Contacts of the helix formed by residues 69 - 92 (chain D) in PDB entry 4G5S
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 TYR 69 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LYS* 4.8 7.8 - - - -
61D TYR* 4.5 17.0 + + - -
65D GLU* 3.0 33.4 + - + -
66D CYS 3.2 9.0 + - - +
68D GLN* 1.3 83.2 - - + +
70D LYS* 1.3 63.0 + - - +
71D VAL 3.4 0.9 - - - -
72D VAL* 3.2 18.7 + - + +
73D VAL* 2.9 26.7 + - + +
169D PRO* 4.5 0.2 - - - -
174D VAL* 3.8 34.5 - - + -
177D THR* 3.6 32.5 - - + -
179D VAL* 4.3 17.6 - - + +
610Z PRO* 4.7 14.1 - - + -
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Residues in contact with LYS 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D CYS 3.6 2.2 + - - -
67D LYS* 3.2 19.2 + - - +
68D GLN 3.1 1.4 - - - -
69D TYR* 1.3 76.7 - - - +
71D VAL* 1.3 64.1 + - - +
73D VAL* 3.0 7.6 + - - +
74D TYR* 3.0 61.5 + - + -
118D VAL* 3.9 27.2 - - - +
164D GLN 5.3 0.4 + - - -
165D SER* 4.3 15.4 + - - +
167D TYR* 4.2 28.9 + - + +
169D PRO* 3.8 16.8 - - + -
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Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS 5.6 0.2 - - - +
68D GLN 3.4 18.6 - - - +
70D LYS* 1.3 76.2 - - + +
72D VAL* 1.3 63.3 + - + +
74D TYR* 3.2 11.2 + - - +
75D SER* 2.8 41.5 + - - +
114D ALA 4.4 16.1 - - - +
115D GLU* 4.6 11.9 - - - -
118D VAL 6.2 0.4 - - - +
607Z CYS* 4.8 7.9 - - - -
610Z PRO* 5.4 5.8 - - + -
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D TYR* 3.3 22.0 - - + +
71D VAL* 1.3 82.0 - - + +
73D VAL* 1.3 64.1 + - - +
75D SER* 3.3 1.9 + - - -
76D ASN* 2.9 42.3 + - - +
177D THR* 4.1 15.0 - - + -
178D ARG 3.8 15.0 - - - +
179D VAL* 4.4 9.6 - - + -
607Z CYS* 4.0 26.5 - - - +
608Z ALA 4.3 2.2 - - - +
610Z PRO* 4.2 25.4 - - + -
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D TYR* 2.9 23.2 + - + +
70D LYS* 3.0 10.1 + - - +
72D VAL* 1.3 76.9 - - - +
74D TYR* 1.3 57.9 + - + +
76D ASN* 3.3 7.4 + - - +
77D THR* 2.4 36.2 + - - +
155D TYR* 3.5 34.2 - - + +
162D ILE* 4.4 12.8 - - + -
167D TYR* 4.1 24.2 - - + +
169D PRO* 4.7 3.6 - - + -
173D ASP* 4.4 6.7 - - + +
177D THR* 3.7 20.4 - - + -
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Residues in contact with TYR 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LYS* 3.0 63.8 + - + -
71D VAL* 3.5 9.6 - - - +
73D VAL* 1.3 76.8 - - + +
75D SER* 1.3 63.1 + - - +
77D THR* 3.1 8.6 + - - -
78D ILE* 2.9 30.5 + - + +
114D ALA* 4.3 20.4 - - + +
118D VAL 4.6 11.7 - - - -
119D MET* 3.5 51.6 + - + +
162D ILE* 2.6 37.0 + - + -
163D SER* 4.4 1.7 - - - -
164D GLN 3.9 7.6 + - - -
167D TYR* 3.6 12.0 - + - -
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Residues in contact with SER 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 2.8 27.5 + - - +
72D VAL 3.3 4.9 + - - -
74D TYR* 1.3 74.0 - - - +
76D ASN* 1.3 64.5 + - - +
78D ILE* 3.7 10.3 - - - +
79D GLN* 2.9 27.7 + - - +
114D ALA 5.5 0.7 + - - -
115D GLU* 5.3 6.2 - - - +
606Z ARG 6.2 0.2 - - - -
607Z CYS* 3.5 30.0 - - - +
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Residues in contact with ASN 76 (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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72D VAL* 2.9 32.7 + - - +
73D VAL* 3.7 5.0 + - - +
75D SER* 1.3 71.9 - - - +
77D THR* 1.3 58.4 + - - +
79D GLN* 3.6 4.8 + - - +
80D SER* 2.9 30.8 + - - -
149D ASN* 4.7 5.3 + - - +
155D TYR* 4.1 17.0 - - + -
177D THR* 3.7 5.2 - - - -
178D ARG* 3.0 50.1 + - + +
605Z GLN 3.3 21.7 + - - +
