Contacts of the helix formed by residues 53 - 80 (chain A) in PDB entry 1FFT
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 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 1.3 79.7 - - - +
54A HIS* 1.3 78.2 + - - +
55A LYS* 2.7 34.0 + - - +
56A ARG* 2.8 50.4 + - + +
57A LEU* 3.0 19.7 + - - +
135A ASP* 3.6 9.3 - - - +
549A PHE 5.1 7.0 - - - +
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Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL 4.0 2.4 + - - -
53A ASP* 1.3 79.1 + - - +
55A LYS* 1.3 90.9 + - + +
57A LEU* 3.0 1.9 + - - -
58A GLY 2.8 19.2 + - - -
124A ASN* 3.0 22.2 + - - +
125A LEU* 5.2 0.9 - - - -
128A PRO* 3.2 41.0 - - + +
129A LEU* 4.2 1.0 - - - +
135A ASP* 2.4 46.6 + - - +
136A VAL* 4.2 21.8 - - + +
142A ASN* 3.9 20.0 - - - +
208A PHE* 5.4 1.3 - - + -
551A ASN* 2.9 24.6 + - - -
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP* 2.7 27.6 + - - +
54A HIS* 1.3 93.8 - - + +
56A ARG* 1.3 64.5 + - - +
58A GLY* 2.9 22.3 + - - -
59A ILE* 3.3 12.8 - - + +
124A ASN 4.3 3.1 - - - -
125A LEU* 3.5 17.2 - - + +
129A LEU* 3.7 23.8 - - + -
547A PRO* 3.5 18.9 + - + +
548A PRO 3.5 3.4 + - - -
549A PHE* 4.2 3.8 + - - +
551A ASN* 2.4 61.5 - - - +
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL 5.8 2.5 - - - +
53A ASP* 2.8 36.8 + - + +
55A LYS* 1.3 81.2 - - - +
57A LEU* 1.3 60.5 + - - +
59A ILE* 3.2 18.7 + - + +
60A MET* 2.8 31.5 + - + +
549A PHE* 3.9 48.1 + - - +
550A TYR* 6.0 1.8 - - - -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL 4.8 11.9 - - - +
53A ASP 3.0 20.6 + - - +
54A HIS* 3.4 5.6 - - - +
56A ARG* 1.3 72.9 - - - +
58A GLY* 1.3 67.2 + - - +
60A MET* 2.5 51.8 + - + +
61A TYR* 2.9 11.9 + - + -
124A ASN* 2.9 13.7 - - - +
142A ASN* 3.2 27.6 - - - +
143A ASN* 3.4 40.8 - - + +
146A PHE* 4.6 14.1 - - + -
147A TRP* 5.6 0.4 - - + -
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS 2.8 4.0 + - - -
55A LYS 2.9 8.5 + - - -
57A LEU* 1.3 78.2 - - - +
59A ILE* 1.3 63.7 + - - +
61A TYR* 2.9 11.8 + - - +
62A ILE* 3.1 18.4 - - - +
121A GLY 3.8 7.1 - - - +
124A ASN* 2.5 21.1 - - - +
125A LEU* 3.7 16.6 - - - -
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 3.3 26.0 + - + +
56A ARG* 3.2 23.9 + - + +
58A GLY* 1.3 71.2 - - - +
60A MET* 1.3 56.4 + - - +
61A TYR 2.6 14.4 + - - -
62A ILE* 2.8 26.3 + - + -
63A ILE* 3.0 31.8 + - + +
125A LEU* 3.4 19.3 - - + +
440A TRP* 6.1 0.2 - - + -
443A ALA* 4.6 12.1 - - + +
444A PHE* 4.2 34.5 - - + -
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Residues in contact with MET 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL 6.1 1.6 - - - +
56A ARG* 2.8 26.3 + - + +
57A LEU* 2.5 43.5 + - + +
59A ILE* 1.3 74.6 - - - +
61A TYR* 1.3 62.3 + - + +
63A ILE* 3.5 21.0 - - - +
64A VAL* 3.3 16.6 - - - +
146A PHE* 3.7 22.4 - - + -
147A TRP* 5.3 14.4 - - + +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 2.9 26.6 + - + -
58A GLY 2.9 9.5 + - - +
59A ILE 2.6 4.4 + - - -
60A MET* 1.3 68.0 - - - +
62A ILE* 1.3 70.9 + - - +
63A ILE 2.9 1.3 - - - -
64A VAL* 2.5 25.7 + - - +
65A ALA 3.3 2.5 + - - -
117A PRO* 3.7 25.4 - - + +
120A ILE* 3.2 56.4 + - + +
121A GLY* 3.6 13.5 - - - -
124A ASN* 4.1 12.8 + - - -
142A ASN 4.9 1.3 + - - -
145A SER* 3.5 8.1 + - - -
146A PHE* 3.1 63.0 + + + +
149A THR* 5.1 7.9 - - + -
204A THR* 4.3 0.2 + - - -
