Contacts of the helix formed by residues 335 - 360 (chain I) in PDB entry 4XLN
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 335 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ILE* 4.0 27.6 - - + +
25I SER* 2.9 28.7 + - - +
28I LYS* 4.3 5.4 - - - -
138I SER* 4.8 5.4 - - - +
332I ARG* 5.8 0.3 + - - -
333I ILE* 3.5 17.9 + - + +
334I ARG* 1.3 75.0 - - - +
336I VAL* 1.3 67.2 + - - +
338I GLU* 3.1 29.6 + - - +
339I LEU* 3.1 16.9 + - - +
461I VAL* 4.3 11.0 - - + -
462I ASP 5.3 3.4 - - - +
465I GLY* 5.9 0.2 - - - -
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Residues in contact with VAL 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ILE 3.8 13.8 + - - +
22I GLN* 3.2 54.9 - - - +
25I SER* 4.4 1.3 - - - -
26I TYR* 4.0 17.3 - - + +
121I MET* 4.6 3.6 - - + -
127I PHE* 5.3 0.4 - - + -
136I ILE* 3.5 42.6 - - + +
137I VAL 5.2 2.2 - - - +
138I SER* 5.3 2.4 + - - +
335I THR* 1.3 69.7 - - - +
337I GLY* 1.3 62.2 + - - +
339I LEU* 3.4 10.5 + - - +
340I MET* 2.9 29.6 + - - +
385I PHE* 5.5 0.2 - - - -
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Residues in contact with GLY 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I SER 3.5 21.1 + - - -
26I TYR* 4.1 7.0 - - - -
28I LYS* 4.4 2.2 - - - -
29I ALA* 3.5 23.6 - - - +
335I THR* 3.3 0.8 + - - -
336I VAL* 1.3 80.9 - - - +
338I GLU* 1.3 59.1 + - - +
340I MET* 3.2 7.6 - - - +
341I ALA* 2.9 27.0 + - - +
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Residues in contact with GLU 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I LYS* 3.5 18.9 + - - +
42I VAL* 5.6 4.5 - - - +
43I GLY* 5.4 5.4 + - - -
165I LEU* 6.3 2.9 - - + -
332I ARG* 3.2 26.2 + - - +
334I ARG* 3.6 27.2 + - - +
335I THR* 3.1 28.5 + - - +
337I GLY* 1.3 76.6 - - - +
339I LEU* 1.3 56.4 + - - +
341I ALA* 3.5 8.6 + - - +
342I ASP* 2.9 27.4 + - - +
463I ALA 3.8 11.4 - - - +
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Residues in contact with LEU 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I ILE* 4.2 18.4 - - + -
137I VAL 4.3 1.6 - - - +
139I GLN* 4.1 11.7 - - - +
334I ARG* 3.9 41.3 - - + +
335I THR 3.1 18.6 + - - +
336I VAL* 3.7 5.2 - - - +
338I GLU* 1.3 72.6 - - - +
340I MET* 1.3 67.2 + - - +
342I ASP* 3.0 11.8 + - - +
343I GLN* 2.9 27.5 + - - +
385I PHE* 4.1 20.1 - - + -
391I LEU* 3.6 29.2 - - + -
415I PRO 6.0 0.4 - - - +
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Residues in contact with MET 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I TYR* 3.6 32.3 - - + -
29I ALA* 4.3 11.4 - - + +
30I LEU* 4.2 9.9 - - + -
44I ILE* 5.3 3.4 - - + -
118I LEU* 3.5 44.9 - - + -
127I PHE* 5.3 0.7 - - + -
136I ILE* 5.8 1.1 - - + -
336I VAL 2.9 14.1 + - - +
337I GLY* 3.2 13.5 - - - +
339I LEU* 1.3 77.4 - - - +
341I ALA* 1.3 57.9 + - - +
343I GLN* 3.4 3.0 + - - +
344I PHE* 2.9 39.1 + - + +
382I LEU* 5.5 3.4 - - - +
385I PHE* 4.9 7.6 - - + -
386I PHE* 4.2 20.9 - - + -
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Residues in contact with ALA 341 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I ALA* 5.1 1.3 - - + +
43I GLY* 3.9 35.7 - - - +
44I ILE* 4.5 2.5 - - - +
47I ALA* 3.7 4.8 - - + +
337I GLY 2.9 15.6 + - - +
338I GLU* 3.8 8.3 - - - +
340I MET* 1.3 77.8 - - - +
342I ASP* 1.3 58.7 + - - +
344I PHE* 3.6 8.0 - - - +
345I ARG* 2.9 42.9 + - - +
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Residues in contact with ASP 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I PRO* 5.1 11.5 - - - +
168I ARG* 5.1 6.2 + - - +
334I ARG* 4.0 22.8 + - - +
338I GLU 2.9 15.3 + - - +
339I LEU* 3.0 21.2 + - - +
341I ALA* 1.3 77.9 - - - +
343I GLN* 1.3 67.6 + - - +
345I ARG* 3.1 28.5 - - - +
346I VAL* 3.4 14.0 - - - +