606Z ARG* 3.6 7.9 - - - +
607Z CYS 3.9 4.0 - - - +
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Residues in contact with THR 77 (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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73D VAL* 2.4 32.4 + - - +
74D TYR* 3.2 10.3 - - - -
76D ASN* 1.3 75.0 - - - +
78D ILE* 1.3 65.1 + - - +
80D SER* 3.2 7.4 + - - -
81D ILE* 3.0 24.2 + - - +
119D MET* 5.3 7.0 - - + -
127D ILE* 5.4 4.9 - - + -
155D TYR* 4.0 27.6 - - + +
156D LEU* 3.6 25.4 - - + +
159D LEU* 4.8 8.7 - - + -
162D ILE* 4.3 13.7 - - + +
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Residues in contact with ILE 78 (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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74D TYR* 2.9 31.4 + - + +
75D SER* 3.7 7.6 - - - +
77D THR* 1.3 72.9 - - - +
79D GLN* 1.3 58.5 + - - +
81D ILE* 3.1 11.3 - - - +
82D ILE* 2.9 53.0 + - + +
107D LEU* 5.0 10.5 - - + -
110D LEU 5.7 0.7 - - - +
111D ALA* 4.4 27.6 - - - +
114D ALA* 4.0 26.0 - - + +
115D GLU 5.7 0.2 - - - +
119D MET* 5.2 5.6 - - + -
123D LEU* 5.2 9.4 - - + -
127D ILE* 5.0 12.1 - - + -
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Residues in contact with GLN 79 (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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75D SER 2.9 18.6 + - - +
76D ASN 3.9 2.2 - - - +
78D ILE* 1.3 73.6 - - - +
80D SER* 1.3 67.1 + - - +
82D ILE* 3.6 10.0 - - - +
83D ALA* 2.9 25.1 + - - +
605Z GLN* 3.5 38.1 - - + +
606Z ARG 4.9 0.7 - - - +
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Residues in contact with SER 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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76D ASN 2.9 15.4 + - - -
77D THR* 3.2 12.1 - - - -
79D GLN* 1.3 75.5 - - - +
81D ILE* 1.3 67.2 + - - +
83D ALA* 2.8 17.2 + - - +
84D ILE* 3.0 14.7 + - - +
148D LEU* 3.7 6.4 - - - +
149D ASN* 3.9 21.1 - - - +
152D ALA* 3.2 29.9 - - - +
155D TYR* 6.5 0.2 - - - -
156D LEU* 4.0 10.5 - - - +
605Z GLN* 4.6 0.6 - - - +
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Residues in contact with ILE 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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77D THR 3.0 10.7 + - - +
78D ILE* 3.1 24.7 - - + +
80D SER* 1.3 78.6 + - - +
82D ILE* 1.3 61.8 + - + +
84D ILE* 3.2 22.0 + - + -
85D ILE* 3.0 41.1 + - + +
107D LEU* 4.7 9.0 - - + -
127D ILE* 4.4 29.2 - - + -
130D LEU* 4.4 23.1 - - + -
131D TRP* 4.8 6.5 - - + +
136D VAL* 4.5 10.8 - - + -
156D LEU* 4.5 16.8 - - + -
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Residues in contact with ILE 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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78D ILE* 2.9 40.6 + - + +
79D GLN* 3.6 8.5 - - - +
81D ILE* 1.3 75.3 - - - +
83D ALA* 1.3 65.3 + - - +
85D ILE* 2.9 9.8 + - - +
86D ARG* 2.9 25.3 + - + +
107D LEU* 4.3 21.5 - - + -
108D PHE* 4.1 27.8 - - + -
111D ALA* 4.5 16.6 - - + -
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Residues in contact with ALA 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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79D GLN 2.9 14.0 + - - +
80D SER 2.8 14.9 + - - +
82D ILE* 1.3 73.9 - - - +
84D ILE* 1.3 61.6 + - - +
86D ARG* 3.5 6.6 + - - +
87D ALA* 2.9 25.2 + - - +
146D TYR* 4.7 4.6 - - + -
147D GLN 4.6 7.0 - - - +
148D LEU* 4.8 4.0 - - + -
604Z ASP* 6.0 0.4 - - - +
605Z GLN* 3.9 26.7 - - + +
