Contacts of the helix formed by residues 56 - 85 (chain A) in PDB entry 4N78
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 ILE 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 1.3 68.7 - - - -
57A ALA* 1.3 59.7 + - - +
58A ARG 2.9 5.3 + - - -
59A TYR* 3.0 9.5 + - + +
60A ILE* 2.9 46.3 + - + +
513A ALA* 4.2 22.7 - - + +
516A LYS* 4.0 33.0 - - + +
517A THR* 5.0 5.2 - - - +
561A MET* 4.0 15.9 - - + -
565A MET* 5.4 4.5 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY 3.5 0.2 - - - -
56A ILE* 1.3 77.7 - - - +
58A ARG* 1.3 60.1 - - - +
60A ILE* 3.8 16.2 - - + +
61A GLU* 3.2 22.5 + - - +
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 3.2 34.1 - - - +
57A ALA* 1.3 76.9 - - - +
59A TYR* 1.3 97.3 + - + +
61A GLU* 3.4 7.0 + - - +
62A GLN* 3.3 18.9 + - - +
152A PHE* 4.4 20.6 + - - +
568A SER* 5.2 2.8 - - - -
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY 3.1 30.7 + - - -
56A ILE* 3.0 6.0 + - - +
58A ARG* 1.3 105.9 + - + +
60A ILE* 1.3 60.4 + - - +
62A GLN* 3.2 8.7 + - + +
63A ALA* 2.8 31.9 + - - +
152A PHE* 4.7 10.1 - + - -
510A VAL* 4.7 12.3 - - + +
560A TYR* 5.1 2.6 - - + -
561A MET* 3.5 23.7 - - + +
564A THR* 3.9 31.2 - - + -
565A MET* 3.4 35.5 - - + +
568A SER* 3.4 22.6 + - - -
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 2.9 37.3 + - + +
57A ALA* 3.8 14.6 - - + +
59A TYR* 1.3 77.1 - - - +
61A GLU* 1.3 57.1 + - - +
63A ALA* 3.5 7.5 + - + +
64A THR* 2.8 34.5 + - - +
561A MET* 4.5 10.5 - - + -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 3.2 15.5 + - - +
58A ARG* 3.7 6.1 - - - +
59A TYR 3.2 0.4 - - - -
60A ILE* 1.3 77.8 - - - +
62A GLN* 1.3 65.5 + - - +
64A THR* 3.0 18.6 + - - +
65A VAL* 3.0 33.8 + - + +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG 3.3 9.8 + - - +
59A TYR* 3.2 14.5 + - + +
61A GLU* 1.3 78.8 - - - +
63A ALA* 1.3 57.2 + - - +
65A VAL* 3.1 12.5 + - - +
66A HIS* 2.8 28.8 + - - +
142A ARG* 4.0 16.5 - - - +
143A LEU* 6.0 0.8 - - - +
148A ARG* 5.1 13.1 - - - +
153A VAL* 6.2 1.6 - - - -
154A SER* 4.0 14.6 + - - -
157A TYR* 3.8 35.5 - - - +
560A TYR* 4.0 13.5 + - - +
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR 2.8 17.9 + - - +
60A ILE* 3.6 8.5 - - + +
62A GLN* 1.3 75.6 - - - +
64A THR* 1.3 56.9 + - - +
66A HIS* 3.8 2.9 - - - +
67A SER* 2.9 31.0 + - - -
560A TYR* 3.7 34.7 + - + -
561A MET* 5.2 3.8 - - - -
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 2.8 24.1 + - - +
61A GLU* 3.0 25.1 + - - +
63A ALA* 1.3 75.5 - - - +
65A VAL* 1.3 61.1 + - + +
67A SER* 3.4 5.6 + - - -
68A SER* 3.0 28.9 + - - -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 3.0 31.8 + - + +
62A GLN* 3.1 14.3 + - - +
64A THR* 1.3 73.6 - - + +
66A HIS* 1.3 68.1 + - - +
68A SER* 3.1 8.0 + - - -
69A MET* 2.9 26.2 + - + +
135A ARG* 5.8 2.0 - - - +
139A GLU* 3.2 31.2 - - - +
142A ARG* 4.4 7.9 - - - +
157A TYR* 3.6 11.4 - - + +
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Residues in contact with HIS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 2.8 21.3 + - - +
63A ALA* 3.8 4.3 - - - +
65A VAL* 1.3 73.1 - - - +
67A SER* 1.3 62.3 + - - +
69A MET* 3.2 2.3 + - - +
70A ASN* 3.1 33.1 + - - -