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY 3.1 23.8 - - - +
59A ILE* 2.8 14.8 + - + +
61A TYR* 1.3 80.5 - - + +
63A ILE* 1.3 66.9 + - + +
65A ALA* 3.0 12.1 + - + +
66A ILE* 2.8 31.7 + - + +
117A PRO* 5.1 1.9 - - - +
118A PHE* 5.8 2.5 - - - +
121A GLY* 4.4 15.5 - - - -
122A LEU* 4.7 12.3 - - + +
125A LEU* 5.7 4.0 - - + -
432A CYS* 6.0 4.7 - - - -
436A MET* 3.8 28.7 - - + -
440A TRP* 5.1 11.4 - - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.0 30.1 + - + +
60A MET* 3.5 23.3 - - - +
61A TYR 2.5 4.4 + - - -
62A ILE* 1.3 75.8 - - + +
64A VAL* 1.3 68.0 + - + +
66A ILE* 3.0 4.5 + - - +
67A VAL* 2.8 42.6 + - + +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET 3.3 16.6 - - - +
61A TYR* 2.5 11.3 + - - +
63A ILE* 1.3 73.9 - - + +
65A ALA* 1.3 63.3 + - - +
67A VAL* 3.4 5.7 + - - +
68A MET* 2.8 32.9 + - + +
113A PHE* 4.5 12.3 - - + +
117A PRO* 5.2 5.6 - - + -
146A PHE* 3.4 28.7 - - + -
149A THR* 6.3 2.9 - - + -
150A VAL* 5.3 3.1 - - + -
153A VAL* 4.5 23.6 - - + -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR 3.3 1.4 + - - -
62A ILE* 3.0 15.3 + - + +
64A VAL* 1.3 78.9 - - - +
66A ILE* 1.3 57.2 + - + +
68A MET* 2.9 3.4 + - - -
69A LEU* 2.7 34.0 + - + +
113A PHE 4.5 1.8 - - - -
114A VAL* 2.9 41.7 - - + +
117A PRO* 4.2 15.6 - - + +
118A PHE 5.7 0.4 - - - +
432A CYS* 6.2 3.8 - - - -
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 2.8 33.2 + - + +
63A ILE* 3.5 8.1 - - - +
65A ALA* 1.3 75.2 - - + +
67A VAL* 1.3 69.4 + - + +
68A MET 3.1 0.5 + - - -
69A LEU* 3.2 22.1 + - + +
70A LEU* 3.2 12.6 + - + +
432A CYS* 6.0 2.9 - - - -
433A PHE* 5.1 11.7 - - + -
436A MET* 4.2 19.7 - - + -
512A LEU* 5.6 1.1 - - + -
513A VAL* 4.9 17.0 - - + -
516A MET* 4.6 24.7 - - + -
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 2.8 42.4 + - + +
64A VAL* 3.8 5.4 - - - +
66A ILE* 1.3 76.7 - - + +
68A MET* 1.3 57.2 + - - +
70A LEU* 3.2 30.1 - - + +
71A ARG* 3.9 3.8 + - - +
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Residues in contact with MET 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 2.8 23.3 + - + +
65A ALA* 3.3 3.4 - - - +
67A VAL* 1.3 74.7 - - - +
69A LEU* 1.3 53.2 + - - +
70A LEU 2.9 5.4 - - - -
71A ARG* 2.6 34.3 + - + +
72A GLY* 2.8 12.7 + - - +
109A ILE* 3.8 11.2 - - + -
113A PHE* 3.5 33.0 - - + +
114A VAL* 3.4 27.9 - - + +
153A VAL* 3.3 36.6 - - + +
156A VAL* 6.0 3.6 - - + -
157A ASN* 5.3 7.2 - - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 2.7 15.5 + - + +
66A ILE* 3.2 15.5 + - + +
68A MET* 1.3 68.0 - - - +
70A LEU* 1.3 58.2 + - - +
71A ARG 2.9 5.8 - - - -
72A GLY* 3.9 2.0 - - - +
73A PHE* 3.0 75.3 + - + +
110A MET* 3.5 35.0 - - + -
114A VAL* 3.2 26.0 - - + +
429A VAL* 5.7 7.0 - - + -
433A PHE* 5.6 9.0 - - + -
509A ILE* 5.5 2.7 - - + -
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE 3.2 10.1 + - - +
67A VAL* 3.2 23.3 - - + +
69A LEU* 1.3 79.5 - - - +
71A ARG* 1.3 57.6 + - + +
73A PHE* 5.1 1.1 - - - +
74A ALA* 3.3 20.9 + - + +
509A ILE* 6.0 4.3 - - - -
513A VAL* 6.1 5.4 - - + -
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL 4.6 2.2 - - - +
68A MET* 2.6 21.7 + - + +
70A LEU* 1.3 81.4 - - + +
72A GLY* 1.3 55.2 + - - +
73A PHE 3.4 0.2 - - - -
74A ALA* 3.3 5.0 - - - +
75A ASP* 2.7 73.4 + - - +
109A ILE* 5.3 5.6 - - + -
