Contacts of the helix formed by residues 79 - 103 (chain D) in PDB entry 4J4L
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 ASN 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D GLY* 3.0 11.8 + - - +
77D GLY 3.3 5.6 + - - +
78D PHE* 1.3 73.1 - - - +
80D GLU* 1.3 66.4 + - - +
81D GLU* 3.1 19.8 + - - +
82D THR* 3.2 31.6 + - - +
83D CYS* 2.9 24.4 + - - +
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Residues in contact with GLU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PHE* 3.9 25.5 - - + -
79D ASN* 1.3 71.3 + - - +
81D GLU* 1.3 63.8 + - - +
83D CYS* 4.0 1.5 - - - +
84D LEU* 3.2 29.8 + - + +
129D LYS* 5.2 8.0 + - - +
131D LYS* 5.4 6.2 + - - +
184D MET* 3.7 46.5 - - - +
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ASN* 3.1 10.7 + - - +
80D GLU* 1.3 84.6 - - - +
82D THR* 1.3 68.8 + - + +
84D LEU* 3.7 4.3 + - - +
85D VAL* 3.5 24.9 + - + +
131D LYS* 4.4 36.3 + - + +
132D ASN* 4.8 9.7 + - - +
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Residues in contact with THR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LYS 4.2 7.1 + - - +
71D ASP* 2.7 29.9 + - - +
72D GLY* 4.3 0.2 - - - -
79D ASN* 3.2 30.4 + - - +
81D GLU* 1.3 83.6 - - + +
83D CYS* 1.3 57.2 + - - +
85D VAL* 3.5 9.7 + - - +
86D LYS* 3.0 25.5 + - - +
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Residues in contact with CYS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ASP 3.3 3.4 - - - -
72D GLY 3.5 9.9 - - - +
73D CYS* 2.1 51.8 - - - -
78D PHE* 4.1 2.0 - - + -
79D ASN 2.9 19.1 + - - +
80D GLU 4.0 3.1 - - - +
82D THR* 1.3 76.9 + - - +
84D LEU* 1.3 59.6 + - - +
86D LYS* 3.2 4.8 + - - +
87D ILE* 2.9 28.1 + - - +
180D ALA* 3.7 11.4 - - - -
184D MET* 3.5 22.7 - - + -
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D GLU* 3.2 21.0 + - + +
81D GLU* 4.2 4.5 - - - +
82D THR 3.5 0.2 - - - -
83D CYS* 1.3 75.4 - - - +
85D VAL* 1.3 57.7 + - + +
87D ILE* 3.3 5.6 + - + +
88D ILE* 3.0 38.1 + - + +
126D LEU* 3.9 41.5 - - + +
129D LYS* 3.8 43.3 - - + +
130D ALA* 4.0 12.3 - - + +
181D LEU* 4.0 12.8 - - + -
184D MET* 3.9 17.2 - - - +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLU* 3.5 17.9 + - + +
82D THR* 3.5 11.8 + - - +
83D CYS 3.3 0.6 - - - -
84D LEU* 1.3 73.3 - - + +
86D LYS* 1.3 64.6 + - - +
88D ILE* 4.1 1.6 - - - +
89D THR* 2.6 39.7 + - - +
130D ALA* 5.9 4.7 - - + -
132D ASN* 4.7 9.4 - - + +
135D ALA* 3.6 46.9 - - + +
136D ILE* 4.4 10.5 - - + +
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PRO* 4.8 4.1 - - - +
66D LYS 2.6 38.9 + - - +
67D MET* 3.7 15.5 - - - -
68D ALA* 5.5 0.4 - - - +
70D LYS* 5.8 0.2 - - - +
71D ASP* 3.1 47.9 + - + +
73D CYS* 4.4 0.7 - - - -
82D THR 3.0 14.3 + - - +
83D CYS* 3.4 8.5 - - - +
85D VAL* 1.3 78.1 - - - +
87D ILE* 1.4 56.6 + - - +
89D THR* 4.4 8.3 - - + -
90D GLY* 2.8 36.4 + - - +
93D GLU* 5.7 1.6 - - - -
173D PHE* 3.9 13.0 - - + -
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Residues in contact with ILE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE* 6.2 0.4 - - + -
67D MET* 3.7 12.3 - - + -
83D CYS* 2.9 38.3 + - - +
84D LEU* 3.3 6.7 + - + +
86D LYS* 1.4 71.4 - - - +
88D ILE* 1.3 62.2 + - - +
91D LEU* 3.1 30.2 + - + +
126D LEU* 3.3 28.9 - - + -
