Contacts of the helix formed by residues 368 - 387 (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 LYS 368 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D VAL* 2.7 35.7 + - + +
316D ALA* 2.8 18.4 + - - +
318D ALA* 2.7 29.6 + - + +
319D ASP* 5.2 0.7 - - - +
320D ASN* 3.7 9.6 - - - +
363D ALA* 2.8 17.2 + - - +
366D THR* 3.4 34.7 + - - +
367D GLY* 1.3 71.5 - - - +
369D ILE* 1.3 58.6 + - - +
370D GLY 3.5 2.2 - - - -
371D ILE* 3.3 19.7 - - + +
372D PHE* 3.0 29.0 + - - +
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Residues in contact with ILE 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ASN* 3.2 10.2 - - - +
363D ALA 5.3 1.1 - - - +
364D ALA* 5.7 4.5 - - - +
367D GLY* 3.6 25.4 - - - +
368D LYS* 1.3 71.2 - - - +
370D GLY* 1.3 60.0 + - - +
372D PHE* 4.1 12.1 - - + -
373D GLN* 2.8 64.0 + - + +
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Residues in contact with GLY 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ASN* 3.1 14.6 - - - +
325D THR* 4.3 25.6 + - - -
329D THR* 4.8 1.1 + - - -
369D ILE* 1.3 78.1 - - - +
371D ILE* 1.3 56.2 + - - +
373D GLN* 4.1 4.5 - - - +
374D HIS* 3.2 26.3 + - - +
377D ARG* 5.0 3.1 + - - -
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Residues in contact with ILE 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D VAL* 4.4 15.0 - - + -
318D ALA* 4.2 11.8 - - + +
320D ASN* 4.8 1.0 - - - +
325D THR* 4.8 3.9 - - - -
328D VAL* 4.0 28.9 - - + -
329D THR* 4.2 14.4 - - - +
332D TYR* 4.2 28.5 - - + -
363D ALA* 3.9 10.1 - - + -
368D LYS* 3.3 28.5 - - + +
370D GLY* 1.3 73.5 - - - +
372D PHE* 1.3 68.6 + - - +
374D HIS* 3.3 11.7 + - + -
375D ILE* 3.0 34.6 + - + +
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Residues in contact with PHE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D LEU* 3.3 48.4 - - + +
361D MET* 5.7 2.0 - - + -
363D ALA* 3.8 10.1 - - + +
364D ALA* 3.4 30.3 - - + -
368D LYS 3.0 20.6 + - - +
369D ILE* 3.8 13.9 - - + +
371D ILE* 1.3 77.4 - - - +
373D GLN* 1.3 74.3 + - + +
375D ILE* 3.1 13.9 + - - +
376D ILE* 3.2 36.7 + - + +
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Residues in contact with GLN 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D ILE* 2.8 46.3 + - + +
370D GLY* 4.2 3.8 - - - +
372D PHE* 1.3 83.3 - - + +
374D HIS* 1.3 62.5 + - - +
376D ILE* 3.9 6.2 - - - +
377D ARG* 3.1 52.3 + - - +
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Residues in contact with HIS 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D THR* 3.2 37.8 + - + +
332D TYR* 5.0 1.1 - + - -
333D ASP* 2.6 43.5 + - - -
370D GLY 3.2 20.3 + - - +
371D ILE* 3.4 18.8 - - + +
372D PHE 3.2 0.2 - - - -
373D GLN* 1.3 77.3 - - - +
375D ILE* 1.3 64.1 + - + +
377D ARG* 3.8 19.7 + - - +
378D ARG* 3.0 33.2 + - + +
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Residues in contact with ILE 375 (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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315D VAL* 5.3 1.3 - - + -
332D TYR* 3.4 44.0 - - + +
349D GLU* 3.8 5.8 - - - +
359D PRO 4.7 2.2 - - - -
360D LEU* 3.5 46.2 - - + +
363D ALA* 5.4 0.9 - - + -
371D ILE* 3.0 31.6 + - + +
372D PHE* 3.1 2.2 + - - +
374D HIS* 1.3 80.0 - - + +
376D ILE* 1.3 55.0 + - - +
378D ARG* 3.4 22.6 + - - +
379D GLU* 2.9 39.3 + - - +
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Residues in contact with ILE 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D LEU* 4.0 27.4 - - + -
372D PHE* 3.2 38.1 + - + +
373D GLN* 3.9 7.4 - - - +
375D ILE* 1.3 75.4 - - - +
377D ARG* 1.3 61.4 + - + +
379D GLU* 3.1 13.0 + - + +
380D ILE* 2.9 46.1 + - + +
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Residues in contact with ARG 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D GLY 5.0 2.6 + - - -
373D GLN* 3.1 52.8 + - + +
374D HIS* 3.8 25.1 + - - +
