Contacts of the helix formed by residues 347 - 381 (chain A) in PDB entry 2NPJ
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 347 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A PHE* 4.5 2.2 - - - -
345A GLY 4.1 4.6 + - - +
346A VAL* 1.3 82.4 - - - +
348A MET* 1.3 65.0 + - - +
349A GLY* 3.6 4.1 + - - -
350A HIS* 3.1 25.7 + - + +
351A GLN* 3.0 19.8 + - - +
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Residues in contact with MET 348 (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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330A GLY 3.5 15.0 - - - +
331A ILE* 3.5 37.7 - - + +
334A ALA* 3.8 16.2 - - + -
336A SER* 5.3 2.7 - - - +
337A LEU* 4.1 13.5 - - + -
342A PHE* 3.7 18.8 - - + -
347A THR* 1.3 73.6 - - - +
349A GLY* 1.3 58.0 + - - +
351A GLN* 3.2 2.1 + - - +
352A LEU* 2.9 41.7 + - + +
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Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A THR* 3.2 6.0 + - - -
348A MET* 1.3 79.2 - - - +
350A HIS* 1.3 61.9 + - - +
352A LEU* 3.4 10.3 + - - +
353A LEU* 3.2 21.5 + - - +
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Residues in contact with HIS 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A HIS 4.6 6.0 + - - -
346A VAL* 3.7 23.7 - - + +
347A THR* 3.1 26.1 + - - +
349A GLY* 1.3 75.8 - - - +
351A GLN* 1.3 65.2 + - - +
353A LEU* 3.4 10.5 + - + +
354A VAL* 3.2 38.5 + - + +
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Residues in contact with GLN 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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157A GLY 3.0 27.7 + - - +
159A LEU* 3.8 20.7 - - + +
330A GLY* 4.0 10.1 - - - +
342A PHE* 3.8 31.9 - - + +
343A ALA* 5.4 2.6 + - - +
346A VAL* 3.6 17.6 - - + +
347A THR 3.0 17.2 + - - +
348A MET 3.7 3.8 - - - +
350A HIS* 1.3 77.2 - - - +
352A LEU* 1.3 60.4 + - - +
354A VAL* 3.2 8.8 + - - +
355A GLN* 2.9 57.6 + - - +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 3.4 41.1 - - + +
330A GLY* 3.9 9.9 - - - +
331A ILE* 3.8 21.5 - - + -
348A MET* 2.9 36.7 + - + +
349A GLY* 3.7 9.0 - - - +
351A GLN* 1.3 76.4 - - - +
353A LEU* 1.3 63.0 + - - +
355A GLN* 3.1 5.6 + - + +
356A LEU* 2.9 34.6 + - + +
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Residues in contact with LEU 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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349A GLY 3.2 10.7 + - - +
350A HIS* 3.7 13.7 - - + +
351A GLN 3.3 0.2 - - - -
352A LEU* 1.3 80.0 - - - +
354A VAL* 1.3 56.5 + - + +
356A LEU* 3.4 16.1 + - + +
357A GLU* 2.9 58.5 + - + +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 6.3 0.4 - - + -
156A HIS* 3.7 33.9 - - + +
158A ALA* 3.6 33.2 - - + +
350A HIS* 3.2 32.9 + - + +
351A GLN* 3.2 15.5 + - - +
353A LEU* 1.3 74.9 - - + +
355A GLN* 1.3 59.8 + - - +
357A GLU* 3.4 14.7 + - - +
358A SER* 2.7 34.9 + - - +
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Residues in contact with GLN 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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158A ALA* 3.8 4.0 - - - -
159A LEU* 2.8 41.0 + - - -
326A CYS* 3.0 40.0 + - + +
327A ILE* 4.5 6.7 - - - +
329A THR* 4.0 7.1 - - - -
330A GLY* 3.9 18.8 - - - -