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Residues in contact with GLN 343 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339I LEU 2.9 13.7 + - - +
340I MET* 4.1 2.7 - - - +
342I ASP* 1.3 87.3 + - - +
344I PHE* 1.3 66.9 - - - +
345I ARG 3.2 2.0 + - - -
346I VAL* 3.3 11.8 + - - +
347I GLY* 3.0 21.8 + - - -
381I ALA* 4.3 19.4 - - - +
382I LEU* 4.9 6.1 - - + -
384I GLU* 6.1 0.9 - - - +
385I PHE* 3.5 45.7 - - + +
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Residues in contact with PHE 344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I ILE* 3.5 31.9 - - + -
47I ALA* 4.0 15.9 - - + -
48I PHE* 4.0 10.3 - + - -
94I LEU* 3.7 26.2 - - + -
118I LEU* 4.5 10.1 - - + -
340I MET* 2.9 24.7 + - + +
341I ALA* 3.3 10.3 + - - +
343I GLN* 1.3 76.4 - - - +
345I ARG* 1.3 56.8 + - - +
348I LEU* 2.9 53.4 + - + +
378I LEU* 3.7 22.7 - - + +
382I LEU* 4.1 33.3 - - + +
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Residues in contact with ARG 345 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I GLY 5.3 0.2 + - - -
46I ALA* 4.0 18.6 - - - +
47I ALA* 3.6 23.1 - - + +
50I GLU* 3.0 43.5 + - + -
51I THR* 3.7 8.6 - - + +
165I LEU* 6.0 2.9 - - - +
168I ARG* 3.3 41.3 + - - +
268I ASP* 3.9 20.7 + - - -
288I ARG* 4.9 5.1 - - - +
341I ALA* 2.9 22.7 + - - +
342I ASP* 3.1 29.0 - - - +
344I PHE* 1.3 76.5 - - - +
346I VAL* 1.3 59.7 + - - +
348I LEU 3.4 1.6 + - - -
349I ALA* 2.9 27.6 + - - +
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Residues in contact with VAL 346 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I LYS* 5.2 23.3 - - + +
168I ARG* 3.7 21.3 - - - +
342I ASP* 3.4 21.1 - - - +
343I GLN* 3.3 14.9 + - - +
345I ARG* 1.3 73.1 - - + +
347I GLY* 1.3 61.0 + - - +
349I ALA* 3.1 9.6 + - + +
350I ARG* 2.9 50.8 + - - +
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Residues in contact with GLY 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343I GLN 3.0 12.6 + - - -
344I PHE 3.9 1.1 - - - -
346I VAL* 1.3 77.7 - - - +
348I LEU* 1.3 56.1 + - - +
350I ARG* 3.2 4.9 + - - -
351I LEU* 2.9 20.4 + - - +
377I PRO 2.9 30.2 - - - +
378I LEU* 4.0 7.6 - - - -
381I ALA* 3.6 19.2 - - - +
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Residues in contact with LEU 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ALA 3.3 11.2 - - - +
48I PHE* 3.5 29.6 - - + -
51I THR* 3.2 29.8 - - + +
52I PHE* 5.4 6.3 - - + -
115I LEU* 4.6 7.4 - - + -
344I PHE* 2.9 28.9 + - + +
345I ARG 3.6 4.9 - - - +
347I GLY* 1.3 75.5 - - - +
349I ALA* 1.3 58.1 + - - +
351I LEU* 3.7 22.0 - - + +
352I ALA* 2.9 24.6 + - - +
378I LEU* 3.8 23.6 - - + +
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Residues in contact with ALA 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I THR* 4.4 6.7 - - + -
168I ARG* 5.8 2.9 - - - +
345I ARG 2.9 13.0 + - - +
346I VAL* 3.1 14.8 + - + +
348I LEU* 1.3 75.6 - - - +
350I ARG* 1.3 60.3 + - - +
351I LEU 3.1 1.3 - - - -
352I ALA* 2.9 23.3 + - + +
353I ARG* 2.9 21.4 + - - +
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Residues in contact with ARG 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I LYS* 6.1 0.6 - - - +
346I VAL* 2.9 31.3 + - - +
347I GLY* 3.4 9.7 - - - +
349I ALA* 1.3 75.5 - - - +
351I LEU* 1.3 57.4 + - - +
353I ARG* 3.5 34.2 + - - +
354I GLY* 2.9 21.1 + - - -
377I PRO* 3.7 24.2 - - + +
381I ALA* 6.2 1.5 - - - +
34R A 5.7 1.8 + - - -
35R G 4.5 14.5 + - - -
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Residues in contact with LEU 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I LEU* 3.6 23.6 - - + -
347I GLY 2.9 12.6 + - - +
348I LEU* 3.8 20.2 - - + +
350I ARG* 1.3 75.1 - - - +
352I ALA* 1.3 59.9 + - - +
354I GLY* 2.8 20.8 + - - +
355I VAL* 2.9 24.6 + - + +
358I ARG* 5.2 0.4 - - - +
373I VAL* 4.6 8.1 - - + -
