Contacts of the helix formed by residues 321 - 343 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ASP* 2.7 29.6 + - + +
320A ASN* 1.3 79.5 - - - +
322A ARG* 1.3 61.6 + - - +
323A GLU* 4.6 1.5 + - - +
324A ASN* 3.4 10.9 + - - +
325A THR* 2.9 29.3 + - - -
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ASN 3.9 1.5 + - - -
321A THR* 1.3 75.3 - - - +
323A GLU* 1.3 88.6 + - - +
325A THR* 3.8 7.0 - - - +
326A LYS* 3.0 32.9 + - + +
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Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A THR* 3.4 1.4 + - - +
322A ARG* 1.3 112.3 + - - +
324A ASN* 1.3 63.1 + - - +
326A LYS* 3.2 29.9 - - - +
327A PHE* 3.3 14.7 + - - +
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Residues in contact with ASN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 3.3 21.8 + - - +
318A ALA* 3.2 9.0 - - - +
319A ASP* 2.6 56.0 + - - +
321A THR* 3.4 9.5 + - - +
323A GLU* 1.3 76.2 - - - +
325A THR* 1.3 65.4 + - - +
326A LYS 3.2 0.3 + - - -
327A PHE* 3.2 18.5 + - - -
328A VAL* 3.0 35.4 + - - +
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA* 6.3 1.1 - - - -
319A ASP 4.0 4.7 + - - -
320A ASN* 3.8 14.7 + - - -
321A THR 2.9 20.6 + - - -
322A ARG* 3.8 7.9 - - - +
324A ASN* 1.3 76.8 + - - +
326A LYS* 1.3 59.2 + - - +
328A VAL* 4.8 3.6 - - - -
329A THR* 2.9 43.1 + - + +
370A GLY* 4.1 30.4 - - - +
371A ILE* 5.1 2.2 + - - +
374A HIS* 6.0 0.4 - - + -
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Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG* 3.0 20.3 + - + +
323A GLU* 3.2 28.9 - - - +
325A THR* 1.3 78.7 - - - +
327A PHE* 1.3 62.5 + - + +
329A THR* 3.6 7.2 - - - +
330A LYS* 3.2 23.7 + - + +
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ALA 3.5 22.4 - - - -
280A CYS 3.6 10.5 - - - -
281A THR 5.2 0.2 - - - -
282A ASN* 3.9 41.7 + - + +
314A LEU* 4.4 2.2 - - + -
317A ILE* 3.3 31.9 - - + -
323A GLU 3.3 11.1 + - - +
324A ASN* 3.2 26.5 + - - -
326A LYS* 1.3 75.6 - - + +
328A VAL* 1.3 75.4 + - + +
329A THR 3.2 1.6 - - - -
330A LYS* 3.2 9.8 + - + +
331A MET* 2.9 31.0 + - + +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU* 3.5 37.7 - - + +
317A ILE* 3.8 29.8 - - + -
318A ALA* 4.3 7.4 - - + -
324A ASN* 3.0 32.5 + - - +
325A THR* 4.3 3.4 - - - +
327A PHE* 1.3 86.3 - - + +
329A THR* 1.3 54.7 + - - +
331A MET* 3.7 1.4 - - - +
332A TYR* 2.8 35.2 + - + +
371A ILE* 4.2 22.9 - - + -
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Residues in contact with THR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A THR* 2.9 28.4 + - + +
326A LYS* 3.6 7.0 - - - +
328A VAL* 1.3 78.5 - - - +
330A LYS* 1.3 61.6 + - + +
332A TYR* 3.7 5.2 - - - +
333A ASP* 3.1 37.5 + - - +
371A ILE* 3.9 12.5 - - - +
374A HIS* 3.2 46.5 - - + +
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ASN* 6.3 0.7 - - - +
284A PRO* 6.5 1.3 - - - -
326A LYS* 3.2 15.3 + - + +
327A PHE* 3.2 10.2 + - + +
329A THR* 1.3 82.5 - - + +
331A MET* 1.3 59.7 + - - +
333A ASP* 3.6 5.7 + - - +
334A LEU* 3.0 33.1 + - + +
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Residues in contact with MET 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ALA 4.5 0.2 - - - +
279A ALA* 3.6 38.8 - - + +
282A ASN* 3.7 30.5 - - - +
283A GLN 4.0 3.4 - - - +
284A PRO* 4.0 20.9 - - + -
287A VAL* 4.5 8.5 - - + -
314A LEU* 3.8 20.4 - - + -
327A PHE* 2.9 18.6 + - + +
328A VAL 3.7 3.4 - - - +
330A LYS* 1.3 77.1 - - - +
332A TYR* 1.3 66.3 + - - +
334A LEU* 3.5 21.5 + - + +
335A LEU* 3.0 34.7 + - + +
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Residues in contact with TYR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LEU* 3.6 51.4 - - + +
314A LEU* 3.6 13.6 - - + +
315A VAL* 4.6 2.5 - - + -
328A VAL 2.8 20.6 + - - +
329A THR* 3.7 8.1 - - - +
331A MET* 1.3 78.6 - - - +
333A ASP* 1.3 72.8 + - - +
335A LEU* 3.3 2.3 + - - +
336A LEU* 3.1 27.8 + - + +
