Contacts of the helix formed by residues 38 - 67 (chain A) in PDB entry 4IF8
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 GLY 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN* 1.3 77.3 + - - +
39A TRP* 1.4 62.4 + - - +
40A LYS 3.5 2.5 - - - -
41A GLN* 3.3 19.2 + - - +
42A ARG* 3.1 33.1 + - - +
118A TYR* 4.8 7.1 - - - -
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Residues in contact with TRP 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN* 3.5 15.7 + - + +
38A GLY* 1.4 75.5 - - - +
40A LYS* 1.3 91.2 + - + +
42A ARG* 3.2 34.6 + - - +
43A MET* 2.9 63.8 + - + +
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY 3.5 0.2 - - - -
39A TRP* 1.3 102.0 - - + +
41A GLN* 1.3 67.2 + - - +
43A MET* 3.2 5.9 + - + +
44A ALA* 2.9 28.7 + - + +
110A LYS* 3.2 24.4 - - - +
111A ASP* 3.1 25.0 + - - +
114A GLU* 2.8 30.9 + - - -
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN 4.0 5.7 + - - +
38A GLY* 3.3 27.1 - - - +
39A TRP 3.3 0.2 - - - -
40A LYS* 1.3 84.0 + - - +
42A ARG* 1.3 56.1 + - - +
44A ALA* 3.3 8.5 + - - +
45A ALA* 2.9 28.2 + - - +
114A GLU* 3.6 49.3 + - + +
115A GLY* 3.8 4.7 - - - -
117A HIS* 6.4 2.0 - - + -
118A TYR* 3.9 25.0 - - + -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN* 4.8 10.9 + - - +
38A GLY* 3.1 37.1 + - - +
39A TRP* 3.3 36.1 - - - +
41A GLN* 1.3 72.6 - - - +
43A MET* 1.3 71.6 + - + +
45A ALA* 3.4 3.2 + - - +
46A LYS* 3.0 27.0 + - - +
118A TYR* 3.6 36.8 - - + +
398A LYS 5.7 4.7 - - - +
400A PRO* 5.4 5.1 - - + +
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Residues in contact with MET 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 2.9 65.5 + - + +
40A LYS* 3.2 8.9 + - + +
42A ARG* 1.3 93.5 - - + +
44A ALA* 1.4 59.9 + - - +
46A LYS* 3.2 22.0 + - + +
47A GLU* 3.2 21.5 + - - +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS 2.9 14.2 + - - +
41A GLN* 3.5 10.3 - - - +
43A MET* 1.4 74.3 - - - +
45A ALA* 1.4 56.4 + - - +
47A GLU* 3.3 4.5 + - - +
48A LEU* 2.9 34.7 + - - +
107A MET* 3.8 21.1 - - + +
111A ASP* 3.5 31.6 - - + +
114A GLU* 5.9 0.4 - - + -
115A GLY* 3.7 6.5 - - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN 2.9 13.4 + - - +
42A ARG 3.5 9.2 - - - +
43A MET 3.3 0.2 - - - -
44A ALA* 1.4 73.1 - - - +
46A LYS* 1.3 58.1 + - - +
48A LEU* 3.2 2.5 + - - +
49A ALA* 2.8 31.9 + - - +
115A GLY* 4.2 3.7 - - - +
118A TYR* 3.7 18.4 - - + -
119A ILE* 3.6 35.2 - - + +
399A ILE* 5.1 2.5 - - + -
400A PRO* 4.2 8.2 - - + +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG 3.0 13.3 + - - +
43A MET* 3.5 26.7 - - + +
45A ALA* 1.3 75.3 - - - +
47A GLU* 1.3 61.4 + - - +
49A ALA* 3.5 3.3 + - - +
50A ARG* 3.4 19.4 + - - +
400A PRO* 3.8 28.3 - - + +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET 3.2 11.2 + - - +
44A ALA 3.3 7.2 + - - +
46A LYS* 1.3 75.7 - - - +
48A LEU* 1.3 63.8 + - + +
50A ARG* 3.3 23.4 + - - +
51A GLN* 3.3 39.8 + - + +
106A LYS* 4.3 24.9 + - + +
107A MET* 3.7 22.9 - - + -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 2.9 22.6 + - - +
45A ALA 3.2 4.0 + - - +
47A GLU* 1.3 77.6 - - + +
49A ALA* 1.3 55.9 + - - +
51A GLN* 3.1 13.8 + - + +
52A ASN* 3.0 29.5 + - - +
104A PHE* 4.3 11.4 - - + -
107A MET* 4.5 11.9 - - + -
112A LEU* 3.6 34.1 - - + +
115A GLY* 3.8 8.5 - - - -
116A PHE* 3.7 54.8 - - + +
119A ILE* 4.1 11.0 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 2.8 16.7 + - - +