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Residues in contact with ILE 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 SER* 3.0 12.3 + - - +
81D ILE* 3.4 31.4 - - + +
82D ILE 3.2 0.2 - - - -
83D ALA* 1.3 76.2 - - - +
85D ILE* 1.3 60.7 + - + +
87D ALA* 3.3 7.0 + - - +
88D MET* 2.9 27.1 + - + +
131D TRP* 4.2 12.1 - - + -
136D VAL* 3.9 26.9 - - + +
139D CYS* 3.8 9.5 - - + -
140D PHE* 4.6 6.1 - - + +
146D TYR* 3.9 17.9 - - - +
148D LEU* 3.9 23.8 - - + -
152D ALA* 5.4 0.4 - - + -
156D LEU* 3.9 18.2 - - + -
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Residues in contact with ILE 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 ILE* 3.0 37.7 + - + +
82D ILE* 2.9 11.2 + - - +
84D ILE* 1.3 78.8 - - + +
86D ARG* 1.3 60.2 + - - +
88D MET* 2.9 46.6 + - + +
89D GLY* 2.9 9.4 + - - -
95D PHE* 5.9 1.8 - - + -
104D ALA* 4.8 12.3 - - + -
107D LEU* 4.6 14.1 - - + -
108D PHE* 3.7 30.7 - - + -
130D LEU* 4.6 14.6 - - + -
136D VAL* 4.5 7.4 - - + -
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Residues in contact with ARG 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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82D ILE* 2.9 19.5 + - + +
83D ALA* 3.9 6.7 - - - +
85D ILE* 1.3 79.5 - - - +
87D ALA* 1.3 58.1 + - - +
89D GLY* 3.0 5.0 + - - +
90D ARG* 3.0 26.0 + - - +
108D PHE* 5.5 6.5 - - + -
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Residues in contact with ALA 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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83D ALA 2.9 19.1 + - - +
84D ILE 3.4 4.9 - - - +
86D ARG* 1.3 74.0 - - - +
88D MET* 1.3 64.6 + - - +
89D GLY 3.0 1.8 - - - -
90D ARG* 3.3 6.5 + - - +
91D LEU* 2.9 30.1 + - + +
139D CYS* 4.2 2.5 - - - -
146D TYR* 3.7 46.4 - - + -
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Residues in contact with MET 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 ILE* 2.9 15.8 + - + +
85D ILE* 2.9 42.5 + - + +
87D ALA* 1.3 75.8 - - - +
89D GLY* 1.3 59.5 + - - +
91D LEU* 4.7 1.1 - - - +
92D LYS* 3.0 17.7 + - - -
93D ILE* 3.2 33.4 + - + +
95D PHE* 3.6 35.4 - - + -
135D GLY 4.5 2.5 - - - +
136D VAL* 3.7 36.3 - - + -
139D CYS* 3.7 22.9 - - + -
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Residues in contact with GLY 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 ILE 2.9 11.1 + - - -
86D ARG* 3.0 7.5 + - - -
88D MET* 1.3 76.1 - - - +
90D ARG* 1.3 63.5 + - - +
92D LYS* 3.0 16.5 + - - +
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Residues in contact with ARG 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ARG 3.0 11.7 + - - +
87D ALA* 4.0 7.9 - - - +
89D GLY* 1.3 74.2 - - - +
91D LEU* 1.3 65.7 + - + +
92D LYS* 3.6 1.7 + - - +
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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 ALA* 2.9 20.7 + - + +
90D ARG* 1.3 82.6 - - + +
92D LYS* 1.3 72.8 + - - +
93D ILE* 4.0 27.1 - - + +
139D CYS* 4.7 2.2 - - - -
142D ARG* 4.6 14.6 + - - +
145D GLU* 3.6 33.0 - - + +
146D TYR* 4.2 28.3 - - + -
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Residues in contact with LYS 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 MET 3.0 5.7 + - - -
89D GLY 3.0 14.1 + - - +
90D ARG 3.3 1.5 - - - +
91D LEU* 1.3 84.5 - - - +
93D ILE* 1.3 59.9 + - - +
94D ASP* 4.1 3.1 + - - +
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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