Contacts of the helix formed by residues 348 - 371 (chain A) in PDB entry 3W0A
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 ASP 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A LEU* 5.5 1.1 - - + -
255A THR* 5.9 5.2 - - + -
258A ASP* 3.0 15.9 + - - +
347A GLN* 1.3 76.1 - - + +
349A ALA* 1.4 59.9 + - - +
350A ALA* 3.6 9.2 + - - +
351A LEU* 3.1 38.8 + - + +
352A ILE* 3.2 25.9 + - - +
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Residues in contact with ALA 349 (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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341A PRO* 3.4 26.1 - - + +
346A VAL* 4.1 9.3 - - + +
347A GLN 3.5 6.4 + - - +
348A ASP* 1.4 73.8 - - - +
350A ALA* 1.4 57.4 + - - +
352A ILE* 3.4 10.7 + - - +
353A GLU* 2.9 33.4 + - - +
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASP* 3.2 7.2 + - - +
349A ALA* 1.4 79.1 - - - +
351A LEU* 1.3 55.9 + - - +
353A GLU* 3.4 9.9 + - - +
354A ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 351 (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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253A ASP* 3.7 31.9 - - + +
254A LEU* 3.7 20.0 - - + -
348A ASP* 3.1 35.3 + - + +
350A ALA* 1.3 72.1 - - - +
352A ILE* 1.3 66.7 + - - +
354A ALA* 3.2 11.2 + - + +
355A ILE* 3.1 35.3 + - + +
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Residues in contact with ILE 352 (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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254A LEU* 3.6 21.5 - - + -
258A ASP* 3.8 15.9 - - - +
262A LEU* 4.1 14.4 - - + -
339A VAL* 3.6 23.6 - - + +
340A SER 3.5 8.7 - - - +
341A PRO* 3.5 25.6 - - + -
346A VAL* 3.7 35.4 - - + -
348A ASP 3.2 17.1 + - - +
349A ALA* 3.7 7.6 - - - +
351A LEU* 1.3 76.1 - - - +
353A GLU* 1.3 55.5 + - - +
355A ILE* 3.3 2.1 + - - -
356A GLN* 2.9 28.1 + - - +
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Residues in contact with GLU 353 (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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341A PRO* 3.8 23.8 - - + +
349A ALA* 2.9 19.3 + - - +
350A ALA* 3.6 9.7 - - - +
352A ILE* 1.3 77.2 - - - +
354A ALA* 1.4 52.2 + - - +
356A GLN* 3.3 4.9 + - - +
357A ASP* 2.7 59.8 + - - +
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Residues in contact with ALA 354 (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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350A ALA 3.0 13.8 + - - +
351A LEU* 3.2 19.5 + - + +
353A GLU* 1.4 73.3 - - - +
355A ILE* 1.3 63.5 + - + +
357A ASP* 3.5 7.0 + - - +
358A ARG* 3.2 23.4 + - - +
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Residues in contact with ILE 355 (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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248A ILE* 4.8 0.4 - - + -
249A PRO 3.5 23.3 - - - +
250A GLY* 3.3 33.4 - - - +
251A PHE* 4.5 0.7 - - - +
253A ASP* 4.9 1.6 - - + +
254A LEU* 3.7 28.9 - - + -
339A VAL* 3.6 23.3 - - + -
351A LEU* 3.1 31.6 + - + +
352A ILE* 3.7 6.1 - - - +
354A ALA* 1.3 74.2 - - + +
356A GLN* 1.4 63.3 + - - +
358A ARG* 3.3 16.3 + - - +
359A LEU* 3.2 26.1 + - + +
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Residues in contact with GLN 356 (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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336A ILE* 3.0 47.8 + - + +
339A VAL* 3.1 23.2 + - - +
340A SER* 3.3 14.6 + - - +
341A PRO* 3.5 16.8 - - + +
342A ASP* 5.4 0.4 + - - -
352A ILE 2.9 13.4 + - - +
353A GLU* 3.8 6.3 - - - +
355A ILE* 1.4 77.0 - - - +
357A ASP* 1.4 55.7 + - - +
359A LEU* 3.2 9.7 + - - +