157A ASN* 5.7 5.5 + - - +
160A LEU* 6.0 3.4 - - - +
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 2.8 16.8 + - - +
69A LEU* 4.7 1.8 - - - -
71A ARG* 1.3 69.1 - - - +
73A PHE* 1.3 70.7 + - - +
75A ASP* 2.8 14.5 + - - +
76A ALA* 2.8 20.3 + - - +
106A HIS* 4.5 6.1 + - - -
109A ILE* 5.1 14.8 - - - +
110A MET* 4.2 15.7 - - - -
114A VAL* 5.9 1.3 - - - -
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.0 62.9 + - + +
70A LEU* 5.1 0.4 - - - -
72A GLY* 1.3 74.2 - - - +
74A ALA* 1.3 69.9 + - - +
76A ALA* 2.8 2.6 + - + +
77A ILE* 2.5 49.1 + - + +
110A MET* 4.0 14.4 - - + +
429A VAL* 5.7 2.9 - - + -
433A PHE* 6.2 0.2 - + - -
460A TRP* 3.7 17.3 - + - -
505A ILE* 4.9 3.8 - - + -
506A ALA* 6.3 0.2 - - - -
509A ILE* 3.5 44.2 - - + -
1001A HEM 3.6 33.9 - + + -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.3 22.9 + - + +
71A ARG* 3.3 9.1 + - - +
73A PHE* 1.3 79.2 - - - +
75A ASP* 1.3 70.8 + - - +
77A ILE* 3.3 11.3 + - - +
78A MET* 3.0 20.0 + - - +
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 2.7 76.3 + - - +
72A GLY* 2.8 15.5 + - - +
74A ALA* 1.3 77.7 - - - +
76A ALA* 1.3 57.9 + - - +
78A MET* 3.1 16.1 + - - +
79A MET* 3.2 24.3 + - + +
102A ILE* 4.8 10.2 - - + +
106A HIS* 5.7 4.2 - - + +
109A ILE* 4.5 9.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY 2.8 10.3 + - - +
73A PHE* 2.8 8.4 + - + +
75A ASP* 1.3 68.5 - - - +
77A ILE* 1.3 65.3 + - + +
78A MET 2.6 7.2 + - - -
79A MET* 3.1 15.4 + - + +
80A ARG* 3.0 27.3 + - - +
103A PHE* 4.4 7.9 - - + -
106A HIS* 3.3 35.7 - - + +
1001A HEM 4.6 14.1 - - + -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 2.5 62.1 + - + +
74A ALA* 3.5 9.6 - - - +
76A ALA* 1.3 71.2 - - + +
78A MET* 1.3 60.2 - - - +
80A ARG* 4.4 9.9 + - - +
81A SER* 4.7 3.1 + - - -
502A ALA* 6.0 8.3 - - + -
506A ALA* 4.0 37.5 - - + +
509A ILE* 5.7 3.1 - - + -
510A LEU* 6.3 2.2 - - + -
1001A HEM 5.7 6.7 - - + +
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Residues in contact with MET 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 3.0 10.5 + - - +
75A ASP* 3.2 11.0 - - - +
76A ALA 2.6 4.9 + - - -
77A ILE* 1.3 72.5 - - - +
79A MET* 1.3 68.4 + - - +
80A ARG 3.2 1.3 - - - -
81A SER* 3.1 23.9 + - - -
93A PHE* 5.7 11.2 - - + -
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Residues in contact with MET 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASP* 3.3 9.0 - - + +
76A ALA* 3.2 33.9 - - + +
78A MET* 1.3 74.2 - - - +
80A ARG* 1.3 53.8 + - - +
81A SER 2.5 18.2 + - - -
82A GLN* 3.1 21.0 + - - +
83A GLN* 4.7 0.5 + - - -
99A TYR* 5.1 7.5 - - + -
102A ILE* 3.1 36.3 - - + -
103A PHE* 2.9 72.5 - - + +
106A HIS* 4.0 8.5 - - + -
----------------------------------------------------------
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA 3.0 17.7 + - - +
77A ILE* 4.4 7.6 - - - +
78A MET 3.2 0.4 - - - -
79A MET* 1.3 74.5 - - - +
81A SER* 1.3 61.9 + - - +
83A GLN* 4.0 22.3 + - - +
103A PHE* 3.3 16.2 - - + -
414A LEU* 6.0 0.2 - - - +
467A ALA* 2.5 34.4 + - - +
468A PHE* 3.7 13.3 - - - -
471A LEU* 4.1 18.6 - - - +
495A LEU* 5.5 1.0 - - - +
498A ALA* 3.4 20.7 + - - +
499A ALA* 3.7 33.9 - - - +
502A ALA* 5.1 12.2 - - + +
1001A HEM 3.2 38.1 - - + +
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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