Contacts of the helix formed by residues 352 - 376 (chain A) in PDB entry 5UAK
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 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A PHE* 3.6 41.2 - - + -
311A PHE* 5.5 5.3 - - - -
348A MET* 3.8 12.0 + - - +
351A THR* 1.3 79.0 - - - +
353A GLN* 1.3 63.5 + - - +
354A PHE 3.6 0.9 - - - -
355A PRO* 3.8 6.4 - - - +
356A TRP* 3.4 59.0 + - + -
993A ASP* 5.0 11.3 + - - -
1145A TRP* 3.3 51.8 - - - -
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Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 3.1 32.6 + - - +
197A LEU* 6.1 0.2 - - + -
200A PHE* 3.2 43.3 - - + +
203A ILE* 5.2 2.8 - - - +
204A ALA* 5.8 4.9 - - + +
348A MET* 3.1 31.0 + - + +
349A ALA* 3.6 12.0 - - - +
352A ARG* 1.3 77.7 - - - +
354A PHE* 1.3 65.3 + - - +
356A TRP* 3.5 29.0 + - + +
357A ALA* 3.5 9.5 + - - +
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Residues in contact with PHE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PHE* 4.1 8.1 - - - -
201A VAL* 3.7 31.6 - - + -
204A ALA* 3.8 25.6 - - + -
205A PRO* 4.3 8.1 - - + -
349A ALA 2.9 21.6 + - - +
350A VAL* 4.3 10.8 - - + +
353A GLN* 1.3 71.6 - - - +
355A PRO* 1.4 74.0 - - + +
357A ALA* 3.0 17.1 + - + +
358A VAL* 3.1 33.7 + - + -
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Residues in contact with PRO 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 6.0 4.3 - - + -
350A VAL 3.5 15.0 - - - +
351A THR 3.4 21.8 - - - +
352A ARG 3.8 5.8 - - - +
353A GLN 3.8 1.8 - - - -
354A PHE* 1.4 98.2 - - + +
356A TRP* 1.3 59.6 + - + +
358A VAL* 3.4 10.5 + - + +
359A GLN* 2.8 29.1 + - - +
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Residues in contact with TRP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 4.1 42.3 - - + +
352A ARG* 3.4 56.3 + - + +
353A GLN* 3.5 19.2 + - + +
354A PHE 3.2 0.6 - - - -
355A PRO* 1.3 77.5 - - + +
357A ALA* 1.3 60.8 + - - +
359A GLN* 3.5 10.3 - - + +
360A THR* 2.8 34.9 + - - +
1145A TRP* 6.0 4.5 - + - -
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Residues in contact with ALA 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU 3.6 23.2 + - - +
198A ALA* 4.8 0.2 - - - +
200A PHE* 4.0 11.0 - - + +
201A VAL* 3.7 32.5 - - + +
353A GLN 3.5 2.6 + - - +
354A PHE* 3.0 15.0 + - + +
356A TRP* 1.3 77.7 - - - +
358A VAL* 1.3 61.5 + - - +
360A THR* 3.9 1.6 - - - -
361A TRP* 3.3 31.4 + - - +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A VAL* 5.4 2.7 - - + -
354A PHE* 3.1 42.8 + - + +
355A PRO* 3.7 9.2 - - + +
356A TRP 3.3 0.2 - - - -
357A ALA* 1.3 74.0 - - - +
359A GLN* 1.3 64.9 + - - +
361A TRP* 4.1 3.0 - - - +
362A TYR* 3.3 25.5 + - + +
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Residues in contact with GLN 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PRO 2.8 18.2 + - - +
356A TRP* 3.5 12.6 - - + +
358A VAL* 1.3 78.7 - - - +
360A THR* 1.3 53.8 + - - +
362A TYR* 3.4 9.6 + - - +
363A ASP* 2.8 53.0 + - + +
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Residues in contact with THR 360 (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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190A LYS 4.8 5.2 + - - -
194A GLY* 3.3 24.5 + - - -
197A LEU* 3.9 9.6 - - + -
198A ALA* 3.4 39.9 - - + +
356A TRP 2.8 22.6 + - - +
357A ALA 3.6 4.3 - - - +
359A GLN* 1.3 73.0 - - - +
361A TRP* 1.3 62.5 + - - +
363A ASP* 3.9 5.7 - - - +
364A SER* 2.8 37.1 + - - -
