Contacts of the helix formed by residues 395 - 418 (chain A) in PDB entry 1XIU
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 ARG 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLU 2.6 41.4 + - - +
327A LEU* 4.0 12.6 - - + +
330A LYS* 3.7 32.0 - - + +
331A MET* 5.9 4.3 - - + -
334A MET* 5.7 6.3 - - - -
336A MET* 5.1 13.9 - - + -
344A LEU* 5.4 3.1 - - + -
391A LYS* 3.6 11.9 + - - +
392A LEU* 3.1 13.2 + - - +
393A LEU 2.9 3.0 + - - -
394A LEU* 1.3 102.2 + - - +
396A LEU* 1.3 61.0 + - + +
397A PRO 3.4 1.1 - - - -
398A ALA* 3.2 17.9 + - - +
399A LEU* 3.1 23.7 + - - +
352B PRO* 5.2 3.6 - - - +
353B ASP* 2.8 36.6 + - - -
367B ARG* 4.3 12.5 - - - +
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Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU* 4.7 2.4 - - - +
344A LEU* 4.3 31.0 - - + -
347A VAL* 3.9 18.4 - - + -
348A VAL* 3.8 25.6 - - + -
367A ARG* 6.0 0.2 - - - +
392A LEU 4.5 0.4 - - - +
393A LEU* 2.9 17.2 + - + +
395A ARG* 1.3 76.4 - - + +
397A PRO* 1.3 70.1 - - + +
399A LEU* 3.2 16.0 + - + +
400A ARG* 2.9 24.4 + - - +
394B LEU* 3.6 29.6 - - + -
397B PRO* 3.8 16.0 - - + +
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Residues in contact with PRO 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU 3.4 11.4 - - - +
394A LEU* 3.6 19.1 - - + +
395A ARG 3.5 3.6 - - - -
396A LEU* 1.3 92.0 - - + +
398A ALA* 1.3 62.2 + - - +
400A ARG* 3.1 4.3 + - + +
401A SER* 2.9 24.3 + - - -
367B ARG* 6.1 1.6 - - - +
393B LEU 5.4 0.2 - - - +
396B LEU* 3.8 29.2 - - + +
397B PRO* 3.9 16.6 - - + -
400B ARG* 3.8 32.8 + - + +
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Residues in contact with ALA 398 (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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326A GLU* 3.5 23.8 - - + +
327A LEU* 4.0 9.9 - - + -
394A LEU 4.9 0.6 + - - -
395A ARG* 3.2 33.6 + - - +
397A PRO* 1.3 79.4 - - - +
399A LEU* 1.3 51.6 + - - +
401A SER* 3.2 6.4 + - - -
402A ILE* 2.8 42.6 + - - +
353B ASP* 4.3 5.6 - - - +
400B ARG* 4.2 6.8 - - - +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU* 3.7 33.8 - - + +
284A ILE* 3.4 33.0 - - + -
285A ALA* 4.0 17.5 - - + +
327A LEU* 4.0 15.7 - - + +
344A LEU* 6.4 0.7 - - + -
348A VAL* 4.3 14.6 - - + -
395A ARG 3.1 12.2 + - - +
396A LEU* 3.5 28.7 - - + +
398A ALA* 1.3 72.2 - - - +
400A ARG* 1.3 67.3 + - - +
402A ILE* 4.6 0.7 - - - +
403A GLY* 2.9 22.9 + - - -
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU* 3.0 37.3 + - - -
348A VAL* 5.8 2.2 - - - +
351A ASN* 4.6 23.2 + - - +
353A ASP* 5.1 5.7 + - - +
367A ARG* 5.9 2.2 - - - +
396A LEU 2.9 13.1 + - - +
397A PRO* 3.3 10.5 - - + +
399A LEU* 1.3 78.7 - - - +
401A SER* 1.3 65.1 + - - +
403A GLY* 3.2 1.4 + - - -
404A LEU* 3.1 29.7 + - + +
322B ARG* 5.0 5.5 - - - +
326B GLU* 5.1 1.8 + - - -
397B PRO* 3.6 31.7 - - + +
398B ALA* 4.0 24.5 - - - +
400B ARG* 4.8 1.8 - - + -
401B SER* 3.6 26.4 + - - +
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Residues in contact with SER 401 (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* 2.8 28.5 + - - -
397A PRO 2.9 16.9 + - - -
398A ALA* 3.3 5.2 - - - -
400A ARG* 1.3 78.9 - - - +
402A ILE* 1.3 63.1 + - - +
404A LEU* 3.2 5.1 + - - +
405A LYS* 3.1 22.3 + - - +
400B ARG* 3.6 21.9 + - - -
404B LEU* 3.8 25.6 - - - +
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Residues in contact with ILE 402 (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 ILE* 4.4 11.4 - - + -
