Contacts of the helix formed by residues 345 - 369 (chain A) in PDB entry 3ECP
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 GLU 345 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.7 4.7 - - - +
110A GLU* 3.8 11.4 - - - +
343A MET* 3.4 1.4 + - - +
344A GLU* 1.3 90.1 - - + +
346A PRO* 1.3 70.3 - - + +
347A ASP* 4.6 2.0 - - + +
348A ASN* 3.2 30.6 + - - +
349A LEU* 2.8 34.5 + - - +
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Residues in contact with PRO 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.6 10.7 - - + -
110A GLU* 3.8 25.4 - - + +
111A LEU* 3.9 30.5 - - + -
124A TRP* 3.6 8.3 - - + -
149A MET* 4.5 7.6 - - + -
345A GLU* 1.3 90.5 - - + +
347A ASP* 1.3 58.3 + - - +
349A LEU* 3.2 6.8 + - + +
350A GLU* 2.7 37.1 + - - +
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Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 5.3 0.2 - - - +
345A GLU* 3.4 1.8 - - + +
346A PRO* 1.3 85.3 - - - +
348A ASN* 1.3 59.1 + - - +
350A GLU* 3.2 10.1 + - - +
351A ARG* 2.8 59.8 + - - +
501A GOL 3.6 27.2 + - - -
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 3.0 19.4 - - + +
65A ARG* 3.3 29.5 - - - +
343A MET* 3.8 19.5 - - + +
344A GLU* 5.0 3.2 - - - +
345A GLU* 3.2 34.7 + - - +
347A ASP* 1.3 77.6 - - - +
349A LEU* 1.3 62.5 + - - +
351A ARG* 2.8 27.0 + - - -
352A MET* 3.2 24.8 + - - +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.9 37.5 - - + +
105A HIS* 4.2 2.9 - - + -
107A VAL* 3.9 28.3 - - + -
111A LEU* 4.4 2.5 - - + -
124A TRP* 3.8 21.8 - - + -
341A GLN* 3.8 30.1 - - + -
343A MET* 3.6 21.7 - - + +
345A GLU 2.8 17.0 + - - +
346A PRO* 3.5 5.2 - - + +
348A ASN* 1.3 76.4 - - - +
350A GLU* 1.3 62.3 + - - +
352A MET* 3.9 0.7 - - - +
353A VAL* 3.1 31.0 + - + +
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 3.4 13.4 - - + +
75A ARG* 2.7 37.7 + - - +
124A TRP* 4.0 15.4 + - + -
147A TRP* 3.4 36.4 - - + +
346A PRO 2.7 18.4 + - - +
347A ASP* 3.7 9.0 - - - +
348A ASN 3.2 0.2 - - - -
349A LEU* 1.3 72.3 - - - +
351A ARG* 1.3 56.5 + - - +
353A VAL 3.1 0.2 + - - -
354A SER* 2.7 38.9 + - - -
501A GOL 3.8 25.5 + - - -
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 4.3 4.0 - - + -
64A ILE* 3.0 30.3 + - + +
65A ARG 3.6 10.9 + - - -
66A ASN 3.0 22.2 + - - -
67A PRO* 4.1 8.3 + - - +
69A VAL* 3.1 40.4 + - + +
71A ALA* 3.8 24.2 - - + +
74A ILE* 4.3 8.0 - - + +
347A ASP* 2.8 44.2 + - - +
348A ASN* 2.8 32.0 + - - +
350A GLU* 1.3 71.2 - - - +
352A MET* 1.3 62.5 + - - +
354A SER* 3.3 4.1 - - - -
355A ILE* 3.1 25.6 + - - +
501A GOL 4.1 5.6 + - - +
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Residues in contact with MET 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 5.6 0.9 - - - -
38A LEU* 3.8 29.6 - - + -
44A LYS 5.8 2.0 - - - +
46A ILE* 3.7 33.7 - - + +
64A ILE* 3.9 19.6 - - + +
341A GLN* 3.3 42.2 - - + +
343A MET* 3.8 16.4 - - - -
348A ASN 3.2 14.3 + - - +
349A LEU 3.9 1.8 - - - +
351A ARG* 1.3 79.7 - - - +
353A VAL* 1.3 57.2 + - - +
355A ILE* 3.0 22.7 + - - +
356A LEU* 3.0 24.7 + - + +
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Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.9 10.1 - - + -
103A TYR* 3.5 22.0 - - - +
124A TRP* 5.9 0.2 - - + -
147A TRP* 3.4 23.8 - - + -
332A TRP* 3.2 26.1 + - + +
338A ALA* 3.6 20.2 - - + +
341A GLN* 4.2 10.1 - - + -
349A LEU* 3.1 27.4 + - + +
352A MET* 1.3 72.6 - - - +
354A SER* 1.3 66.1 + - - +
356A LEU* 3.2 5.5 + - - -
357A SER 3.1 17.8 + - - -
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Residues in contact with SER 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 3.6 6.5 - - - +