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Residues in contact with TRP 361 (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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74A ARG* 3.9 27.1 - - - -
81A PHE* 6.5 0.7 - + - -
198A ALA* 2.9 43.9 + - + +
201A VAL* 3.7 16.8 - - + +
357A ALA 3.3 22.3 + - - +
358A VAL* 4.1 4.3 - - - +
359A GLN 3.4 0.2 - - - -
360A THR* 1.3 78.9 - - - +
362A TYR* 1.3 57.1 + - - +
364A SER* 4.7 2.0 - - - -
365A LEU* 2.8 59.8 + - + +
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Residues in contact with TYR 362 (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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358A VAL* 3.3 19.4 + - + +
359A GLN* 3.8 11.2 - - - +
361A TRP* 1.3 77.9 - - - +
363A ASP* 1.3 65.6 + - + +
365A LEU* 4.6 3.5 - - - +
366A GLY* 3.5 18.2 + - - -
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Residues in contact with ASP 363 (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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190A LYS* 3.5 46.4 + - - +
359A GLN* 2.8 39.0 + - + +
360A THR* 3.9 6.2 - - - +
362A TYR* 1.3 77.2 - - - +
364A SER* 1.3 61.9 + - - +
366A GLY* 4.4 0.7 - - - -
367A ALA* 3.5 19.6 + - - +
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LYS* 5.7 5.6 - - - -
191A PHE* 3.2 38.0 - - - -
195A LEU* 5.9 1.4 - - - +
198A ALA* 6.6 0.4 - - - -
360A THR* 2.8 26.1 + - - -
361A TRP* 4.0 2.7 - - - -
363A ASP* 1.3 73.5 - - - +
365A LEU* 1.3 54.3 + - - +
367A ALA* 2.9 10.5 + - - +
368A ILE* 2.8 39.1 + - - +
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Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.7 41.1 - - + -
361A TRP* 2.8 41.5 + - + +
362A TYR* 4.6 3.1 - - - +
364A SER* 1.3 73.8 - - - +
366A GLY* 1.3 52.1 + - - +
368A ILE* 3.3 11.8 + - + +
369A ASN* 2.8 36.0 + - + +
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Residues in contact with GLY 366 (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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362A TYR 3.5 14.5 + - - -
363A ASP 4.4 0.7 - - - -
364A SER 3.2 0.6 - - - -
365A LEU* 1.3 78.3 - - - +
367A ALA* 1.3 50.9 + - - +
369A ASN* 3.4 7.7 + - - +
370A LYS* 2.8 35.6 + - - +
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Residues in contact with ALA 367 (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 MET* 5.1 1.9 - - - +
186A ASN* 5.9 2.2 - - - +
187A ASN* 4.1 19.4 - - + +
190A LYS* 4.4 17.3 - - + +
191A PHE* 5.9 2.5 - - + -
363A ASP 3.5 13.8 + - - +
364A SER* 2.9 11.7 + - - +
366A GLY* 1.3 72.8 - - - +
368A ILE* 1.3 65.4 + - + +
370A LYS* 3.4 10.9 + - + +
371A ILE* 3.3 30.0 + - - +
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Residues in contact with ILE 368 (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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69A LEU* 3.7 22.8 - - + +
70A ILE* 3.7 28.5 - - + -
73A LEU* 4.4 15.3 - - + -
156A MET* 5.1 6.1 - - + -
191A PHE* 3.9 24.2 - - + -
364A SER* 2.8 37.4 + - - +
365A LEU* 3.3 17.2 + - + +
367A ALA* 1.3 73.2 - - + +
369A ASN* 1.3 60.6 + - - +
371A ILE* 3.5 10.3 - - + +
372A GLN* 3.3 21.0 + - - +
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Residues in contact with ASN 369 (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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70A ILE* 5.5 6.2 - - + +
365A LEU* 2.8 18.1 + - - +
366A GLY* 3.6 9.0 - - - +