360A SER* 2.7 42.4 + - - +
387A LEU* 5.6 1.4 - - - +
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Residues in contact with ASP 357 (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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353A GLU* 2.7 46.8 + - - +
354A ALA* 3.9 7.0 + - - +
355A ILE 3.3 0.2 - - - -
356A GLN* 1.4 78.8 - - - +
358A ARG* 1.3 53.9 + - - +
360A SER* 3.7 8.2 + - - -
361A ASN* 2.8 49.0 + - - +
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Residues in contact with ARG 358 (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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127A GLU* 3.6 27.6 + - - +
128A GLN* 5.0 2.4 - - + +
131A ILE* 3.8 22.4 - - + +
249A PRO* 3.0 42.9 + - - +
250A GLY* 3.4 11.5 - - - +
253A ASP* 5.2 2.6 + - - -
354A ALA 3.2 13.7 + - - +
355A ILE* 3.5 18.8 + - - +
357A ASP* 1.3 74.3 - - - +
359A LEU* 1.4 56.1 + - + +
361A ASN* 4.0 7.4 - - - +
362A THR* 2.7 35.6 + - - -
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Residues in contact with LEU 359 (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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131A ILE* 3.9 25.6 - - + -
135A LEU* 4.0 17.9 - - + -
248A ILE* 3.9 20.9 - - + -
249A PRO* 4.7 6.7 - - + +
332A LEU* 3.7 7.3 - - + +
335A ALA* 3.9 33.7 - - + +
336A ILE* 3.7 14.8 - - + +
339A VAL* 4.3 8.5 - - + -
355A ILE* 3.2 17.6 + - + +
356A GLN* 3.2 12.4 + - - +
358A ARG* 1.4 77.1 - - + +
360A SER* 1.4 59.7 + - - +
362A THR* 3.2 7.9 + - - -
363A LEU* 3.0 27.9 + - - +
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Residues in contact with SER 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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336A ILE* 4.0 19.7 - - - +
356A GLN* 2.7 34.9 + - - +
357A ASP* 3.7 11.4 + - - -
359A LEU* 1.4 73.0 - - - +
361A ASN* 1.4 60.5 + - - +
363A LEU* 3.3 3.2 + - - +
364A GLN* 2.9 31.0 + - - +
380A TYR* 3.7 24.0 + - - -
384A ILE* 5.5 0.7 - - - +
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Residues in contact with ASN 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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128A GLN* 3.9 10.8 - - - +
357A ASP* 2.8 32.1 + - - +
358A ARG* 4.0 6.3 - - - +
360A SER* 1.4 71.0 - - - +
362A THR* 1.3 62.5 + - - +
364A GLN* 3.5 12.5 + - - +
365A THR* 2.7 36.1 + - - +
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Residues in contact with THR 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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124A LEU* 3.8 1.4 - - - +
128A GLN* 3.4 38.5 + - + +
131A ILE* 4.0 14.0 - - + +
132A ILE* 3.6 33.9 - - + -
332A LEU* 3.8 14.1 - - + -
358A ARG 2.7 21.6 + - - -
359A LEU* 3.4 9.6 - - - -
361A ASN* 1.3 75.6 - - - +
363A LEU* 1.4 52.2 + - - +
365A THR* 3.7 2.1 - - - -
366A TYR* 2.8 34.8 + - - +
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Residues in contact with LEU 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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329A GLU* 3.8 30.7 - - + -
332A LEU* 3.9 18.6 - - + +
333A LEU* 4.9 4.0 - - + +
336A ILE* 3.7 24.0 - - + -
359A LEU 3.0 13.8 + - - +
360A SER 3.6 7.0 - - - +
362A THR* 1.4 74.3 - - - +
364A GLN* 1.3 65.5 + - - +
366A TYR* 3.3 2.0 + - + +
367A ILE* 3.0 46.6 + - + +
380A TYR* 4.0 18.4 - - + -
383A MET* 3.7 30.1 - - + -
384A ILE* 5.6 1.6 - - + -
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Residues in contact with GLN 364 (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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360A SER* 2.9 18.9 + - - +
361A ASN* 4.0 13.0 + - - +