351A GLN* 2.9 42.7 + - - +
352A LEU* 3.1 7.8 + - + +
354A VAL* 1.3 76.6 - - - +
356A LEU* 1.3 62.2 + - + +
358A SER* 3.3 7.2 + - - -
359A ILE* 3.0 29.9 + - - +
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Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 3.8 37.5 - - + -
352A LEU* 2.9 26.9 + - + +
353A LEU* 3.7 17.0 - - + +
355A GLN* 1.3 77.0 - - - +
357A GLU* 1.3 57.7 + - + +
359A ILE* 3.3 8.5 + - + +
360A ALA* 2.9 29.9 + - - +
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Residues in contact with GLU 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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153A LEU* 5.9 1.1 - - + -
156A HIS* 5.7 5.2 - - - +
353A LEU* 2.9 46.9 + - + +
354A VAL* 3.7 18.2 - - - +
355A GLN 3.3 0.2 - - - -
356A LEU* 1.3 75.4 - - + +
358A SER* 1.3 57.6 + - - +
360A ALA* 3.4 6.2 + - - +
361A ILE* 2.9 42.9 + - + +
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Residues in contact with SER 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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153A LEU* 3.7 31.6 - - - +
158A ALA* 3.3 25.7 - - - +
165A THR* 4.5 11.0 - - - -
354A VAL* 2.7 23.9 + - - +
355A GLN* 3.3 7.8 + - - -
357A GLU* 1.3 72.9 - - - +
359A ILE* 1.3 57.7 + - - +
361A ILE* 3.6 1.9 + - - +
362A THR* 2.8 37.6 + - - -
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Residues in contact with ILE 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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165A THR* 4.7 4.0 - - + -
169A ILE* 4.1 10.0 - - + +
323A ILE* 3.8 25.8 - - + +
326A CYS* 3.7 28.9 - - + -
327A ILE* 3.6 32.1 - - + +
355A GLN 3.0 22.8 + - - +
356A LEU* 3.5 10.8 - - + +
357A GLU 3.3 0.2 - - - -
358A SER* 1.3 72.4 - - - +
360A ALA* 1.3 67.2 + - - +
362A THR* 3.2 6.4 + - - -
363A ILE* 3.0 43.9 + - + +
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Residues in contact with ALA 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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356A LEU 2.9 17.1 + - - +
357A GLU* 3.8 6.7 - - - +
359A ILE* 1.3 78.7 - - - +
361A ILE* 1.3 63.1 + - + +
363A ILE* 3.4 6.9 + - - +
364A VAL* 3.1 31.8 + - + +
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Residues in contact with ILE 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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146A MET* 4.3 28.7 - - + -
152A LEU* 4.3 14.8 - - + -
153A LEU* 3.8 25.1 - - + -
357A GLU* 2.9 28.1 + - + +
358A SER* 3.9 4.9 - - - +
360A ALA* 1.3 76.5 - - + +
362A THR* 1.3 58.8 + - - +
364A VAL* 4.2 2.6 - - - +
365A TRP* 2.9 41.9 + - + +
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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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143A ILE* 4.1 22.9 - - + +
153A LEU* 4.5 7.4 - - - +
165A THR* 3.4 43.3 - - - +
169A ILE* 3.9 10.1 - - + -
170A ASN* 3.9 17.7 - - - +
358A SER 2.8 23.7 + - - -
359A ILE* 3.2 4.7 + - - -
361A ILE* 1.3 78.7 - - - +
363A ILE* 1.3 56.9 + - - +
365A TRP* 4.0 0.2 - - - +
366A SER* 2.9 30.8 + - - -
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Residues in contact with ILE 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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169A ILE* 3.6 17.7 - - + -