376D ILE* 1.3 82.1 - - + +
378D ARG* 1.3 52.8 + - - +
380D ILE* 3.4 10.7 + - + +
381D ALA* 2.8 36.7 + - - +
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Residues in contact with ARG 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D TYR* 4.3 4.0 - - - -
333D ASP* 3.6 26.9 + - - +
336D LEU* 3.6 21.8 - - - +
349D GLU* 2.8 39.6 + - - -
374D HIS* 3.0 23.7 + - + +
375D ILE* 3.5 22.2 + - - +
377D ARG* 1.3 74.8 - - - +
379D GLU* 1.3 70.8 + - - +
381D ALA* 3.5 7.3 + - + +
382D ASP* 2.9 55.2 + - - +
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Residues in contact with GLU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D GLU* 4.1 7.8 - - - +
360D LEU* 4.8 9.0 - - - +
375D ILE* 2.9 28.5 + - - +
376D ILE* 3.1 15.8 + - + +
378D ARG* 1.3 94.9 + - - +
380D ILE* 1.3 60.5 + - + +
382D ASP* 3.6 6.4 + - - +
383D ALA* 3.2 24.6 + - - +
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Residues in contact with ILE 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D ILE* 2.9 37.9 + - + +
377D ARG* 3.7 11.2 - - + +
379D GLU* 1.3 73.7 - - + +
381D ALA* 1.3 66.7 + - - +
382D ASP 3.1 1.5 + - - -
383D ALA* 3.1 8.8 + - + +
384D ALA* 3.0 25.4 + - + +
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Residues in contact with ALA 381 (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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377D ARG 2.8 22.3 + - - +
378D ARG* 3.8 8.7 - - + +
380D ILE* 1.3 73.9 - - - +
382D ASP* 1.3 56.7 + - - +
384D ALA* 3.6 8.2 + - - +
385D ALA* 3.0 26.7 + - - +
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Residues in contact with ASP 382 (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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378D ARG* 2.9 44.0 + - - +
379D GLU* 3.7 8.5 - - + +
380D ILE 3.1 0.2 - - - -
381D ALA* 1.3 74.0 - - - +
383D ALA* 1.3 66.8 + - - +
384D ALA 3.1 1.1 + - - -
385D ALA* 3.3 12.5 + - - +
386D HIS* 2.9 36.5 + - + -
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Residues in contact with ALA 383 (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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379D GLU 3.2 11.5 + - - +
380D ILE* 3.1 10.9 + - - +
382D ASP* 1.3 77.2 - - - +
384D ALA* 1.3 58.0 + - - +
386D HIS* 3.2 4.0 + - - -
387D HIS* 2.8 46.0 + - + +
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Residues in contact with ALA 384 (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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380D ILE* 3.0 19.0 + - + +
381D ALA* 3.7 8.7 - - - +
383D ALA* 1.3 73.6 - - - +
385D ALA* 1.3 65.0 + - - +
386D HIS 3.1 2.1 + - - -
387D HIS* 3.4 14.2 + - - +
388D HIS* 3.3 21.1 + - - -
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Residues in contact with ALA 385 (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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381D ALA 3.0 15.1 + - - +
382D ASP* 3.5 15.9 - - - +
384D ALA* 1.3 75.1 - - - +
386D HIS* 1.3 63.1 + - + +
388D HIS* 3.4 23.7 + - - -
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Residues in contact with HIS 386 (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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382D ASP* 2.9 37.6 + - + -
383D ALA* 3.2 3.9 + - - +
384D ALA 3.1 0.6 - - - -
385D ALA* 1.3 83.1 - - + +
387D HIS* 1.3 81.5 + - + +
388D HIS* 4.0 3.6 + - - -
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Residues in contact with HIS 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D ALA* 2.8 35.3 + - + +
384D ALA* 3.4 15.3 + - - +
386D HIS* 1.3 93.9 - + + +
388D HIS* 1.3 63.0 + - - +
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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
------------------------------------------------------------
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