46A LYS 3.6 6.5 - - - +
47A GLU 3.3 0.2 - - - -
48A LEU* 1.3 71.8 - - - +
50A ARG* 1.4 61.0 + - - +
52A ASN* 3.0 29.2 - - - +
53A MET* 3.1 14.8 + - + +
119A ILE* 4.9 0.8 - - - +
395A TYR* 5.7 2.9 - - + +
400A PRO* 3.1 45.3 - - + +
401A SER* 3.7 4.4 - - - +
402A VAL* 5.1 0.3 + - - +
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS 3.4 8.4 + - - +
47A GLU* 3.3 19.1 + - - +
49A ALA* 1.4 76.4 - - - +
51A GLN* 1.4 73.5 + - - +
53A MET* 3.5 12.9 + - + +
54A ASP* 3.2 18.5 + - - +
289A VAL* 3.5 45.9 + - + +
290A ASP* 3.6 13.1 + - - -
293A SER* 5.3 4.8 + - - -
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Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 3.3 37.2 + - + +
48A LEU* 3.1 16.7 + - + +
50A ARG* 1.4 87.2 - - - +
52A ASN* 1.4 60.5 + - - +
54A ASP* 3.5 10.5 + - - +
55A LEU* 3.0 27.6 + - - +
102A PHE 4.3 12.9 - - - +
103A ASN* 3.3 44.1 + - - +
104A PHE* 5.6 4.3 - - + -
106A LYS* 4.0 18.4 + - + +
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Residues in contact with ASN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 3.0 13.6 + - - +
49A ALA* 3.0 24.2 - - - +
51A GLN* 1.4 71.8 - - - +
53A MET* 1.3 64.6 + - - +
55A LEU* 4.1 5.8 - - - -
56A GLY* 2.8 26.2 + - - -
76A PRO* 3.3 24.2 - - + +
77A LEU* 3.5 29.5 - - - +
80A SER* 4.1 10.0 - - - +
116A PHE* 5.5 1.4 - - - -
119A ILE* 5.4 0.4 - - - +
401A SER* 2.8 24.7 + - - -
402A VAL* 3.0 26.6 + - - +
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Residues in contact with MET 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.1 16.3 + - + +
50A ARG* 3.5 15.3 - - + +
52A ASN* 1.3 78.3 + - - +
54A ASP* 1.4 61.7 + - - +
56A GLY* 3.3 1.4 + - - -
57A PHE* 3.1 44.9 + - + -
289A VAL* 4.4 14.6 - - + +
292A PHE* 3.5 51.4 - - + -
395A TYR* 4.0 21.8 - - + +
402A VAL* 3.9 23.3 - - + -
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Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG 3.2 5.9 + - - +
51A GLN* 3.7 14.7 - - - +
53A MET* 1.4 78.7 - - - +
55A LEU* 1.4 55.8 + - - +
57A PHE* 3.3 8.1 + - - +
58A LYS* 3.0 61.9 + - - +
103A ASN* 4.0 10.4 + - - -
288A GLN* 5.1 6.6 - - - +
289A VAL* 3.6 27.3 + - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN 3.0 17.4 + - - +
52A ASN* 3.6 4.7 - - - +
54A ASP* 1.4 74.7 + - - +
56A GLY* 1.3 56.8 + - - +
58A LYS* 3.2 11.6 + - - +
59A LEU* 2.8 55.1 + - + +
76A PRO* 3.7 20.2 - - + +
79A ILE* 4.6 4.3 - - + -
80A SER* 3.4 25.6 - - - +
101A GLY 5.3 1.6 - - - +
102A PHE* 4.0 19.3 - - + +
323A LEU* 6.0 0.2 - - + -
326A ILE* 3.9 41.3 - - + -
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASN 2.8 16.5 + - - -
53A MET* 3.3 2.0 + - - -
55A LEU* 1.3 73.5 - - - +
57A PHE* 1.3 57.0 + - - +
59A LEU* 3.3 5.6 + - - +
60A LEU 2.8 26.3 + - - -
74A LEU* 5.0 2.3 - - - +
76A PRO* 3.6 27.6 - - - -
402A VAL* 6.0 0.2 - - - -
405A LEU* 3.2 18.8 - - - +
----------------------------------------------------------
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Residues in contact with PHE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 3.1 42.2 + - + +
54A ASP* 3.9 5.8 - - - +
55A LEU 3.3 0.2 - - - -
56A GLY* 1.3 74.7 - - - +
58A LYS* 1.3 61.3 + - - +
60A LEU* 3.9 2.8 - - - +
61A LYS* 3.0 31.6 + - - +
287A LEU* 3.9 48.3 - - + +
288A GLN* 3.2 39.5 - - - -
289A VAL 4.4 0.4 - - - -
291A THR* 5.1 0.4 - - - -
292A PHE* 4.6 8.5 - + + -
295A TRP* 5.0 4.3 - + - -