173A ILE* 3.6 34.9 - - + +
323A ILE* 4.2 17.5 - - + -
359A ILE* 3.0 39.2 + - + +
360A ALA* 3.8 7.2 - - - +
362A THR* 1.3 75.2 - - - +
364A VAL* 1.3 63.4 + - + +
367A GLY* 2.9 26.5 + - - -
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Residues in contact with VAL 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 ALA* 3.1 19.2 + - + +
361A ILE* 4.2 2.9 - - - +
363A ILE* 1.3 80.6 - - + +
365A TRP* 1.3 64.8 + - - +
367A GLY* 3.8 0.8 - - - -
368A VAL* 2.9 45.0 + - + +
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Residues in contact with TRP 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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74A PHE* 3.6 45.3 - + + -
138A LEU 2.7 25.9 + - - -
139A SER* 3.9 5.2 - - - +
142A PRO* 3.5 26.6 - - + +
143A ILE* 4.0 20.4 - - + -
146A MET* 3.7 17.9 - - + -
361A ILE* 2.9 27.8 + - + +
362A THR 4.0 1.6 - - - +
364A VAL* 1.3 77.0 - - - +
366A SER* 1.3 63.5 + - - +
368A VAL* 4.0 3.2 - - - +
369A VAL* 3.1 36.8 + - + +
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Residues in contact with SER 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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135A TRP* 3.2 11.6 + - - -
139A SER* 3.4 10.7 + - - -
143A ILE* 4.4 0.2 - - - +
170A ASN* 2.7 47.4 + - - -
173A ILE* 4.3 5.6 - - - -
174A ALA 3.8 5.4 + - - -
362A THR 2.9 18.8 + - - -
363A ILE 4.1 1.3 - - - -
365A TRP* 1.3 75.9 - - - +
367A GLY* 1.3 57.3 + - - +
369A VAL 3.5 0.2 + - - -
370A ALA* 2.8 31.4 + - - +
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Residues in contact with GLY 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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173A ILE* 3.6 16.7 - - - +
177A VAL* 3.9 14.1 - - - +
363A ILE 2.9 18.9 + - - -
364A VAL* 3.8 1.1 - - - -
366A SER* 1.3 73.6 - - - +
368A VAL* 1.3 59.4 + - - +
370A ALA* 3.8 1.7 - - - +
371A PHE* 3.0 29.3 + - - +
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL* 2.9 35.8 + - + +
365A TRP* 4.0 3.6 - - - +
367A GLY* 1.3 73.0 - - - +
369A VAL* 1.3 69.6 + - + +
371A PHE* 3.2 7.2 + - - +
372A ILE* 3.0 40.6 + - + +
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.0 6.0 - - + +
135A TRP* 3.9 16.9 - - + +
138A LEU* 3.5 42.0 - - + +
139A SER* 3.7 21.8 - - - -
365A TRP* 3.1 27.6 + - + +
366A SER 4.0 0.4 - - - +
368A VAL* 1.3 79.0 - - + +
370A ALA* 1.3 57.9 + - - +
372A ILE* 3.2 12.0 + - + +
373A GLY* 2.8 26.7 + - - -
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 3.7 10.2 - - + -
135A TRP* 3.8 4.0 - - + -
174A ALA* 3.8 30.5 - - + -
177A VAL* 4.2 5.8 - - + -
366A SER 2.8 20.3 + - - +
367A GLY 3.8 3.8 - - - +
369A VAL* 1.3 75.7 - - - +
371A PHE* 1.3 63.6 + - - +
373A GLY* 3.1 1.2 + - - -
374A TYR* 2.9 42.9 + - + -
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Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 4.0 13.8 - - + +
181A LEU* 4.3 21.3 - - + -
367A GLY 3.0 17.8 + - - +
368A VAL* 3.2 7.8 + - - +
370A ALA* 1.3 77.8 - - - +
372A ILE* 1.3 62.9 + - + +
374A TYR* 3.4 3.1 + - - +
375A LYS* 3.0 73.0 + - + +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.5 12.3 - - + -
138A LEU* 5.6 8.1 - - + -
368A VAL* 3.0 35.6 + - + +
