Contacts of the helix formed by residues 369 - 386 (chain C) in PDB entry 2XLR
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 369 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368C VAL* 1.3 85.5 - - + +
370C ALA* 1.3 65.3 + - - +
371C GLU* 3.6 11.0 + - - +
372C GLU* 2.6 56.4 + - - +
373C MET* 3.2 16.1 + - - +
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Residues in contact with ALA 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C TRP* 3.9 26.0 - - + -
368C VAL 4.1 0.6 + - - -
369C THR* 1.3 72.3 - - - +
371C GLU* 1.3 64.2 + - - +
373C MET* 3.1 13.6 + - - +
374C TYR* 3.1 22.8 + - + -
403C LEU* 5.9 1.3 - - + -
406C LYS* 4.8 18.8 - - + -
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Residues in contact with GLU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C THR* 3.1 10.6 + - - +
370C ALA* 1.3 80.5 - - - +
372C GLU* 1.3 61.6 + - + +
374C TYR* 3.7 3.9 + - - +
375C THR* 2.7 34.3 + - - +
400C LYS* 5.5 5.6 - - - +
403C LEU* 4.1 40.4 - - + +
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Residues in contact with GLU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C THR* 4.8 9.5 - - - +
367C LEU* 4.1 19.7 - - + +
368C VAL* 3.0 17.3 + - - +
369C THR* 2.6 51.8 + - - +
371C GLU* 1.3 78.5 - - + +
373C MET* 1.3 58.6 + - - +
375C THR* 3.4 7.4 + - - -
376C TYR* 2.9 27.4 + - - +
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Residues in contact with MET 373 (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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298C LEU* 3.7 28.5 - - + +
324C TRP* 3.7 36.6 - - + -
367C LEU* 4.0 28.7 - - + +
368C VAL 3.7 25.1 - - - +
369C THR 3.2 8.2 + - - +
370C ALA* 3.1 7.3 + - - +
372C GLU* 1.3 74.6 - - - +
374C TYR* 1.3 65.1 + - - +
375C THR 3.1 1.1 - - - -
376C TYR* 3.0 5.1 + - - +
377C GLN* 3.0 24.0 + - - +
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Residues in contact with TYR 374 (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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324C TRP* 3.1 50.6 - + + -
325C TYR* 3.7 7.6 - + - -
370C ALA* 3.1 25.2 + - + -
371C GLU* 4.0 7.6 - - - +
373C MET* 1.3 73.4 - - - +
375C THR* 1.3 59.2 + - - +
377C GLN* 3.5 2.4 + - - +
378C GLY* 2.8 27.0 + - - -
399C ASN* 3.6 20.6 - - + +
402C PHE* 3.3 55.4 - + + -
403C LEU* 4.7 7.6 - - + -
405C TRP* 3.0 28.8 - - - -
406C LYS* 3.9 16.5 - - + -
501C NAP 3.5 7.3 + - - -
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Residues in contact with THR 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C GLU* 2.7 27.2 + - - +
372C GLU* 3.5 8.5 - - - -
373C MET 3.1 0.4 - - - -
374C TYR* 1.3 80.7 - - - +
376C TYR* 1.3 57.5 + - - +
378C GLY* 3.3 1.0 + - - -
379C ASP* 2.8 49.3 + - - +
399C ASN* 3.9 20.6 + - - +
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Residues in contact with TYR 376 (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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298C LEU* 4.0 39.3 - - + -
299C TRP* 3.4 20.2 - + - +
360C TRP* 2.8 51.9 + + - -
363C LYS* 3.7 33.9 - - + -
364C GLU* 3.8 13.7 - - + -
367C LEU* 3.7 18.6 - - + -
372C GLU 2.9 17.7 + - - +
373C MET 3.0 4.7 + - - +
375C THR* 1.3 77.4 - - - +
377C GLN* 1.3 66.5 + - - +
379C ASP* 3.1 9.8 + - + +
380C TYR* 2.9 24.3 + - + +
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Residues in contact with GLN 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LEU* 3.7 22.6 + - + +
321C GLN* 4.2 8.1 - - - +
322C ASP 3.0 21.0 + - - -
324C TRP* 2.7 32.3 + - + +
325C TYR* 2.8 24.4 + - + +
329C MET* 3.6 29.5 - - - -
373C MET 3.0 14.5 + - - +
374C TYR 4.1 2.9 - - - +
376C TYR* 1.3 80.3 - - - +
378C GLY* 1.3 57.2 + - - +
380C TYR* 3.2 11.2 + - + +
381C ILE* 2.9 38.2 + - + +
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Residues in contact with GLY 378 (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 TYR* 3.8 11.6 - - - -
374C TYR 2.8 18.6 + - - -
375C THR* 3.5 2.2 - - - -
