Contacts of the helix formed by residues 385 - 408 (chain A) in PDB entry 1XZQ
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 ASN 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLU* 3.4 22.7 + - - +
128A ASP* 4.8 6.0 + - - +
206A ILE* 3.4 16.7 - - + +
209A ASN* 5.5 3.1 - - - +
210A ARG* 6.2 3.8 - - + -
383A ILE* 3.6 4.0 - - - +
384A THR* 1.3 84.9 + - - +
386A LEU* 1.3 65.2 + - - +
387A ARG* 3.4 15.9 + - - +
388A GLN* 3.3 34.9 + - - +
389A LYS* 3.1 19.6 + - - +
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Residues in contact with LEU 386 (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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203A ASP* 5.9 0.7 - - - +
206A ILE* 3.9 12.3 - - + +
385A ASN* 1.3 72.8 - - - +
387A ARG* 1.3 71.8 + - - +
389A LYS* 2.5 34.7 + - + +
390A GLN* 2.7 46.8 + - + +
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Residues in contact with ARG 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.1 15.6 - - - +
121A THR* 4.5 0.6 - - - +
124A GLU* 3.0 38.6 + - - +
385A ASN* 3.4 7.9 + - - +
386A LEU* 1.3 79.7 - - - +
388A GLN* 1.3 72.1 + - - +
390A GLN* 3.0 6.8 + - - +
391A LEU* 2.9 45.0 + - + +
428A GLU 2.8 26.1 + - - -
429A VAL* 3.1 24.2 + - - +
438A LEU* 3.6 35.8 - - + +
442A ILE* 3.7 15.9 - - - +
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Residues in contact with GLN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 3.9 13.2 + - + +
124A GLU* 3.1 27.3 + - - +
144A ASN* 4.4 4.0 + - - -
149A LEU* 3.7 26.8 - - + +
382A LEU 4.1 0.3 - - - +
383A ILE* 3.7 10.5 - - + -
384A THR* 2.9 35.6 + - - -
385A ASN* 3.3 27.2 + - - +
386A LEU 3.1 0.4 - - - -
387A ARG* 1.3 88.1 - - - +
389A LYS* 1.3 60.2 + - - +
391A LEU* 4.2 6.1 - - - +
392A LEU* 3.2 31.7 + - + +
429A VAL* 4.8 6.0 - - + +
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Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 4.3 4.7 - - + +
202A ALA* 3.6 28.0 - - + -
203A ASP* 3.3 28.6 + - - +
206A ILE* 3.8 15.3 - - + -
383A ILE* 3.7 12.3 - - + +
385A ASN 3.1 13.8 + - - +
386A LEU* 2.5 26.3 + - + +
388A GLN* 1.3 70.5 - - - +
390A GLN* 1.3 68.5 + - - +
392A LEU* 3.2 5.4 + - - +
393A GLU* 2.9 60.4 + - + +
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Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 2.7 52.1 + - + +
387A ARG* 3.5 7.2 - - - +
389A LYS* 1.3 74.2 - - + +
391A LEU* 1.3 64.0 + - + +
393A GLU* 3.1 16.4 + - - +
394A ASN* 3.0 24.6 + - - +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ARG* 2.9 55.7 + - + +
388A GLN* 4.2 1.1 - - - +
390A GLN* 1.3 73.0 - - + +
392A LEU* 1.3 64.1 + - - +
394A ASN* 3.1 11.1 + - + +
395A VAL* 3.0 24.3 + - - +
425A LEU* 4.3 21.4 - - + +
428A GLU* 3.5 44.6 - - + +
429A VAL* 3.8 16.2 - - + -
438A LEU* 6.1 0.9 - - + -
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Residues in contact with LEU 392 (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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149A LEU* 4.9 13.0 - - + -
152A PHE* 4.9 7.6 - - + -
153A VAL* 4.7 9.9 - - + -
156A LEU* 5.0 4.9 - - + -
195A LEU* 3.9 23.5 - - + +
199A LEU* 4.0 10.5 - - + -
383A ILE* 3.5 31.6 - - + -
388A GLN* 3.2 21.0 + - + +
389A LYS 3.2 6.0 + - - +
391A LEU* 1.3 79.5 - - - +
393A GLU* 1.3 61.4 + - - +
395A VAL* 3.2 6.6 + - + +
396A LYS* 3.1 19.4 + - - +
426A LEU* 4.0 25.4 - - + -
429A VAL* 4.4 14.6 - - + -
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 3.9 21.5 - - + +
389A LYS* 2.9 52.0 + - + +