349A GLU* 3.0 40.5 + - - +
359A PRO* 3.6 12.3 - - + +
360A LEU 4.7 0.5 + - - -
371A ILE* 4.1 15.5 - - + -
374A HIS* 5.4 0.7 - + - -
375A ILE* 3.5 32.9 - - + +
378A ARG* 6.4 0.7 - - - -
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A THR* 3.1 17.5 + - - +
330A LYS* 4.0 5.5 - - - +
332A TYR* 1.3 87.0 - - - +
334A LEU* 1.3 65.4 + - - +
336A LEU* 3.5 4.7 + - - +
337A ILE* 3.3 31.1 + - + +
374A HIS* 2.6 40.4 + - - -
378A ARG* 3.4 32.9 + - - +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A PRO* 4.5 17.9 - - + -
287A VAL* 4.3 15.9 - - + -
288A HIS* 4.5 20.2 - - + +
330A LYS* 3.0 26.6 + - + +
331A MET* 3.5 21.3 - - + +
333A ASP* 1.3 74.6 - - - +
335A LEU* 1.3 74.8 + - + +
337A ILE* 3.6 7.2 + - - +
338A LYS* 3.1 35.9 + - + +
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU* 4.9 3.8 - - + -
279A ALA* 4.1 2.0 - - + -
287A VAL* 4.1 21.8 - - + -
300A LEU* 3.0 34.7 - - + +
310A VAL* 3.6 36.8 - - + -
311A LEU* 4.0 9.2 - - + -
314A LEU* 3.6 15.5 - - + -
331A MET* 3.0 33.1 + - + +
332A TYR 3.3 3.1 + - - +
334A LEU* 1.3 82.2 - - + +
336A LEU* 1.3 60.7 + - - +
338A LYS* 3.5 4.5 - - + +
339A CYS* 2.9 31.5 + - - +
348A LEU* 4.5 3.1 - - + +
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LEU* 4.4 10.4 - - + +
332A TYR* 3.1 20.2 + - + +
333A ASP 3.7 8.7 - - - +
335A LEU* 1.3 76.5 - - - +
337A ILE* 1.3 56.7 + - - +
339A CYS* 3.5 4.7 + - - +
340A ALA* 3.1 28.1 + - + +
347A ASN* 3.7 25.4 - - - +
348A LEU* 3.9 19.7 - - + +
349A GLU* 3.7 31.9 - - + +
378A ARG* 3.5 35.7 - - - +
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ASP* 3.3 19.6 + - + +
334A LEU* 3.8 6.5 - - - +
336A LEU* 1.3 73.4 - - - +
338A LYS* 1.3 56.5 + - - +
340A ALA* 3.0 7.0 + - - +
341A LYS* 2.7 37.9 + - + +
378A ARG* 4.1 21.5 - - - +
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Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A VAL* 4.8 4.5 - - - -
288A HIS* 3.1 21.0 + - + +
291A THR* 2.6 34.3 + - - -
292A GLU* 2.6 36.8 + - - +
300A LEU* 3.8 23.1 - - + -
334A LEU* 3.1 26.0 + - + +
335A LEU* 3.5 8.5 - - + +
337A ILE* 1.3 79.5 - - - +
339A CYS* 1.3 57.9 + - - +
341A LYS* 3.4 12.2 + - + +
342A LEU* 3.0 42.9 + - + +
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Residues in contact with CYS 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU* 3.5 15.0 - - + +
301A ARG* 4.2 6.7 - - - -
335A LEU 2.9 18.6 + - - +
336A LEU 3.6 5.4 - - - +
337A ILE 3.2 0.2 - - - -
338A LYS* 1.3 77.7 - - - +
340A ALA* 1.3 54.3 + - - +
343A PHE* 2.6 55.0 + - - +
346A THR* 3.6 27.8 - - - +
348A LEU* 3.8 30.7 - - + +
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Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A LEU* 3.1 16.2 + - + +
337A ILE* 3.0 7.9 + - - +
339A CYS* 1.3 75.0 - - - +
341A LYS* 1.3 60.9 + - - +
343A PHE 4.0 7.0 - - - -
344A PRO* 3.1 29.1 - - + +
346A THR 4.7 7.1 + - - +
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Residues in contact with LYS 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ILE* 2.7 17.2 + - + +
338A LYS* 3.4 16.6 - - + +
340A ALA* 1.3 79.7 - - - +
342A LEU* 1.3 79.0 + - + +
344A PRO* 3.8 7.4 - - - +
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A THR* 4.3 19.7 - - - +
292A GLU* 6.2 1.1 - - + -
297A GLN* 5.3 5.4 - - - +
300A LEU* 4.5 5.8 - - + -
338A LYS* 3.0 39.3 + - + +
341A LYS* 1.3 94.7 - - + +
343A PHE* 1.3 94.6 + - + +
344A PRO* 3.4 7.3 - - - +
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Residues in contact with PHE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ASP* 3.8 14.4 - - - -
300A LEU* 4.6 10.3 - - + -
301A ARG* 3.3 50.9 - - + -
339A CYS* 2.6 33.2 + - - +
340A ALA* 4.0 0.5 - - - -
342A LEU* 1.3 103.9 - - + +
344A PRO* 1.3 68.4 - - - +
345A ASP* 3.1 3.8 - - - +
346A THR* 3.0 36.6 + - + +
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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