319A ILE* 3.7 16.6 - - + -
322A ARG* 3.7 48.5 - - + +
323A VAL* 3.7 23.8 - - + +
326A GLU* 4.0 12.6 - - + +
327A LEU* 3.7 21.5 - - + -
398A ALA 2.8 24.3 + - - +
399A LEU* 4.1 3.6 - - - +
401A SER* 1.3 72.8 - - - +
403A GLY* 1.3 58.6 + - - +
405A LYS* 3.2 2.6 + - - +
406A CYS* 2.9 36.3 + - - -
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Residues in contact with GLY 403 (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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280A ASN* 2.9 30.9 + - - -
281A GLU* 4.5 5.4 - - - -
284A ILE* 3.9 15.9 - - - +
399A LEU 2.9 15.4 + - - -
400A ARG 3.5 4.9 - - - -
402A ILE* 1.3 78.7 - - - +
404A LEU* 1.3 60.8 + - - +
406A CYS* 3.3 3.5 + - - +
407A LEU* 3.2 14.6 + - - +
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Residues in contact with LEU 404 (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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280A ASN* 5.8 0.2 - - - +
400A ARG* 3.1 23.3 + - + +
401A SER 3.6 5.2 - - - +
403A GLY* 1.3 72.1 - - - +
405A LYS* 1.3 65.7 - - - +
407A LEU* 3.2 20.2 + - + +
408A GLU* 3.1 27.1 + - - +
401B SER* 3.5 31.6 - - - +
404B LEU* 3.9 28.5 - - + -
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Residues in contact with LYS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE* 3.7 27.8 - - + -
322A ARG* 4.3 11.9 - - - +
401A SER 3.1 15.9 + - - +
402A ILE 3.2 4.0 + - - +
404A LEU* 1.3 75.5 - - - +
406A CYS* 1.3 63.3 + - - +
408A GLU* 3.1 31.2 + - + +
409A HIS* 3.1 40.8 + - + -
404B LEU* 6.6 0.2 - - - -
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Residues in contact with CYS 406 (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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201A 9CR 3.6 61.1 - - + +
280A ASN* 5.3 0.9 - - + +
284A ILE* 4.1 9.0 - - + -
319A ILE* 3.9 15.9 - - - -
402A ILE* 2.9 27.1 + - - +
403A GLY 3.6 8.5 - - - +
404A LEU 3.3 0.2 - - - -
405A LYS* 1.3 77.9 - - - +
407A LEU* 1.3 56.4 + - - +
409A HIS* 2.8 20.2 + - - +
410A LEU* 2.9 18.7 + - + +
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Residues in contact with LEU 407 (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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279A TRP* 3.9 32.5 - - + +
280A ASN* 3.4 28.7 - - + +
403A GLY 3.2 3.3 + - - +
404A LEU* 3.2 24.0 + - + +
406A CYS* 1.3 75.0 - - - +
408A GLU* 1.3 68.0 + - - +
410A LEU* 3.1 9.5 + - + +
411A PHE* 2.9 55.6 + - + -
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Residues in contact with GLU 408 (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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404A LEU* 3.1 15.6 + - - +
405A LYS* 3.1 40.3 + - + +
407A LEU* 1.3 76.7 - - + +
409A HIS* 1.3 65.6 + - + +
411A PHE* 3.3 6.2 + - - +
412A PHE* 3.1 21.0 + - - +
408B GLU* 3.9 19.1 - - - +
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Residues in contact with HIS 409 (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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201A 9CR 3.4 18.8 - - + +
315A GLY 4.9 5.0 + - - -
316A VAL* 4.1 24.3 - - + +
319A ILE* 3.9 25.4 - - + +
405A LYS* 3.1 41.8 + - + +
406A CYS* 2.8 10.2 + - - +
408A GLU* 1.3 79.4 - - + +
410A LEU* 1.3 57.7 + - - +
412A PHE* 3.1 9.5 + + - +
413A PHE* 2.9 46.4 + + + -
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Residues in contact with LEU 410 (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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201A 9CR 3.7 43.3 - - + -