377C GLN* 1.3 76.3 - - - +
379C ASP* 1.3 56.8 + - - +
381C ILE* 3.4 3.2 + - - +
382C GLN* 3.0 28.5 + - - +
395C ILE* 3.7 31.3 - - - +
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Residues in contact with ASP 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C TRP* 4.2 11.6 - - + -
363C LYS* 5.9 2.9 + - - -
375C THR* 2.8 36.2 + - - +
376C TYR* 3.1 9.9 + - + +
378C GLY* 1.3 72.5 - - - +
380C TYR* 1.3 59.7 + - - +
382C GLN* 3.6 7.8 - - - +
383C ASN* 3.0 30.0 + - - +
395C ILE* 5.9 0.9 - - - +
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Residues in contact with TYR 380 (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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298C LEU 5.9 0.7 - - - -
299C TRP* 3.7 26.2 - + - -
305C LYS* 2.5 34.7 + - + -
306C GLY* 3.5 7.4 - - - -
321C GLN* 4.6 8.7 - - + -
329C MET* 4.0 22.0 - - + -
333C GLN* 3.1 32.8 + - - +
360C TRP* 3.6 24.3 - + + -
376C TYR* 2.9 16.4 + + + +
377C GLN* 3.3 16.8 - - + +
379C ASP* 1.3 77.0 - - - +
381C ILE* 1.3 64.8 + - + +
383C ASN* 3.3 5.5 + - + +
384C LEU* 3.2 44.0 + - + +
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Residues in contact with ILE 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C TYR* 3.4 48.7 - - + -
328C ASN* 4.6 4.3 - - + +
329C MET* 3.9 28.7 - - + +
332C ALA* 4.1 9.9 - - + -
377C GLN* 2.9 23.4 + - + +
378C GLY* 3.7 3.8 - - - +
380C TYR* 1.3 74.4 - - + +
382C GLN* 1.3 61.2 + - - +
384C LEU* 3.0 12.5 + - - +
385C ILE* 2.9 41.2 + - + +
393C PHE* 4.3 18.4 - - + -
395C ILE* 4.3 4.5 - - + -
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Residues in contact with GLN 382 (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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378C GLY 3.0 18.3 + - - +
379C ASP* 3.6 9.4 - - - +
380C TYR 3.3 0.2 - - - -
381C ILE* 1.3 76.7 - - - +
383C ASN* 1.3 63.3 + - - +
385C ILE* 3.3 27.7 + - - +
386C ASP* 2.9 60.9 + - - +
392C SER* 3.5 9.6 + - - -
393C PHE 4.6 4.7 - - - +
395C ILE* 3.5 21.2 - - + +
396C PRO* 5.6 1.4 - - - +
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Residues in contact with ASN 383 (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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305C LYS* 3.1 32.3 + - - +
360C TRP* 4.5 20.7 - - + +
379C ASP 3.0 18.4 + - - +
380C TYR* 3.5 7.8 - - + +
382C GLN* 1.3 79.2 - - - +
384C LEU* 1.3 61.4 + - - +
386C ASP* 3.8 10.6 + - - +
387C MET* 3.5 23.8 + - - +
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Residues in contact with LEU 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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305C LYS* 4.0 26.7 - - + +
307C VAL* 5.0 1.1 - - + -
329C MET 5.0 0.2 - - - +
332C ALA* 3.9 25.4 - - + +
333C GLN* 3.9 17.9 - - + +
336C TYR* 4.0 28.9 - - + +
380C TYR* 3.2 45.5 + - + +
381C ILE* 3.0 10.1 + - + +
383C ASN* 1.3 75.4 - - - +
385C ILE* 1.3 65.6 + - - +
387C MET* 3.2 25.0 + - + +
388C THR* 3.9 10.0 + - - +
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Residues in contact with ILE 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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332C ALA* 3.7 21.3 - - + +
381C ILE* 2.9 27.0 + - + +
382C GLN* 3.3 38.5 + - - +
384C LEU* 1.3 71.9 - - - +
386C ASP* 1.3 62.5 + - - +
388C THR* 3.0 31.8 + - - +
390C TYR* 3.7 32.5 - - + +
391C PRO 4.5 0.2 - - - +
392C SER* 3.6 33.0 - - - +
393C PHE* 4.3 17.3 - - + +
395C ILE* 4.4 2.7 - - + -
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Residues in contact with ASP 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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382C GLN* 2.9 50.4 + - - +
383C ASN* 4.0 8.4 - - - +
384C LEU 3.2 0.6 - - - -
385C ILE* 1.3 76.8 - - - +
387C MET* 1.3 62.0 + - + +
388C THR 3.4 1.5 + - - +
392C SER* 4.2 4.2 + - - -
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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