Contacts of the helix formed by residues 368 - 384 (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 LYS 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A VAL* 2.8 32.4 + - + +
316A ALA* 2.9 16.2 + - - +
318A ALA* 2.5 33.1 + - + +
319A ASP* 5.0 1.6 - - - +
320A ASN* 3.6 11.4 - - - +
363A ALA* 2.8 18.7 + - - +
366A THR* 3.5 35.3 + - - +
367A GLY* 1.3 71.3 - - - +
369A ILE* 1.3 63.6 + - - +
370A GLY 3.3 2.9 + - - -
371A ILE* 3.4 20.9 - - + +
372A PHE* 3.0 24.5 + - - +
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Residues in contact with ILE 369 (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* 3.2 15.0 + - + +
367A GLY* 2.9 20.7 + - - +
368A LYS* 1.3 70.3 - - - +
370A GLY* 1.3 60.2 + - - +
372A PHE* 4.3 6.3 - - - -
373A GLN* 2.9 60.7 + - + +
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Residues in contact with GLY 370 (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* 3.3 12.2 + - - -
325A THR* 4.1 29.0 - - - +
369A ILE* 1.3 83.5 - - - +
371A ILE* 1.3 61.7 + - - +
373A GLN* 3.6 6.2 + - - +
374A HIS* 3.2 22.0 + - - +
377A ARG* 4.9 1.7 + - - -
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Residues in contact with ILE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 4.1 17.0 - - + -
318A ALA* 4.1 13.5 - - + -
320A ASN* 5.0 0.4 + - - -
325A THR* 4.9 3.1 + - - +
328A VAL* 4.2 21.5 - - + -
329A THR* 3.9 22.7 - - - +
332A TYR* 4.1 24.2 - - + -
363A ALA* 3.9 10.1 - - + -
368A LYS* 3.4 30.7 - - + +
370A GLY* 1.3 75.1 - - - +
372A PHE* 1.3 57.6 + - - +
374A HIS* 3.2 10.0 + - + +
375A ILE* 3.0 50.5 + - + +
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Residues in contact with PHE 372 (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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360A LEU* 3.5 47.3 - - + -
361A MET* 4.9 5.2 - - + -
363A ALA* 4.1 9.2 - - + -
364A ALA* 3.7 28.0 - - + -
368A LYS 3.0 21.3 + - - +
369A ILE* 3.6 5.8 - - - +
371A ILE* 1.3 77.7 - - - +
373A GLN* 1.3 73.6 + - + +
375A ILE* 3.4 2.7 + - - +
376A ILE* 3.0 43.3 + - + +
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Residues in contact with GLN 373 (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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369A ILE* 2.9 45.4 + - + +
370A GLY* 4.1 4.4 - - - +
372A PHE* 1.3 82.7 - - + +
374A HIS* 1.3 57.5 + - - +
376A ILE* 3.8 7.4 - - - +
377A ARG* 2.9 52.6 + - - +
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Residues in contact with HIS 374 (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* 6.0 0.4 - - + -
329A THR* 3.2 36.8 - - + +
332A TYR* 5.4 0.7 - + - -
333A ASP* 2.6 42.4 + - - -
370A GLY 3.2 14.6 + - - +
371A ILE* 3.2 17.4 + - + +
373A GLN* 1.3 78.3 - - - +
375A ILE* 1.3 58.2 + - + +
377A ARG* 3.5 23.5 + - - +
378A ARG* 2.8 38.7 + - + +
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 5.2 0.2 - - + -
332A TYR* 3.5 42.4 - - + +
349A GLU* 4.1 11.4 - - - +
359A PRO 4.6 3.1 - - - +
360A LEU* 3.2 47.1 - - + +
363A ALA* 5.1 0.9 - - + -
371A ILE* 3.0 35.0 + - + +
372A PHE* 4.7 1.1 - - - -
374A HIS* 1.3 76.7 - - + +
376A ILE* 1.3 64.7 + - - +
378A ARG* 3.3 7.5 + - - +
379A GLU* 3.1 39.6 + - - +
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Residues in contact with ILE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 3.9 18.6 - - + -
372A PHE* 3.0 46.0 + - + +
373A GLN* 3.8 6.3 - - - +
375A ILE* 1.3 75.6 - - - +
377A ARG* 1.3 65.2 + - + +
379A GLU* 3.3 20.2 + - - +
380A ILE* 3.2 37.7 + - + +
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Residues in contact with ARG 377 (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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370A GLY 4.9 1.8 + - - -
373A GLN* 2.9 50.6 + - - +
374A HIS* 3.5 24.3 + - - +
376A ILE* 1.3 81.1 - - + +
378A ARG* 1.3 60.6 + - - +
380A ILE* 3.5 10.8 + - + +
381A ALA* 3.2 21.0 + - - +
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Residues in contact with ARG 378 (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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332A TYR* 6.4 0.2 - - - -
333A ASP* 3.4 44.9 + - - +
336A LEU* 3.5 38.7 - - - +
337A ILE* 4.1 21.6 - - - +
349A GLU* 5.6 2.6 + - - +
374A HIS* 2.8 22.9 + - + +
375A ILE* 3.3 9.6 + - - +
377A ARG* 1.3 76.4 - - - +
379A GLU* 1.3 59.0 + - + +
381A ALA* 3.3 6.1 + - - +
382A ASP* 2.9 57.9 + - - +
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Residues in contact with GLU 379 (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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349A GLU* 3.8 17.3 - - - +
360A LEU* 4.2 11.9 - - - +
375A ILE* 3.1 30.2 + - - +
376A ILE* 3.3 26.1 + - + +
378A ARG* 1.3 77.1 - - + +
380A ILE* 1.3 59.0 + - + +
382A ASP* 3.8 5.4 - - - +
383A ALA* 3.0 31.2 + - - +
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Residues in contact with ILE 380 (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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376A ILE* 3.2 30.0 + - + +
377A ARG* 3.8 11.0 - - + +
379A GLU* 1.3 73.0 - - + +
381A ALA* 1.3 61.5 + - - +
383A ALA* 3.8 4.4 - - - +
384A ALA* 2.9 30.9 + - + +
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Residues in contact with ALA 381 (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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377A ARG 3.2 14.7 + - - +
378A ARG* 3.4 10.5 - - - +
380A ILE* 1.3 77.2 - - - +
382A ASP* 1.3 62.2 + - - +
384A ALA* 3.1 30.7 + - - +
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Residues in contact with ASP 382 (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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378A ARG* 2.9 49.0 + - - +
379A GLU* 3.8 5.4 - - - +
381A ALA* 1.3 80.4 - - - +
383A ALA* 1.3 57.2 - - - +
384A ALA 4.2 3.4 - - - +
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Residues in contact with ALA 383 (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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379A GLU 3.0 19.0 + - - +
380A ILE* 4.0 5.8 - - - +
382A ASP* 1.3 73.7 - - - +
384A ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 384 (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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380A ILE* 2.9 21.9 + - + +
381A ALA* 3.1 17.2 + - - +
382A ASP* 4.2 4.2 - - - +
383A ALA* 1.3 80.5 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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