243A CYS* 3.9 17.3 - - - -
279A TRP* 4.0 28.0 - - + -
406A CYS 2.9 16.4 + - - +
407A LEU* 3.7 15.9 - - + +
409A HIS* 1.3 78.1 - - - +
411A PHE* 1.3 59.4 + - + +
413A PHE* 3.4 11.6 + - + +
414A LYS* 2.9 29.5 + - - +
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Residues in contact with PHE 411 (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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407A LEU* 2.9 59.5 + - + +
408A GLU* 3.3 5.8 + - - +
410A LEU* 1.3 74.6 - - + +
412A PHE* 1.3 62.8 + - - +
414A LYS* 3.4 25.6 + - + +
415A LEU* 3.1 24.1 + - - +
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Residues in contact with PHE 412 (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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408A GLU 3.1 11.0 + - - +
409A HIS* 3.1 13.6 + + - +
411A PHE* 1.3 74.1 - - - +
413A PHE* 1.3 85.3 + + - +
415A LEU* 3.2 10.1 + - + +
416A ILE* 2.9 50.2 + - + +
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Residues in contact with PHE 413 (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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201A 9CR 4.2 16.6 - + + -
239A VAL* 3.4 34.5 - - + -
243A CYS* 4.5 5.2 - - - -
316A VAL* 4.4 12.6 - - + -
409A HIS* 2.9 47.2 + + + -
410A LEU* 3.4 20.2 + - + +
412A PHE* 1.3 91.7 - + - +
414A LYS* 1.3 62.6 + - - +
416A ILE* 3.3 11.4 + - + +
417A GLY* 3.1 21.0 + - - -
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Residues in contact with LYS 414 (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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410A LEU 2.9 19.5 + - - +
411A PHE* 3.7 26.5 - - + +
412A PHE 3.2 0.2 - - - -
413A PHE* 1.3 77.9 - - - +
415A LEU* 1.3 59.0 + - + +
417A GLY* 3.7 1.8 + - - +
418A ASP* 3.4 20.1 + - - +
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Residues in contact with LEU 415 (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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411A PHE 3.1 16.2 + - - +
412A PHE* 3.8 8.7 - - + +
414A LYS* 1.3 73.3 - - + +
416A ILE* 1.3 71.2 + - + +
417A GLY 3.0 1.8 - - - -
418A ASP* 2.8 37.4 - - + +
419A GLN* 4.3 1.2 + - - +
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Residues in contact with ILE 416 (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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412A PHE* 2.9 50.8 + - + +
413A PHE* 3.4 13.0 - - + +
415A LEU* 1.3 79.8 - - + +
417A GLY* 1.3 62.1 + - - +
418A ASP 3.3 0.3 + - - -
419A GLN* 3.2 25.1 + - - +
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Residues in contact with GLY 417 (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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413A PHE 3.1 10.8 + - - -
414A LYS* 4.2 2.2 - - - -
415A LEU 3.0 1.0 - - - -
416A ILE* 1.3 80.0 - - - +
418A ASP* 1.3 56.2 + - - +
419A GLN 3.1 11.2 + - - -
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Residues in contact with ASP 418 (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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414A LYS* 3.4 13.3 + - - +
415A LEU* 2.8 39.1 + - + +
417A GLY* 1.3 72.9 - - - +
419A GLN* 1.3 70.5 + - + +
420A PRO* 4.9 0.2 - - - +
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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
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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