Contacts of the helix formed by residues 368 - 387 (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 LYS 368 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C VAL* 2.9 24.7 + - + +
316C ALA* 2.8 26.1 + - - +
318C ALA* 2.6 33.3 + - + +
319C ASP* 4.9 1.1 - - - +
320C ASN* 3.6 9.9 - - - +
363C ALA* 2.8 14.0 + - + +
366C THR* 3.5 35.0 + - - +
367C GLY* 1.3 70.1 - - - +
369C ILE* 1.3 58.4 + - - +
370C GLY 3.3 2.9 + - - -
371C ILE* 3.5 20.0 - - + +
372C PHE* 2.9 31.7 + - - +
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Residues in contact with ILE 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ASN* 3.2 8.9 - - + +
363C ALA 5.4 0.9 - - - +
364C ALA* 5.6 5.2 - - - +
367C GLY* 3.0 28.9 + - - +
368C LYS* 1.3 70.3 - - - +
370C GLY* 1.3 61.3 + - - +
372C PHE* 4.0 14.4 - - + -
373C GLN* 2.8 58.9 + - + +
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Residues in contact with GLY 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ASN* 3.3 13.9 - - - +
325C THR* 4.3 21.0 - - - -
329C THR* 4.4 2.4 + - - -
369C ILE* 1.3 80.5 - - - +
371C ILE* 1.3 60.3 + - - +
373C GLN* 4.3 5.6 - - - +
374C HIS* 3.4 20.4 + - - +
377C ARG* 4.9 2.9 + - - -
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Residues in contact with ILE 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C VAL* 4.3 11.4 - - + +
318C ALA* 4.0 12.3 - - + +
320C ASN* 5.0 0.2 - - - +
325C THR* 4.7 6.1 - - + +
328C VAL* 4.0 25.1 - - + -
329C THR* 3.8 19.3 - - - +
332C TYR* 4.0 31.6 - - + -
363C ALA* 3.8 10.5 - - + -
368C LYS* 3.5 26.6 - - + +
370C GLY* 1.3 73.0 - - - +
372C PHE* 1.3 69.3 + - - +
374C HIS* 3.2 8.6 + - + -
375C ILE* 3.1 39.0 + - + +
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Residues in contact with PHE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 3.3 49.4 - - + +
361C MET* 4.4 6.3 - - + -
363C ALA* 3.8 9.4 - - + -
364C ALA* 3.5 29.8 - - + +
368C LYS 2.9 22.9 + - - +
369C ILE* 3.8 13.7 - - + +
371C ILE* 1.3 81.0 - - - +
373C GLN* 1.3 74.8 + - + +
375C ILE* 3.3 1.0 + - - -
376C ILE* 3.2 40.4 + - + +
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Residues in contact with GLN 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C ILE* 2.8 46.2 + - + +
370C GLY* 4.4 4.8 - - - +
372C PHE* 1.3 84.1 - - + +
374C HIS* 1.3 61.4 - - - +
376C ILE* 3.4 7.6 + - - +
377C ARG* 3.1 44.1 + - - +
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Residues in contact with HIS 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C THR* 3.3 45.4 + - + +
332C TYR* 5.1 3.4 - + - -
333C ASP* 2.9 38.0 + - - -
370C GLY 3.4 9.9 + - - +
371C ILE* 3.2 19.8 + - + +
373C GLN* 1.3 79.2 - - - +
375C ILE* 1.3 61.4 + - + +
377C ARG* 3.4 28.7 + - - +
378C ARG* 3.1 32.3 + - + +
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Residues in contact with ILE 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C VAL* 5.0 2.0 - - + -
332C TYR* 3.4 40.6 - - + +
349C GLU* 3.5 7.9 - - - +
359C PRO 4.6 2.0 - - - -
360C LEU* 3.6 50.5 - - + +
363C ALA* 5.1 0.7 - - + -
371C ILE* 3.1 29.5 + - + +
372C PHE* 3.7 1.3 - - - +
374C HIS* 1.3 76.8 - - + +
376C ILE* 1.3 56.7 + - - +
378C ARG* 3.3 25.7 + - - +
379C GLU* 3.0 36.0 + - - +
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Residues in contact with ILE 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 3.8 26.7 - - + -
372C PHE* 3.2 38.5 + - + +
373C GLN* 3.7 9.4 - - - +
374C HIS 3.3 0.2 - - - -
375C ILE* 1.3 74.1 - - - +
377C ARG* 1.3 61.9 + - + +
379C GLU* 3.3 8.9 + - + +
380C ILE* 3.0 47.4 + - + +
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Residues in contact with ARG 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C GLY 4.9 3.0 + - - -
373C GLN* 3.1 41.7 + - - +
374C HIS* 3.6 36.5 + - - +
376C ILE* 1.3 76.3 - - + +