74A ILE* 4.3 12.8 - - - -
75A ARG* 2.6 47.5 + - - +
147A TRP* 3.9 8.4 - - - -
350A GLU 2.7 23.4 + - - -
351A ARG* 3.3 9.2 - - - -
353A VAL* 1.3 71.8 - - - +
355A ILE* 1.3 61.8 + - - +
357A SER* 2.6 28.5 + - - -
358A PHE* 3.8 5.7 - - - -
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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
----------------------------------------------------------
17A PHE* 4.6 10.7 - - + -
31A LEU* 3.9 17.9 - - + -
34A VAL* 4.0 16.8 - - + -
35A ALA* 4.1 24.0 - - + -
38A LEU* 3.9 22.2 - - + -
63A PHE* 3.7 30.3 - - + -
64A ILE* 4.3 8.1 - - + -
74A ILE* 4.3 8.3 - - + -
351A ARG 3.1 14.1 + - - +
352A MET* 3.0 9.7 + - - +
354A SER* 1.3 75.6 - - - +
356A LEU* 1.3 62.2 + - - +
358A PHE* 3.0 18.4 + - - +
359A VAL* 3.4 12.0 + - + +
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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
----------------------------------------------------------
38A LEU* 4.3 15.9 - - + +
43A GLY 5.9 0.9 - - - +
332A TRP* 3.7 10.9 - - + +
336A ALA* 3.6 34.9 - - + +
337A GLY 4.0 7.9 - - - -
338A ALA* 4.0 3.4 - - - +
341A GLN* 3.6 40.2 - - + +
352A MET* 3.0 31.9 + - + +
353A VAL* 3.6 10.5 - - - +
354A SER 3.2 0.4 - - - -
355A ILE* 1.3 78.3 - - - +
357A SER* 1.3 55.8 + - - +
359A VAL* 3.2 14.9 + - + +
360A ALA* 2.9 28.1 + - - +
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 5.3 0.7 - - - +
142A LEU* 3.6 18.4 - - - +
145A GLN* 4.1 7.4 + - - -
328A PHE* 3.4 5.7 - - - -
332A TRP* 3.2 35.4 - - - +
353A VAL 3.1 4.4 + - - -
354A SER* 2.6 21.2 + - - -
356A LEU* 1.3 77.2 - - - +
358A PHE* 1.3 71.4 + - - +
360A ALA* 3.3 5.4 - - - +
361A VAL* 3.3 25.1 + - - +
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Residues in contact with PHE 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 3.2 25.8 - - + -
16A VAL* 4.2 8.5 - - + -
17A PHE* 3.6 29.2 - + + -
74A ILE* 4.7 0.4 - - + -
75A ARG* 3.4 43.3 - - + -
78A GLY* 3.4 31.4 - - - -
79A ALA* 3.8 0.9 - - + -
82A THR* 4.9 1.6 - - - -
142A LEU* 4.1 34.8 - - + -
354A SER 3.8 9.2 - - - -
355A ILE 3.0 6.6 + - - +
357A SER* 1.3 90.5 + - - +
359A VAL* 1.3 63.9 + - - +
361A VAL* 3.4 11.3 + - + +
362A ARG 3.2 15.9 + - - -
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 4.0 17.0 - - + -
35A ALA 4.6 2.2 - - - +
38A LEU* 4.2 28.7 - - + +
39A ALA* 4.3 9.4 - - + +
42A SER* 3.9 28.4 + - - +
43A GLY 5.3 0.4 - - - +
336A ALA* 3.8 16.4 - - + -
355A ILE* 3.4 16.7 + - + +
356A LEU* 3.2 19.8 + - + +
358A PHE* 1.3 72.5 - - - +
360A ALA* 1.3 67.2 + - - +
362A ARG* 3.0 15.3 + - - +
363A LEU* 3.1 13.2 + - + +
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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
----------------------------------------------------------
328A PHE* 3.9 9.9 - - + -
331A ALA* 3.6 13.4 - - + +
332A TRP* 3.5 34.5 - - - +
336A ALA* 4.1 2.9 - - + +
356A LEU 2.9 12.6 + - - +
357A SER 3.3 12.8 - - - +
359A VAL* 1.3 76.4 - - - +
361A VAL* 1.3 62.3 + - - +
363A LEU* 3.1 17.1 + - - +
364A LEU* 3.3 15.4 + - - +
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 6.2 0.2 - - - +
130A LEU* 4.4 8.5 - - + -
139A THR* 4.4 6.5 - - + -
141A GLY* 4.0 16.8 - - - -
142A LEU* 3.9 19.7 - - + +
328A PHE* 3.7 20.0 - - + -
357A SER 3.3 14.3 + - - +
358A PHE* 3.6 14.4 - - + +
359A VAL 3.3 0.2 - - - -
360A ALA* 1.3 78.3 - - - +
362A ARG* 1.3 59.1 + - - +
364A LEU* 3.2 13.1 + - - +
365A GLN* 3.0 49.6 + - - +
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Residues in contact with ARG 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 2.9 36.2 + - + +