363A LEU* 1.3 73.5 - - - +
365A THR* 1.3 62.2 + - - +
367A ILE* 3.4 5.4 + - - +
368A ARG* 3.2 48.0 + - + +
380A TYR* 3.8 47.5 + - + +
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Residues in contact with THR 365 (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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122A PRO* 3.4 29.5 - - + +
123A LYS 4.1 2.0 - - - +
124A LEU* 3.8 25.4 - - + +
128A GLN* 3.8 18.5 + - - +
361A ASN* 2.7 23.9 + - - +
362A THR 3.7 3.4 - - - -
364A GLN* 1.3 72.4 - - - +
366A TYR* 1.4 65.1 + - - +
368A ARG* 3.3 23.2 + - - +
369A CYS* 3.0 26.3 + - - +
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Residues in contact with TYR 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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124A LEU* 3.7 16.7 - - + +
132A ILE* 3.8 24.0 - - + -
326A HIS* 2.7 27.8 + + - -
328A GLU* 3.5 39.5 + - + -
329A GLU* 3.5 36.8 - - + -
332A LEU* 4.8 3.4 - - + -
362A THR 2.8 21.4 + - - +
363A LEU* 3.3 7.8 + - + +
365A THR* 1.4 72.2 - - - +
367A ILE* 1.4 56.9 + - - +
369A CYS* 4.8 0.2 - - - -
370A ARG* 2.7 65.0 + - + +
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Residues in contact with ILE 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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329A GLU* 3.6 16.4 - - + +
363A LEU* 3.0 42.6 + - + +
364A GLN* 3.8 4.5 - - - +
366A TYR* 1.4 73.5 - - - +
368A ARG* 1.3 67.0 + - + +
371A HIS* 3.1 36.1 + - + +
378A LEU 6.2 0.2 - - - +
379A LEU* 4.1 25.8 - - + +
380A TYR* 3.8 38.4 - - + +
383A MET* 3.8 11.2 - - - -
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Residues in contact with ARG 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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120A LEU* 3.2 24.3 + - - +
121A ARG* 2.8 47.3 + - + -
122A PRO* 3.6 30.3 - - - +
364A GLN* 3.2 33.1 + - + +
365A THR* 3.3 24.8 + - - +
367A ILE* 1.3 81.9 - - + +
369A CYS* 1.3 52.6 + - - +
371A HIS 4.9 2.6 - - - +
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Residues in contact with CYS 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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121A ARG* 3.3 25.8 + - + +
122A PRO 4.3 10.8 - - - +
123A LYS* 4.5 23.1 - - - -
124A LEU* 4.8 7.9 - - + -
365A THR 3.0 18.3 + - - +
366A TYR* 4.2 1.6 - - - +
368A ARG* 1.3 77.3 - - - +
370A ARG* 1.4 82.0 + - + +
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Residues in contact with ARG 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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121A ARG* 5.9 0.2 - - - -
124A LEU* 3.8 26.5 - - + +
129A GLN* 3.9 18.6 + - - +
132A ILE* 6.0 0.4 - - - +
326A HIS* 3.6 9.5 - - - -
366A TYR* 2.7 55.1 + - + +
369A CYS* 1.4 93.5 + - + +
371A HIS* 1.4 59.3 + - - +
372A PRO* 3.4 11.4 - - - +
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Residues in contact with HIS 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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121A ARG* 5.6 2.1 + - - -
323A LEU 4.5 5.9 + - - -
324A ASN* 4.0 12.4 + - - +
326A HIS* 3.5 23.2 + + + -
329A GLU* 2.6 42.2 + - - +
366A TYR* 3.7 1.0 + - - -
367A ILE* 3.1 28.6 + - + +
368A ARG 4.9 2.9 - - - +
369A CYS 4.0 0.4 - - - -
370A ARG* 1.4 76.4 - - - +
372A PRO* 1.4 91.9 - - + +
373A PRO* 3.9 1.4 - - - +
374A PRO 5.8 3.3 - - - -
379A LEU* 3.4 19.2 - - + +
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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
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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