378C ARG* 1.3 57.3 + - - +
380C ILE* 3.8 10.0 - - + +
381C ALA* 2.8 31.6 + - - +
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Residues in contact with ARG 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS* 3.6 17.6 - - - +
332C TYR* 4.3 4.2 - - - -
333C ASP* 4.1 22.3 + - - +
336C LEU* 3.5 23.0 - - - +
349C GLU* 2.6 33.3 + - - -
374C HIS* 3.1 22.4 + - + +
375C ILE* 3.3 16.4 - - - +
376C ILE 3.2 0.4 - - - -
377C ARG* 1.3 75.1 - - - +
379C GLU* 1.3 82.3 + - - +
381C ALA* 3.7 6.0 - - + +
382C ASP* 2.7 46.9 + - - +
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Residues in contact with GLU 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS* 4.2 22.6 + - + +
349C GLU* 4.6 5.5 - - - +
360C LEU* 5.8 4.3 - - + +
375C ILE* 3.0 20.6 + - - +
376C ILE* 3.5 10.8 - - + +
378C ARG* 1.3 114.1 + - - +
380C ILE* 1.3 65.2 + - + +
382C ASP* 3.2 7.7 - - + +
383C ALA* 3.1 22.7 + - - +
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Residues in contact with ILE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ILE* 3.0 40.3 + - + +
377C ARG* 3.8 8.5 - - + +
379C GLU* 1.3 77.6 - - + +
381C ALA* 1.3 61.0 + - - +
383C ALA* 3.4 6.7 + - - +
384C ALA* 3.2 23.6 + - + +
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Residues in contact with ALA 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ARG 2.8 20.0 + - - +
378C ARG* 3.8 7.2 - - + +
380C ILE* 1.3 75.1 - - - +
382C ASP* 1.3 65.3 + - - +
384C ALA* 3.6 6.4 + - - +
385C ALA* 3.0 24.8 + - - +
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Residues in contact with ASP 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS* 3.6 32.8 + - + +
378C ARG* 2.7 32.7 + - - +
379C GLU* 3.2 11.7 - - + +
381C ALA* 1.3 72.7 - - - +
383C ALA* 1.3 62.5 + - - +
385C ALA* 3.3 12.9 + - - +
386C HIS* 3.2 38.2 + - - -
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Residues in contact with ALA 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C GLU 3.1 12.0 + - - +
380C ILE* 3.9 6.5 - - - +
381C ALA 3.3 0.2 - - - -
382C ASP* 1.3 79.1 - - - +
384C ALA* 1.3 57.3 + - - +
386C HIS* 2.9 20.3 + - - -
387C HIS* 3.0 29.7 + - + +
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Residues in contact with ALA 384 (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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380C ILE* 3.2 16.3 + - + +
381C ALA* 3.8 7.6 - - - +
383C ALA* 1.3 79.2 - - - +
385C ALA* 1.3 59.9 - - - +
386C HIS 3.1 1.2 + - - -
387C HIS* 3.1 25.1 + - - +
388C HIS 3.6 8.7 - - - -
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Residues in contact with ALA 385 (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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381C ALA 3.0 19.1 + - - +
382C ASP* 3.3 8.5 + - - +
384C ALA* 1.3 75.0 - - - +
386C HIS* 1.3 65.5 + - + +
388C HIS 4.2 11.4 + - - +
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Residues in contact with HIS 386 (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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163B LYS 5.4 7.6 + - - -
165B ARG* 3.1 49.8 + - - +
168B ASP* 5.0 10.4 + - - -
211B GLU* 5.1 0.3 - - - +
382C ASP* 3.2 37.6 + - - -
383C ALA* 2.9 9.6 + - - +
385C ALA* 1.3 83.1 + - + +
387C HIS* 1.3 65.9 + - + +
388C HIS 3.7 2.4 + - - -
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Residues in contact with HIS 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ARG* 2.8 36.5 + - - -
206B THR 5.0 4.0 - - - -
207B GLY* 3.2 22.1 + - - -
210B ARG* 4.5 11.0 - - - +
211B GLU* 3.7 13.7 - - - -
383C ALA* 3.0 33.0 + - + +
384C ALA* 3.1 9.7 + - - +
386C HIS* 1.3 79.8 - - + +
388C HIS* 1.3 67.4 + - - +
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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