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Residues in contact with ILE 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ASP* 3.2 20.7 + - + +
334C LEU* 3.2 14.9 + - + +
336C LEU* 1.3 75.0 - - + +
338C LYS* 1.3 67.3 + - + +
340C ALA* 3.3 6.8 + - - +
341C LYS* 3.2 43.1 + - + +
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Residues in contact with LYS 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C VAL* 5.3 6.7 - - + -
288C HIS* 4.2 12.3 - - + +
291C THR* 3.4 25.8 - - + +
292C GLU* 2.8 40.8 + - - +
300C LEU* 3.6 19.7 - - + -
334C LEU* 3.0 27.6 + - + +
335C LEU* 3.9 6.7 - - + +
337C ILE* 1.3 78.4 - - + +
339C CYS* 1.3 53.0 + - - +
341C LYS* 3.3 14.1 + - + +
342C LEU* 2.7 56.0 + - + +
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Residues in contact with CYS 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C LEU* 3.4 31.9 - - + -
301C ARG* 4.8 1.1 - - - -
335C LEU 3.0 15.2 + - - +
336C LEU* 3.7 7.0 - - - +
337C ILE 3.2 0.2 - - - -
338C LYS* 1.3 75.1 - - - +
340C ALA* 1.3 60.1 + - - +
342C LEU* 4.8 0.7 - - - -
343C PHE* 2.7 55.6 + - - +
346C THR* 4.2 17.9 - - - -
348C LEU* 3.8 24.7 - - + -
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Residues in contact with ALA 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C LEU 3.0 17.6 + - - +
337C ILE* 3.3 8.0 + - - +
339C CYS* 1.3 76.7 - - - +
341C LYS* 1.3 62.8 + - + +
344C PRO* 3.7 26.4 - - - +
346C THR 6.1 0.4 - - - -
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Residues in contact with LYS 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ILE* 3.2 31.0 + - + +
338C LYS* 3.6 19.1 - - + +
340C ALA* 1.3 79.3 - - + +
342C LEU* 1.3 69.1 + - + +
344C PRO* 4.2 5.0 - - - +
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C THR* 3.9 41.1 - - + +
292C GLU* 6.1 0.4 - - + -
297C GLN* 4.8 8.5 - - - +
298C ALA 5.7 0.7 - - - +
300C LEU* 4.2 12.6 - - + -
338C LYS* 2.7 36.7 + - - +
341C LYS* 1.3 79.1 - - + +
343C PHE* 1.3 91.6 + - + +
344C PRO* 3.6 5.6 - - - +
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Residues in contact with PHE 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C GLN* 6.1 2.5 - - - -
298C ALA 5.9 0.2 - - - -
299C ASP* 3.8 28.3 - - + -
300C LEU* 4.2 21.8 - - + -
301C ARG* 3.6 42.0 - - + -
339C CYS* 2.7 23.6 + - - +
340C ALA* 4.9 0.2 - - - -
342C LEU* 1.3 101.2 - - + +
344C PRO* 1.3 65.9 - - - +
345C ASP 3.1 3.1 - - - -
346C THR* 3.1 35.1 + - + +
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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