369A VAL* 3.5 13.2 - - + +
371A PHE* 1.3 82.7 - - + +
373A GLY* 1.3 58.1 + - - +
375A LYS* 3.4 5.1 + - - +
376A LEU* 2.9 33.8 + - + +
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Residues in contact with GLY 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 4.6 1.7 - - - +
131A PHE* 3.9 18.2 - - - -
134A VAL* 3.7 25.4 - - - -
135A TRP 5.4 0.4 - - - -
369A VAL 2.8 13.9 + - - -
370A ALA 3.6 3.4 - - - -
372A ILE* 1.3 78.5 - - - +
374A TYR* 1.3 61.2 + - - +
376A LEU* 3.5 2.1 + - - +
377A ALA* 3.1 23.7 + - - +
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Residues in contact with TYR 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 4.0 2.1 - - - +
119A LEU* 3.1 24.9 - - + +
123A ILE* 4.6 10.3 - - + -
131A PHE* 3.4 39.4 - + + -
174A ALA 2.8 29.9 + - - -
177A VAL* 3.8 15.3 - - + -
178A GLY* 3.5 20.6 - - - -
181A LEU* 3.6 23.1 - - + -
370A ALA* 2.9 27.3 + - + +
371A PHE 3.9 0.7 - - - +
373A GLY* 1.3 74.9 - - - +
375A LYS* 1.3 57.5 + - - +
377A ALA* 3.5 1.4 + - - +
378A ASP* 2.9 30.0 + - - +
383A LEU* 3.4 31.8 - - + +
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Residues in contact with LYS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.5 18.4 - - - +
371A PHE* 3.0 63.1 + - + +
372A ILE* 3.8 5.6 - - - +
373A GLY 3.3 0.2 - - - -
374A TYR* 1.3 73.8 - - + +
376A LEU* 1.3 59.7 + - - +
378A ASP* 3.3 16.5 + - + +
379A LEU* 2.9 43.7 + - + +
383A LEU* 6.2 1.8 - - - -
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 4.3 9.9 - - + -
134A VAL* 3.7 26.7 - - + -
372A ILE* 2.9 22.7 + - + +
373A GLY* 3.9 4.0 - - - +
375A LYS* 1.3 74.6 - - - +
377A ALA* 1.3 60.8 + - - +
379A LEU* 3.4 11.0 + - + -
380A THR* 2.7 44.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA* 3.6 37.5 - - + +
130A ILE* 3.9 17.9 - - + +
131A PHE* 4.7 0.9 - - + +
373A GLY 3.1 17.7 + - - +
374A TYR* 3.7 4.9 - - - +
376A LEU* 1.3 76.5 - - - +
378A ASP* 1.3 56.3 + - - +
381A VAL* 2.8 32.3 + - - +
382A GLY 3.0 6.2 + - - -
383A LEU* 4.2 6.3 - - + -
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Residues in contact with ASP 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TYR 2.9 18.5 + - - +
375A LYS* 3.3 19.3 + - + +
377A ALA* 1.3 75.6 - - - +
379A LEU* 1.3 62.2 + - + +
382A GLY* 3.3 14.6 + - - -
383A LEU* 2.7 46.7 + - + +
384A ARG 4.6 0.5 + - - -
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LYS* 2.9 28.7 + - + +
376A LEU* 3.8 11.0 - - + +
378A ASP* 1.3 78.7 - - + +
380A THR* 1.3 62.7 + - - +
----------------------------------------------------------
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Residues in contact with THR 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 4.2 15.2 - - + +
376A LEU* 2.7 36.6 + - - +
377A ALA 3.9 1.1 - - - -
379A LEU* 1.3 81.3 - - - +
381A VAL* 1.3 70.6 + - + +
----------------------------------------------------------
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 3.1 25.6 + - - -
126A SER* 3.4 31.0 - - - +
127A ALA* 3.7 23.8 - - - +
130A ILE* 3.9 18.8 - - + -
377A ALA 2.8 16.7 + - - +
380A THR* 1.3 84.9 - - + +
382A GLY* 1.3 63.0 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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).
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