374I ASN* 3.5 44.0 - - + +
377I PRO* 3.4 26.8 - - + +
378I LEU* 4.7 5.6 - - + -
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Residues in contact with ALA 352 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I THR* 4.5 7.2 - - - +
54I ILE* 3.6 25.4 - - + +
348I LEU 2.9 16.8 + - - +
349I ALA* 2.9 17.4 + - - +
351I LEU* 1.3 77.2 - - - +
353I ARG* 1.3 58.9 + - + +
355I VAL* 3.4 19.0 + - - +
356I ARG* 3.6 21.6 + - - +
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Residues in contact with ARG 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349I ALA 2.9 16.8 + - - +
350I ARG* 3.7 39.3 - - - +
352I ALA* 1.3 73.7 - - + +
354I GLY* 1.3 62.8 + - - +
355I VAL 3.1 2.1 + - - -
356I ARG* 3.5 30.4 + - + +
357I GLU* 3.8 17.5 + - - +
33R G 5.8 1.4 + - - -
34R A 2.4 36.1 + - - -
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Residues in contact with GLY 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350I ARG 2.9 13.2 + - - -
351I LEU* 2.8 17.9 + - - -
353I ARG* 1.3 77.5 - - - +
355I VAL* 1.3 59.9 + - - +
357I GLU* 4.6 1.1 + - - +
358I ARG* 3.4 37.8 + - - +
372I LEU 5.2 0.2 - - - -
377I PRO* 5.2 4.0 - - - -
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Residues in contact with VAL 355 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I ILE* 3.6 22.9 - - + -
66I LEU* 4.0 15.5 - - + -
351I LEU* 2.9 25.1 + - + +
352I ALA* 3.5 12.3 - - - +
354I GLY* 1.3 79.1 - - - +
356I ARG* 1.3 65.9 + - - +
358I ARG* 3.1 7.5 + - - +
359I MET* 2.9 31.2 + - - +
372I LEU* 3.6 39.9 - - + +
373I VAL* 5.6 1.6 - - + -
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Residues in contact with ARG 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I PRO 5.1 1.6 + - - -
54I ILE* 3.4 39.0 - - - +
55I GLU 2.9 27.6 + - - +
56I GLU* 3.3 50.8 - - + +
352I ALA* 3.6 18.7 + - - +
353I ARG* 3.5 23.9 + - + +
355I VAL* 1.3 76.6 - - - +
357I GLU* 1.3 64.0 + - + +
359I MET* 2.9 25.1 + - - +
360I VAL* 3.4 3.6 + - - +
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Residues in contact with GLU 357 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLU* 5.0 0.2 - - - -
353I ARG* 3.8 16.2 + - - +
354I GLY 5.4 0.9 - - - +
356I ARG* 1.3 82.3 - - + +
358I ARG* 1.3 57.7 + - - +
359I MET 3.3 0.2 - - - -
360I VAL* 3.3 16.8 - - + +
361I MET* 3.1 31.1 - - - +
215L LYS 5.4 0.7 - - - +
216L LYS* 3.4 52.9 - - + +
33R G 5.8 0.3 + - - -
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Residues in contact with ARG 358 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351I LEU* 5.2 0.4 - - - +
354I GLY* 3.4 25.3 + - - +
355I VAL 3.2 12.1 - - - +
356I ARG 3.0 0.6 - - - -
357I GLU* 1.3 79.8 - - - +
359I MET* 1.3 61.1 + - - +
361I MET* 3.9 19.7 - - + +
367I LEU* 4.7 9.7 - - + +
371I LYS 3.2 23.2 + - - +
372I LEU* 3.8 23.5 + - + +
373I VAL 3.9 6.1 + - - -
374I ASN* 3.2 51.6 - - - +
291L ARG* 3.9 11.9 - - - +
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Residues in contact with MET 359 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I ILE* 4.4 14.1 - - - +
56I GLU* 3.5 40.4 - - - +
63I GLY 5.1 0.2 - - - -
64I LEU* 3.6 52.9 - - + +
66I LEU* 5.7 0.7 - - - -
355I VAL* 2.9 33.3 + - - +
356I ARG* 2.9 10.1 + - - +
358I ARG* 1.3 78.9 - - - +
360I VAL* 1.3 58.1 + - - +
361I MET 3.3 8.7 + - - +
364I PRO* 5.1 12.0 - - - +
367I LEU* 5.9 3.3 - - - +
372I LEU* 3.7 11.9 - - + -
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Residues in contact with VAL 360 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLU* 3.2 36.1 - - - +
356I ARG 3.7 0.2 - - - +
357I GLU* 3.3 25.6 - - + +
359I MET* 1.3 76.0 - - - +
361I MET* 1.3 56.9 + - + +
364I PRO* 6.0 2.9 - - - -
216L LYS* 3.5 26.3 + - + +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il