7A HIS* 3.4 17.8 + - - +
9A ALA* 4.3 10.0 - - - +
12A TRP* 3.5 43.4 - - + +
39A ALA* 3.0 40.0 + - - +
40A LYS* 5.5 1.2 - - - +
42A SER* 4.0 6.3 + - - -
358A PHE 3.2 11.2 + - - +
359A VAL* 3.0 11.3 + - - +
361A VAL* 1.3 76.2 - - - +
363A LEU* 1.3 59.4 + - - +
365A GLN* 3.7 9.3 - - - -
366A LEU* 2.8 51.3 + - + +
450A TRP* 4.2 2.4 - - - -
453A TRP* 4.5 6.3 - - - +
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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
----------------------------------------------------------
42A SER* 3.9 17.5 - - - +
331A ALA* 4.0 23.1 - - + +
335A GLY* 4.0 11.9 - - - +
336A ALA* 4.0 15.3 - - + +
359A VAL 3.1 11.0 + - - +
360A ALA* 3.1 14.5 + - - +
362A ARG* 1.3 72.2 - - - +
364A LEU* 1.3 68.2 + - - +
366A LEU* 3.4 14.1 + - + +
367A ARG* 3.5 8.0 + - - +
446A TRP* 4.1 32.1 - - + +
450A TRP* 3.8 46.9 - - + +
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Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.9 4.7 - - + -
139A THR* 4.6 17.5 - - + +
324A ARG* 5.1 0.7 - - - +
327A GLU* 3.6 35.9 - - + +
328A PHE* 3.9 31.6 - - + +
331A ALA* 4.0 10.8 - - + -
360A ALA 3.6 11.7 - - - +
361A VAL* 3.2 14.5 + - - +
363A LEU* 1.3 80.2 - - - +
365A GLN* 1.3 61.2 + - - +
367A ARG* 3.4 7.2 + - - +
368A GLU* 3.2 35.8 + - - +
446A TRP* 3.7 21.5 - - + +
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Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR 5.4 8.0 - - - +
6A LEU* 3.6 24.7 - - + +
12A TRP* 4.5 6.6 + - - -
85A LEU* 6.1 1.4 - - - +
139A THR* 2.8 39.4 + - - +
140A VAL* 3.7 17.4 + - - +
361A VAL* 3.0 33.9 + - - +
362A ARG* 3.8 11.7 - - - +
363A LEU 3.3 0.2 - - - -
364A LEU* 1.3 74.9 - - - +
366A LEU* 1.3 53.8 + - - +
368A GLU* 3.5 10.3 - - + +
369A SER* 2.7 36.0 + - - -
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.4 7.0 - - + -
7A HIS* 3.5 31.6 - - + +
362A ARG* 2.8 47.2 + - + +
363A LEU* 3.7 7.4 - - - +
364A LEU 3.3 0.4 - - - -
365A GLN* 1.3 74.1 - - - +
367A ARG* 1.3 61.8 + - - +
369A SER* 2.7 22.5 + - - -
370A PHE* 2.9 19.7 - - + -
449A LEU* 5.6 1.3 - - + -
450A TRP* 3.5 41.7 - - + -
453A TRP* 4.2 21.8 - - + +
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Residues in contact with ARG 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A TRP* 4.8 3.2 - - - -
324A ARG* 5.8 1.0 - - - +
327A GLU* 3.1 32.9 + - - -
363A LEU 3.5 3.0 + - - +
364A LEU* 3.4 10.2 + - - +
365A GLN 3.4 0.2 - - - -
366A LEU* 1.3 77.0 - - - +
368A GLU* 1.3 65.4 + - - +
370A PHE* 2.9 22.9 + - - +
371A THR* 3.1 24.2 + - + +
426A TYR* 4.3 6.9 - - + -
443A ILE* 4.3 3.5 - - - +
444A ALA 3.0 26.6 + - - -
445A SER* 3.8 3.7 - - - +
446A TRP* 3.5 37.3 - - + +
449A LEU* 3.7 33.3 - - + +
4C A 4.7 0.2 + - - -
5C C 2.8 26.4 + - - -
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 2.8 49.0 + - + +
139A THR* 2.6 55.0 + - - +
324A ARG* 3.7 13.5 + - - +
327A GLU* 5.1 2.4 - - - +
364A LEU* 3.2 23.4 + - - +
365A GLN* 3.5 11.6 - - - +
367A ARG* 1.3 84.5 + - + +
369A SER* 1.3 60.7 + - - +
370A PHE 3.1 0.2 - - - -
371A THR* 3.1 20.4 + - + +
372A PRO* 4.0 0.2 - - - +
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Residues in contact with SER 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR 5.8 1.1 - - - -
6A LEU* 3.7 11.4 - - - -
7A HIS* 2.9 33.2 - - - -
138A ARG* 3.6 12.2 + - - +
365A GLN 2.7 18.8 + - - -
366A LEU 2.7 17.0 + - - -
368A GLU* 1.3 73.3 - - - +
370A PHE* 1.3 60.6 + - - +
372A PRO* 4.9 2.8 - - - +
396A VAL* 3.8 21.4 - - - +
422A LEU* 4.5 1.0 - - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il