156A ALA* 3.4 37.2 - - + -
157A TYR* 3.6 29.7 - + + +
160A THR* 2.6 30.0 + - + -
560A TYR* 3.3 28.3 + + + +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA 2.9 19.6 + - - -
64A THR* 3.7 6.3 - - - -
66A HIS* 1.3 77.5 - - - +
68A SER* 1.3 61.6 + - - +
70A ASN* 3.5 11.4 + - - +
71A GLU* 3.2 33.2 + - - +
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 3.0 20.0 + - - -
65A VAL* 3.4 7.6 - - - -
67A SER* 1.3 76.2 - - - +
69A MET* 1.3 65.1 + - - +
71A GLU* 3.3 26.3 + - - +
72A MET* 3.6 6.1 + - - +
135A ARG* 2.5 33.8 + - - -
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Residues in contact with MET 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 2.9 21.5 + - + +
66A HIS 3.7 6.1 - - - +
68A SER* 1.3 76.8 - - - +
70A ASN* 1.3 64.0 + - - +
72A MET* 3.0 17.4 + - - +
73A LEU 3.2 8.3 + - - -
135A ARG* 3.9 33.4 - - + +
136A PHE* 4.4 15.3 - - - -
139A GLU* 4.5 11.4 - - + +
157A TYR* 3.4 27.8 - - + +
160A THR* 4.2 10.5 - - + -
161A LEU* 4.1 16.2 - - + -
164A PHE* 3.4 41.6 - - + -
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS* 3.1 33.9 + - - -
67A SER* 3.7 11.7 - - - +
68A SER 3.3 0.2 - - - -
69A MET* 1.3 75.3 - - - +
71A GLU* 1.3 64.2 + - + +
73A LEU* 3.1 25.7 + - - +
74A GLU* 3.1 22.1 + - + +
160A THR* 3.2 27.4 + - - +
163A LYS* 5.4 1.7 - - - -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 3.2 27.7 + - - +
68A SER* 3.3 14.7 + - - +
69A MET 3.2 0.2 - - - -
70A ASN* 1.3 77.7 - - + +
72A MET* 1.3 57.9 + - - +
74A GLU* 3.4 11.8 + - - +
75A GLU* 3.1 26.0 + - - +
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Residues in contact with MET 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER 3.6 5.2 + - - +
69A MET* 3.0 13.3 + - - +
71A GLU* 1.3 77.8 - - - +
73A LEU* 1.3 58.6 + - - +
75A GLU* 3.2 14.0 + - - +
76A GLY* 2.9 24.3 + - - -
128A PHE* 3.5 29.5 - - + +
131A ASN* 3.1 30.5 - - + +
132A ALA* 3.4 32.1 - - + +
135A ARG* 3.8 35.0 - - + +
164A PHE* 3.9 15.9 - - + -
167A MET* 4.1 2.1 - - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET 3.2 3.3 + - - +
70A ASN* 3.1 30.9 + - - +
72A MET* 1.3 74.3 - - - +
74A GLU* 1.3 67.7 + - + +
76A GLY* 3.3 1.9 + - - -
77A GLN* 3.0 23.0 + - - +
160A THR* 3.9 22.0 - - + +
163A LYS* 3.6 47.1 - - + +
164A PHE* 3.8 25.8 - - + -
167A MET* 3.9 20.4 - - + +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 3.1 19.9 + - + +
71A GLU* 3.5 11.0 - - - +
72A MET 3.3 0.2 - - - -
73A LEU* 1.3 78.3 - - - +
75A GLU* 1.3 62.6 + - - +
77A GLN* 3.3 13.3 + - - +
78A GLU* 3.2 30.0 + - - +
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU 3.1 13.1 + - - +
72A MET* 3.5 17.3 - - - +
73A LEU 3.2 0.2 - - - -
74A GLU* 1.3 75.3 - - - +
76A GLY* 1.3 65.1 + - - +
78A GLU* 3.1 29.1 + - - +
79A TYR* 3.2 32.6 + - + -
128A PHE* 3.5 29.8 - - + +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET 2.9 12.0 + - - -
73A LEU 3.3 3.6 + - - -
75A GLU* 1.3 71.5 - - - +
77A GLN* 1.3 60.0 + - - +
79A TYR* 3.0 6.4 + - - +
80A ALA* 2.9 27.6 + - - +
128A PHE* 3.3 28.0 - - - -
167A MET* 3.9 12.8 - - - -
171A LEU* 3.7 6.6 - - - +
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU 3.0 12.6 + - - +
74A GLU* 3.4 17.9 - - - +