368A ILE* 1.3 77.5 - - - +
370A LYS* 1.3 59.1 + - - +
372A GLN* 3.1 17.9 + - - +
373A ASP* 2.9 32.4 + - - +
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Residues in contact with LYS 370 (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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183A LEU* 4.3 27.6 - - + +
186A ASN* 4.9 14.4 - - - +
190A LYS* 5.7 4.4 - - - +
366A GLY 2.8 21.9 + - - +
367A ALA* 3.4 13.0 + - + +
369A ASN* 1.3 74.1 - - - +
371A ILE* 1.3 61.8 + - + +
373A ASP* 3.4 7.5 + - - +
374A PHE* 3.3 18.5 + - - +
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Residues in contact with ILE 371 (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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69A LEU* 3.9 25.6 - - + -
156A MET* 3.7 34.3 - - + -
160A ILE* 4.9 18.5 - - + +
183A LEU* 4.0 31.9 - - + +
187A ASN* 5.6 7.2 - - - +
367A ALA 3.3 12.7 + - - +
368A ILE 3.5 13.7 - - - +
370A LYS* 1.3 74.3 - - + +
372A GLN* 1.3 56.8 + - - +
374A PHE* 3.2 10.9 + - + +
375A LEU* 2.8 41.1 + - + +
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Residues in contact with GLN 372 (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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57A TRP* 5.0 5.6 - - + -
67A PRO 3.6 13.9 + - - -
68A LYS* 4.2 3.8 - - - +
69A LEU* 3.4 53.9 + - + +
70A ILE* 4.0 16.7 - - - +
368A ILE 3.3 15.6 + - - +
369A ASN* 3.1 17.7 + - - +
371A ILE* 1.3 77.0 - - - +
373A ASP* 1.3 65.4 + - - +
375A LEU* 3.5 3.0 + - - +
376A GLN* 3.4 22.2 + - - +
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Residues in contact with ASP 373 (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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369A ASN* 2.9 16.4 + - - +
370A LYS* 3.5 11.7 - - - +
372A GLN* 1.3 77.9 - - - +
374A PHE* 1.3 60.5 + - - +
375A LEU 3.6 0.2 + - - -
376A GLN* 3.5 18.7 - - - +
377A LYS* 4.3 4.3 - - - +
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Residues in contact with PHE 374 (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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160A ILE* 5.3 17.5 - - + -
163A LYS* 4.5 13.4 - - + +
164A THR* 5.3 5.8 - - - -
167A LEU* 4.6 26.7 - - + -
171A VAL* 5.5 1.8 - - + -
176A SER* 5.2 11.9 - - - -
180A LEU* 3.9 35.2 - - + -
183A LEU* 4.7 19.1 - - + -
370A LYS 3.3 9.2 + - - +
371A ILE* 3.2 13.3 + - - +
373A ASP* 1.3 77.7 + - - +
375A LEU* 1.3 66.6 + - - +
377A LYS* 3.3 46.9 - - + +
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Residues in contact with LEU 375 (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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57A TRP* 3.4 39.7 - - + +
61A LEU* 6.0 0.4 - - + -
69A LEU* 3.9 22.0 - - + -
159A LEU* 3.6 31.2 - - + -
160A ILE* 5.1 10.1 - - + -
163A LYS* 3.1 50.1 + - + +
371A ILE* 2.8 24.5 + - + +
372A GLN* 3.7 8.1 - - - +
373A ASP 3.3 0.4 - - - -
374A PHE* 1.3 76.2 - - - +
376A GLN* 1.3 59.3 + - + +
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Residues in contact with GLN 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 6.1 4.5 - - + -
61A LEU* 5.7 6.9 - - - +
67A PRO* 5.4 13.9 - - - +
163A LYS* 4.9 1.6 - - - +
372A GLN 3.4 11.9 + - - +
373A ASP* 3.5 12.6 + - - +
374A PHE 3.4 0.2 - - - -
375A LEU* 1.3 78.4 - - + +
377A LYS* 1.3 61.6 + - - +
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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