390A GLN* 3.7 13.7 + - - +
392A LEU* 1.3 73.1 - - - +
394A ASN* 1.3 66.2 + - - +
396A LYS* 3.0 19.6 + - + +
397A GLY* 3.0 10.6 + - - -
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Residues in contact with ASN 394 (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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390A GLN 3.0 12.6 + - - +
391A LEU* 3.1 17.7 - - + +
393A GLU* 1.3 77.9 - - - +
395A VAL* 1.3 59.5 + - - +
397A GLY* 3.1 10.8 + - - -
398A HIS* 3.0 44.9 + - - -
421A ARG* 4.5 5.4 + - - +
425A LEU* 3.3 15.3 - - + +
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Residues in contact with VAL 395 (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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156A LEU* 5.7 0.9 - - + -
160A LEU* 5.5 0.2 - - + -
195A LEU* 3.7 17.7 - - + -
391A LEU 3.0 14.6 + - - +
392A LEU* 3.4 11.0 - - + +
393A GLU 3.1 0.4 - - - -
394A ASN* 1.3 78.5 - - - +
396A LYS* 1.3 62.5 + - - +
398A HIS* 3.6 2.1 + - - +
399A LEU* 3.1 37.5 + - + +
422A ALA* 3.6 13.0 - - + +
425A LEU* 3.5 31.2 - - + -
426A LEU* 3.2 38.6 - - + +
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Residues in contact with LYS 396 (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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192A LYS* 4.4 21.5 - - + +
195A LEU* 3.8 13.0 - - + +
196A THR* 3.5 35.5 - - - +
199A LEU* 4.2 16.7 - - + +
392A LEU 3.1 11.5 + - - +
393A GLU* 3.0 15.2 + - + +
395A VAL* 1.3 77.0 - - - +
397A GLY* 1.3 65.1 + - - +
399A LEU* 3.3 6.2 + - - +
400A GLU* 3.1 42.2 + - - +
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Residues in contact with GLY 397 (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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393A GLU 3.0 12.8 + - - -
394A ASN* 3.1 5.9 + - - -
396A LYS* 1.3 75.7 - - - +
398A HIS* 1.3 54.6 + - - +
400A GLU* 2.7 45.3 + - - +
401A ASP* 3.3 10.9 + - - +
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Residues in contact with HIS 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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394A ASN* 3.0 37.5 + - - -
395A VAL 4.2 4.5 - - - +
397A GLY* 1.3 73.6 - - - +
399A LEU* 1.3 62.7 + - - +
401A ASP* 3.3 18.0 + - - -
402A ALA* 3.2 19.4 + - - +
418A ASP* 3.6 37.6 - - + +
421A ARG* 3.2 46.8 + - + +
422A ALA* 4.2 6.3 + - + -
425A LEU* 3.6 8.9 - - + +
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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
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156A LEU* 6.4 0.7 - - + -
160A LEU* 4.1 16.2 - - + -
188A LEU* 4.8 8.6 - - + +
191A ILE* 4.5 13.7 - - + -
192A LYS* 4.0 39.7 - - + +
195A LEU* 4.2 18.4 - - + -
395A VAL* 3.1 25.1 + - + +
396A LYS 3.4 9.6 - - - +
397A GLY 3.0 0.8 + - - -
398A HIS* 1.3 77.1 - - - +
400A GLU* 1.3 61.2 - - - +
402A ALA* 3.8 6.0 + - - +
403A ILE* 3.3 27.9 + - - +
419A LEU* 4.7 8.9 - - + +
422A ALA* 3.5 25.6 - - + -
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Residues in contact with GLU 400 (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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192A LYS* 4.0 19.2 - - + +
396A LYS* 3.1 30.1 + - - +
397A GLY* 2.7 27.7 + - - +
399A LEU* 1.3 76.7 - - - +
401A ASP* 1.3 63.4 + - - +
403A ILE* 2.7 37.3 - - + +
404A LYS* 2.9 6.2 + - - +
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Residues in contact with ASP 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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397A GLY 3.6 11.0 - - - +