76A GLY* 1.3 75.0 - - - +
78A GLU* 1.3 63.2 + - + +
80A ALA* 3.2 6.2 + - - +
81A VAL* 3.0 32.4 + - + +
167A MET* 5.1 0.8 - - - +
170A VAL* 6.1 0.8 - - - +
308A PHE* 3.6 29.6 - - - -
677A TYR* 5.2 6.1 + - - -
682A PHE* 6.1 0.2 - - - -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.2 19.4 - - - +
75A GLU* 3.1 22.0 + - - +
77A GLN* 1.3 78.3 - - + +
79A TYR* 1.3 59.7 + - + +
81A VAL* 3.4 10.0 + - - +
82A MET* 3.1 24.1 + - - +
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Residues in contact with TYR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 3.2 39.9 + - + -
76A GLY* 3.0 8.1 + - - +
78A GLU* 1.3 77.3 - - + +
80A ALA* 1.3 66.4 + - - +
82A MET* 3.2 18.3 + - + +
83A LEU* 3.0 27.4 + - - +
121A LYS* 3.9 7.4 - - - -
124A ASN* 3.2 30.5 + - + +
125A PHE* 3.4 49.4 - + + -
128A PHE* 3.6 29.8 - + + +
171A LEU* 4.2 7.0 - - + -
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY 2.9 13.1 + - - +
77A GLN* 3.4 14.4 - - - +
79A TYR* 1.3 76.5 - - - +
81A VAL* 1.3 56.9 + - - +
83A LEU* 3.3 1.7 + - - -
84A TYR* 3.0 30.7 + - - +
170A VAL* 4.3 5.4 - - + -
171A LEU* 3.8 10.7 - - + +
174A LEU* 3.5 22.6 - - + +
308A PHE* 3.5 25.6 - - + -
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN* 3.0 30.0 + - + +
78A GLU* 3.5 10.3 - - - +
79A TYR 3.2 0.2 - - - -
80A ALA* 1.3 73.9 - - - +
82A MET* 1.3 58.5 + - - +
84A TYR* 4.7 0.9 - - - -
85A THR* 2.6 40.9 + - - +
308A PHE* 4.1 17.7 - - + -
681A ARG* 4.2 13.5 - - + +
682A PHE* 3.6 45.3 - - + +
684A LYS* 4.5 4.7 - - - +
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU 3.1 13.8 + - - +
79A TYR* 3.2 19.7 + - + +
81A VAL* 1.3 78.4 - - - +
83A LEU* 1.3 95.8 + - + +
85A THR* 3.7 4.7 + - - -
86A TRP* 3.2 40.3 + - + +
121A LYS* 3.5 45.5 - - + +
122A LEU* 4.3 8.5 - - + -
125A PHE* 4.3 19.1 - - + -
684A LYS* 5.2 5.6 - - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR 3.0 18.1 + - - +
80A ALA 3.7 4.9 - - - +
82A MET* 1.3 93.1 - - + +
84A TYR* 1.3 65.8 + - - +
86A TRP* 3.0 16.7 + - - +
122A LEU* 5.0 3.8 - - + -
125A PHE* 3.8 30.7 - - + -
171A LEU* 3.8 20.9 - - + +
174A LEU* 3.8 31.4 - - + +
175A LYS* 4.1 11.9 - - + +
177A MET* 5.1 0.2 - - - -
178A LYS* 3.2 20.7 - - + +
181A VAL* 4.4 21.1 - - + -
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA 3.0 8.7 + - - +
81A VAL 4.1 2.2 - - - +
83A LEU* 1.3 78.5 - - - +
85A THR* 1.3 71.7 + - + +
86A TRP 3.3 0.6 + - - -
174A LEU* 4.2 15.5 - - + +
177A MET* 4.7 4.9 - - + -
178A LYS* 3.7 12.4 + - - +
308A PHE* 3.4 36.3 - + + -
309A GLY* 3.7 15.0 - - - -
310A ASP* 2.6 37.8 + - - -
623A PHE* 3.6 15.6 - + + +
625A GLU* 3.3 49.2 + - + +
626A PHE* 4.1 7.0 - - + -
682A PHE* 3.9 29.4 - + - -
687A LEU* 5.8 0.2 - - + -
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 2.6 23.9 + - + +
82A MET* 3.7 3.9 + - - -
84A TYR* 1.3 89.4 - - + +
86A TRP* 1.3 59.4 + - - +
87A ARG* 3.3 8.9 + - - +
625A GLU* 4.9 4.0 - - + -
682A PHE* 4.2 14.8 - - + -
684A LYS* 3.4 37.9 + - + -
686A PHE* 3.7 24.9 - - - -
687A LEU* 4.0 24.5 - - + -
----------------------------------------------------------
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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