173D PHE* 3.9 6.6 - - - -
177D SER* 3.4 51.4 - - - +
180D ALA* 4.4 1.1 - - + -
181D LEU* 4.1 19.3 - - + -
184D MET* 4.3 2.7 - - + -
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Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 3.0 21.4 + - + +
85D VAL* 4.1 2.2 - - - +
87D ILE* 1.3 74.4 - - - +
89D THR* 1.3 66.1 + - - +
91D LEU* 3.2 8.3 + - - +
92D LEU* 3.0 29.3 + - + +
123D ILE* 4.7 7.3 - - + +
126D LEU* 3.8 44.6 - - + +
127D GLN* 4.0 21.8 - - + +
130D ALA* 4.1 13.5 - - + -
136D ILE* 3.8 40.4 - - + -
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Residues in contact with THR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D VAL* 2.6 27.9 + - - +
86D LYS* 3.8 11.7 - - + -
88D ILE* 1.3 73.4 - - - +
90D GLY* 1.3 64.5 + - - +
92D LEU* 3.1 10.5 + - - +
93D GLU* 3.1 36.4 + - - +
136D ILE* 3.8 6.9 - - - -
137D THR* 3.3 50.8 + - - +
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Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PRO* 3.7 14.0 - - - +
86D LYS* 2.8 24.7 + - - +
89D THR* 1.3 74.8 - - - +
91D LEU* 1.3 60.6 + - - +
93D GLU* 3.1 16.5 + - - +
94D PHE* 3.1 18.0 + - - -
173D PHE* 3.6 20.9 - - - -
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ILE* 3.1 26.4 + - + +
88D ILE* 3.2 4.7 + - - +
90D GLY* 1.3 76.3 - - - +
92D LEU* 1.3 61.2 + - - +
94D PHE* 3.4 12.9 + - - +
95D GLU* 3.5 17.8 + - - +
119D THR* 4.6 6.5 - - + +
122D LEU* 3.9 25.1 - - + -
123D ILE* 3.8 25.5 - - + +
126D LEU* 3.9 20.2 - - + -
170D PHE* 3.8 28.7 - - + -
173D PHE* 3.8 13.0 - - + -
174D LEU* 4.0 17.9 - - + -
177D SER* 5.5 0.4 - - - +
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ILE* 3.0 25.7 + - + +
89D THR* 3.1 7.8 + - - +
91D LEU* 1.3 78.4 - - - +
93D GLU* 1.3 62.1 + - - +
95D GLU* 3.1 38.9 + - - +
96D VAL 4.5 1.0 + - - -
123D ILE* 4.1 19.3 - - + -
127D GLN* 4.9 5.6 - - - +
136D ILE* 3.8 28.9 - - + -
138D THR* 4.4 9.4 - - - -
139D PRO* 3.7 31.7 - - + +
144D ASN* 5.7 1.2 + - - -
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Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PRO* 3.8 25.1 - - + +
86D LYS* 5.7 1.7 - - - -
89D THR* 3.1 34.7 + - - +
90D GLY* 3.1 7.3 + - - +
92D LEU* 1.3 77.2 - - - +
94D PHE* 1.3 61.4 - - - +
95D GLU 3.3 0.7 + - - -
96D VAL* 3.7 9.9 - - - +
97D TYR* 3.3 22.3 - - + -
137D THR* 4.1 16.2 - - - +
139D PRO* 4.0 21.1 - - + +
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Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LEU* 3.9 26.0 - - + -
65D PRO* 3.5 32.8 - - + -
90D GLY 3.1 20.2 + - - -
91D LEU* 3.7 9.6 - - - +
92D LEU 3.2 0.4 - - - -
93D GLU* 1.3 77.9 - - - +
95D GLU* 1.3 61.6 + - - +
97D TYR* 3.1 29.3 + + + +
98D LEU* 3.3 16.6 + - + +
166D ILE* 4.2 4.9 - - + -
169D SER 3.8 8.7 - - - -
170D PHE* 3.5 60.1 - + + -
173D PHE* 3.8 30.7 - + + -
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Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU 3.5 13.7 + - - +
92D LEU* 3.1 32.5 + - - +
94D PHE* 1.3 76.7 - - - +
96D VAL* 1.3 62.8 + - - +
98D LEU* 3.2 11.5 + - + +
99D GLU* 3.2 21.9 + - - +
116D GLN* 4.7 4.3 - - + +
119D THR* 4.7 8.8 - - + +
120D LYS* 2.7 51.6 + - - +
123D ILE* 3.8 14.9 - - + +
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU 4.5 1.2 + - - -