398A HIS* 3.3 25.2 + - - +
400A GLU* 1.3 78.3 - - - +
402A ALA* 1.3 62.5 + - - +
404A LYS* 3.0 10.7 + - - +
405A SER* 2.9 26.6 + - - -
418A ASP* 3.0 31.3 - - - +
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Residues in contact with ALA 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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188A LEU* 4.4 7.6 - - + -
398A HIS 3.2 8.9 + - - +
399A LEU 4.0 3.8 - - - +
401A ASP* 1.3 79.8 - - - +
403A ILE* 1.3 61.6 + - - +
405A SER* 3.8 0.5 - - - -
406A LEU* 3.1 31.7 + - + +
415A ALA* 3.8 21.8 - - + +
418A ASP* 4.0 2.8 + - + -
419A LEU* 3.4 39.5 - - + -
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Residues in contact with ILE 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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185A VAL* 4.4 9.6 - - + +
188A LEU* 3.4 43.5 - - + +
189A GLU* 4.5 17.0 - - + +
192A LYS* 5.3 9.9 - - + -
399A LEU 3.3 10.5 + - - +
400A GLU* 2.7 44.0 - - + +
402A ALA* 1.3 73.8 - - - +
404A LYS* 1.3 76.7 + - + +
406A LEU 4.3 0.9 - - - -
407A LYS* 3.0 37.2 + - + +
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Residues in contact with LYS 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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400A GLU 2.9 17.2 + - - +
401A ASP* 3.4 8.3 - - - +
403A ILE* 1.3 82.5 - - + +
405A SER* 1.3 69.8 + - - +
407A LYS* 2.8 20.4 + - - +
408A GLU* 3.1 46.1 + - + +
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Residues in contact with SER 405 (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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401A ASP 2.9 14.2 + - - -
402A ALA 3.8 3.4 - - - -
404A LYS* 1.3 82.8 - - - +
406A LEU* 1.3 66.0 + - - +
408A GLU* 3.1 13.4 + - - +
409A GLY 3.3 6.8 + - - -
410A MET* 3.4 34.1 + - - +
411A PRO 4.3 1.9 + - - -
414A MET* 3.9 19.4 - - - +
415A ALA* 3.9 15.5 + - - +
418A ASP* 5.6 1.3 - - - -
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Residues in contact with LEU 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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167A ILE* 4.6 8.3 - - + -
179A THR* 5.6 0.4 - - + -
181A THR* 3.2 31.2 + - + +
184A VAL* 3.4 33.9 - - + -
185A VAL* 3.5 27.6 - - + -
188A LEU* 3.7 12.8 - - + -
402A ALA 3.1 14.0 + - - +
405A SER* 1.3 78.0 - - - +
407A LYS* 1.3 64.2 + - - +
409A GLY* 3.0 14.6 + - - -
410A MET 4.9 5.2 - - - +
412A VAL* 4.5 23.1 - - + -
415A ALA* 3.3 25.6 - - + -
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Residues in contact with LYS 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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181A THR* 4.9 3.1 - - - -
185A VAL* 4.6 15.7 - - + -
189A GLU* 5.5 9.3 + - - +
403A ILE* 3.0 29.6 - - + +
404A LYS* 2.8 16.6 + - - +
406A LEU* 1.3 71.3 - - - +
408A GLU* 1.3 56.4 + - + +
409A GLY* 2.7 16.4 + - - -
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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
----------------------------------------------------------
404A LYS* 3.1 51.3 + - + +
405A SER* 3.1 7.3 + - - +
407A LYS* 1.3 73.3 - - + +
409A GLY* 1.3 56.0 + - - +
410A MET* 2.8 33.4 + - + +
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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
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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