393A LEU* 4.0 31.9 - - + -
402A VAL* 6.2 0.9 - - + -
405A LEU* 4.0 21.5 - - + -
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP* 3.0 49.3 + - - +
55A LEU* 3.2 10.3 + - - +
57A PHE* 1.3 78.6 - - + +
59A LEU* 1.3 61.5 + - - +
61A LYS* 3.7 10.8 - - + +
62A LYS* 3.2 29.2 + - + +
101A GLY 4.4 4.9 + - - -
103A ASN* 3.7 18.0 - - - +
325A TYR* 5.7 3.4 - - + +
326A ILE* 4.1 28.1 - - + +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 2.8 41.2 + - + +
56A GLY* 3.8 4.7 - - - +
58A LYS* 1.3 74.7 - - - +
60A LEU* 1.3 59.0 + - - +
62A LYS* 3.3 3.8 + - - +
63A LEU* 2.9 38.9 + - + +
74A LEU* 4.2 18.2 - - + -
76A PRO* 5.5 0.4 - - + -
79A ILE* 4.0 29.6 - - + -
322A THR* 3.8 35.9 - - + +
323A LEU* 5.6 2.7 - - + -
325A TYR* 4.1 14.1 - - + -
326A ILE* 4.4 16.4 - - + -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY 2.8 20.9 + - - +
57A PHE 3.9 3.4 - - - +
59A LEU* 1.3 72.5 - - - +
61A LYS* 1.3 58.3 + - - +
63A LEU* 4.6 5.4 - - - +
64A ALA* 2.9 37.7 + - + +
72A ILE* 3.7 30.7 - - + -
74A LEU* 5.5 2.3 - - + +
284A GLU* 5.0 6.5 - - + +
287A LEU* 3.7 28.3 - - + -
391A LEU* 4.1 21.3 - - + -
405A LEU* 3.9 25.6 - - + -
406A GLY 5.4 0.2 - - - +
407A LYS* 3.9 22.2 - - + +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE 3.0 21.4 + - - +
58A LYS* 3.7 10.4 - - + +
60A LEU* 1.3 75.4 - - - +
62A LYS* 1.3 60.0 + - + +
64A ALA* 4.0 4.3 - - - +
65A PHE* 3.0 29.1 + - - +
284A GLU* 3.3 33.2 - - - +
285A LYS* 3.4 19.0 + - + +
287A LEU* 2.8 33.9 + - + -
288A GLN* 3.1 21.4 - - - +
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS* 3.2 17.7 + - + +
59A LEU 3.8 0.7 - - - +
61A LYS* 1.3 76.9 - - + +
63A LEU* 1.3 66.4 + - - +
65A PHE* 3.2 8.7 + - + +
66A TYR* 3.1 52.7 + - + -
325A TYR* 3.7 54.7 - - + +
----------------------------------------------------------
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 2.9 26.4 + - + +
60A LEU 3.9 0.7 - - - +
62A LYS* 1.3 76.8 - - - +
64A ALA* 1.3 56.7 + - - +
66A TYR* 3.4 3.0 + - - +
67A ASN* 2.9 39.6 + - - +
72A ILE* 3.8 25.8 - - + -
74A LEU* 3.7 30.7 - - + -
317A PHE* 3.7 28.7 - - + -
322A THR* 4.7 7.0 - - + +
325A TYR* 3.9 24.9 - - + +
----------------------------------------------------------
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 2.9 23.1 + - + +
61A LYS* 4.1 3.1 - - - +
63A LEU* 1.3 69.8 - - - +
65A PHE* 1.3 65.5 + - - +
67A ASN 4.2 4.7 - - - -
68A PRO* 3.3 25.3 - - - +
72A ILE* 3.5 13.1 - - + +
284A GLU* 3.5 35.8 - - + +
407A LYS* 3.8 8.6 + - + +
----------------------------------------------------------
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS 3.0 20.2 + - - +
62A LYS* 3.2 10.5 + - + +
64A ALA* 1.3 78.3 - - - +
66A TYR* 1.4 98.4 + + - +
68A PRO* 3.8 9.4 - - - +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 3.1 51.3 + - + +
63A LEU* 4.3 2.2 - - - +
65A PHE* 1.4 103.8 - + - +
67A ASN* 1.3 72.6 + - - +
68A PRO* 3.6 5.7 - - - +
325A TYR* 3.4 40.2 - + - +
----------------------------------------------------------
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 2.9 22.1 + - - +
64A ALA* 3.6 8.3 - - - +
66A TYR* 1.3 89.3 - - - +
68A PRO* 1.3 67.7 - - - +
70A ARG* 3.2 65.7 + - + +
72A ILE* 5.0 3.2 - - + +
407A LYS* 4.9 0.5 + - - -
----------------------------------------------------------
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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