93D GLU 3.7 15.6 + - - +
95D GLU* 1.3 76.6 - - - +
97D TYR* 1.3 73.7 + - + +
99D GLU* 3.1 12.7 - - + +
100D TYR* 3.1 23.7 + - - +
144D ASN* 3.7 53.9 - - + +
147D LEU* 3.9 17.7 - - + -
148D LEU* 4.0 19.3 - - + +
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Residues in contact with TYR 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LEU* 4.2 19.7 - - + +
63D ASN* 3.6 19.8 + - - -
64D LEU* 3.5 33.0 - - + +
65D PRO* 5.3 2.9 - - + -
93D GLU* 3.3 27.6 - - + -
94D PHE* 3.1 16.5 + + + +
96D VAL* 1.3 83.3 - - + +
98D LEU* 1.3 58.3 + - + +
100D TYR* 3.2 9.8 - - - +
101D LEU* 3.1 28.8 + - - +
147D LEU* 3.7 30.6 - - + +
151D LEU* 4.3 16.2 - - + -
166D ILE* 3.9 31.5 - - + +
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D PHE* 3.4 18.6 - - + +
95D GLU* 3.2 13.7 + - + +
97D TYR* 1.3 76.0 - - - +
99D GLU* 1.3 64.6 + - - +
101D LEU* 3.4 28.0 + - + +
102D GLN* 3.0 25.9 + - - +
115D VAL* 4.4 5.6 - - + +
116D GLN* 4.2 28.9 - - + +
119D THR* 3.8 38.1 - - + +
166D ILE* 4.7 7.9 - - + -
170D PHE* 4.0 31.2 - - + -
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLU 3.2 11.6 + - - +
96D VAL* 3.1 15.5 - - + +
98D LEU* 1.3 73.3 - - - +
100D TYR* 1.3 65.9 + - - +
102D GLN* 3.0 27.3 + - - +
103D ASN* 4.3 5.9 + - - -
116D GLN* 3.0 25.7 + - - +
148D LEU* 4.6 19.9 - - + +
152D GLN* 5.8 0.5 + - - -
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Residues in contact with TYR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D VAL 3.1 8.6 + - - +
97D TYR* 3.2 10.1 - - - +
99D GLU* 1.3 77.9 - - - +
101D LEU* 1.3 66.2 + - + +
102D GLN 3.2 1.2 + - - -
103D ASN* 3.5 10.4 + - - +
104D ARG* 3.4 24.8 - - + +
148D LEU* 3.9 15.2 - - + +
151D LEU* 3.5 40.3 + - + -
152D GLN* 4.2 17.6 + - + +
159D GLN* 2.6 59.4 + - - +
162D THR* 4.2 10.7 - - + +
163D THR* 3.6 19.7 - - - -
166D ILE* 3.7 24.2 - - + -
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 4.4 12.3 - - + -
97D TYR 3.1 17.8 + - - +
98D LEU* 3.5 28.3 - - + +
99D GLU 3.1 0.8 - - - -
100D TYR* 1.3 84.3 - - + +
102D GLN* 1.3 66.2 + - - +
103D ASN 3.3 0.2 - - - -
104D ARG* 3.1 12.7 + - + -
105D PHE* 3.2 25.7 - - + -
112D ALA* 4.3 3.9 - - + +
115D VAL* 5.6 3.8 - - + -
163D THR* 3.9 35.9 - - + +
166D ILE* 4.2 15.3 - - + -
167D LEU* 3.7 26.9 - - + -
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Residues in contact with GLN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.0 21.5 - - - +
99D GLU* 3.0 21.2 + - - +
101D LEU* 1.3 78.7 - - - +
103D ASN* 1.3 70.6 + - - +
104D ARG 3.4 0.7 + - - -
105D PHE* 3.9 12.6 + - - +
109D GLU* 4.5 10.4 + - - +
112D ALA* 2.9 28.2 - - - +
113D ARG* 3.5 29.1 - - - +
116D GLN* 3.4 27.0 + - - +
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Residues in contact with ASN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D GLU* 4.6 5.2 + - - -
100D TYR 3.5 8.3 + - - +
101D LEU 3.3 0.4 - - - -
102D GLN* 1.3 87.3 - - - +
104D ARG* 1.3 69.2 + - - +
105D PHE 3.4 2.3 + - - -
106D GLU* 4.9 10.2 + - - +
152D GLN* 3.9 21.8 + - - +
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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
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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