Contacts of the helix formed by residues 80 - 103 (chain A) in PDB entry 5DSV
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 LEU 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 4.6 7.6 + - + -
79A GLY* 1.3 69.8 - - - -
81A LEU* 1.3 67.3 + - - +
82A ALA* 4.3 13.9 - - + +
83A ASP* 3.2 25.8 + - - +
84A ALA 3.3 9.0 + - - -
129A ARG* 4.2 17.3 - - - +
132A GLY* 2.9 27.3 + - - +
133A CYS* 3.8 5.4 - - - +
14G PHE* 4.5 5.8 - - + -
18G GLY 5.8 1.1 - - - +
20G VAL* 4.5 18.6 - - + +
154G SER* 5.2 11.0 - - - +
156G VAL* 5.9 1.1 - - + -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 4.2 12.8 - - - +
64A LYS 4.5 1.6 - - - +
65A ARG* 4.4 13.5 - - + -
67A PHE* 4.4 16.6 - - + -
77A VAL* 4.1 24.9 - - + -
79A GLY 3.2 9.4 + - - +
80A LEU* 1.3 74.2 - - - +
82A ALA* 1.3 64.6 + - - +
84A ALA* 3.3 5.0 + - + -
85A ARG* 3.0 52.5 + - - +
156G VAL* 4.8 6.9 - - + +
158G TYR* 3.8 23.3 - - + +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.4 8.0 - - + +
81A LEU* 1.3 77.9 - - - +
83A ASP* 1.3 63.2 + - - +
85A ARG* 3.5 8.6 + - - +
86A SER* 3.3 16.1 + - - -
120G HIS* 3.7 20.2 + - + +
154G SER* 2.9 31.4 - - - +
155G GLY 4.2 8.7 - - - +
156G VAL* 3.7 22.4 - - + +
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.4 19.7 - - - +
81A LEU 3.2 0.6 - - - -
82A ALA* 1.3 74.3 - - - +
84A ALA* 1.3 68.9 + - - +
86A SER* 2.9 17.5 + - - -
87A LEU* 2.9 13.0 + - - +
129A ARG* 2.4 34.2 + - - -
131A PHE* 3.6 17.8 - - + -
132A GLY* 3.0 21.6 + - - +
133A CYS* 4.0 9.9 - - - -
120G HIS* 2.8 27.7 + - - -
123G THR* 4.6 0.7 + - - -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 5.1 1.1 - - + -
75A MET* 3.9 4.8 - - + +
77A VAL* 3.9 37.2 - - + -
78A ALA 5.6 0.4 - - - +
80A LEU 3.3 6.6 + - - +
81A LEU* 3.5 12.8 - - + +
83A ASP* 1.3 79.2 - - - +
85A ARG* 1.3 57.6 + - - +
87A LEU* 2.9 7.0 + - - +
88A ALA* 2.8 29.2 + - - +
133A CYS* 3.4 23.7 - - + -
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 4.2 23.2 - - - +
64A LYS 4.2 5.1 + - - +
67A PHE* 3.8 30.2 - - + -
81A LEU* 3.0 50.9 + - + +
82A ALA* 3.8 6.9 - - - +
83A ASP 3.1 0.4 + - - -
84A ALA* 1.3 73.0 - - - +
86A SER* 1.3 63.0 + - - +
88A ALA* 3.3 9.6 + - - +
89A ASP* 3.1 24.4 + - - +
92A ARG* 4.7 1.4 + - - -
113G ASP* 4.5 16.1 + - - -
117G MET* 5.4 0.9 - - - -
155G GLY 5.5 0.2 + - - -
156G VAL* 4.1 9.7 - - - +
157G SER* 3.7 37.9 + - - +
158G TYR* 4.5 1.8 - - - -
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA 3.3 3.7 + - - -
83A ASP 2.9 10.0 + - - -
85A ARG* 1.3 78.9 - - - +
87A LEU* 1.3 63.3 + - - +
89A ASP* 3.2 6.2 + - - +
90A ILE* 3.2 29.2 + - - +
131A PHE* 3.8 13.5 - - - -
117G MET* 3.9 25.3 - - - +
120G HIS* 3.5 33.4 - - - -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A MET* 4.3 8.2 - - + +
83A ASP 2.9 10.0 + - - +
84A ALA* 2.9 8.7 + - - +
86A SER* 1.3 75.1 + - - +
88A ALA* 1.3 65.2 + - - +
90A ILE* 3.2 16.2 + - + +
91A ALA* 3.0 22.5 + - - +
115A VAL* 4.6 11.3 - - + +
118A TYR* 4.4 4.7 - - + -
119A VAL* 3.6 32.1 - - + -
131A PHE* 3.8 37.7 - - + -
133A CYS* 3.3 34.1 - - - +
135A PHE* 4.1 13.9 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 4.7 9.4 - - + -
69A VAL* 4.5 3.3 - - + +
75A MET* 3.8 26.4 - - + +
84A ALA 2.8 11.7 + - - +
85A ARG* 3.3 14.1 - - - +
86A SER 3.2 0.2 - - - -
87A LEU* 1.3 76.8 - - - +
89A ASP* 1.3 51.8 + - - +
91A ALA* 3.1 5.6 + - - +
92A ARG* 2.7 60.2 + - - +
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG 3.1 10.4 + - - +
86A SER* 3.3 11.7 - - - +
88A ALA* 1.3 78.0 - - - +
90A ILE* 1.3 62.4 + - + +
92A ARG* 2.9 31.7 + - - +
93A GLU* 3.0 24.1 + - - +
117G MET* 3.2 33.6 - - - +
100L SER 4.4 8.5 - - - +
101L ASN 5.3 2.6 - - - +
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Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER* 3.2 23.6 + - - +
87A LEU* 3.4 17.9 - - + +
88A ALA 3.1 0.8 - - - -
89A ASP* 1.3 77.0 - - + +
91A ALA* 1.3 62.8 + - - +
93A GLU* 3.3 6.0 + - - +
94A GLU* 3.0 29.1 + - + +
115A VAL* 4.4 15.5 - - + -
118A TYR* 3.4 66.0 - - + +
131A PHE* 5.0 0.9 - - + -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 3.7 24.5 - - + -
75A MET* 4.9 4.3 - - - -
87A LEU 3.0 11.7 + - - +
88A ALA* 3.4 8.5 - - - +
90A ILE* 1.3 76.7 - - - +
92A ARG* 1.3 62.5 + - - +
94A GLU* 3.2 1.4 + - - +
95A ALA* 2.9 27.5 + - - +
111A LEU* 3.7 9.0 - - + +
115A VAL* 3.6 27.6 - - + +
137A LEU* 5.3 4.3 - - + -
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 3.8 25.1 - - - +
68A ASN 3.3 24.2 + - - -
69A VAL* 3.2 28.5 + - - +
85A ARG 4.7 1.4 + - - -
88A ALA* 2.7 28.9 + - - +
89A ASP* 2.9 42.9 + - - +
91A ALA* 1.3 72.0 - - - +
93A GLU* 1.3 63.3 + - - +
95A ALA* 3.4 2.1 + - - +
96A SER* 3.0 24.4 + - - -
99L ARG* 4.2 14.2 - - + +
100L SER* 3.9 25.1 - - - +
101L ASN 5.8 0.2 - - - -
103L GLY* 5.1 14.4 + - - -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASP 3.0 15.8 + - - +
90A ILE* 3.8 5.8 - - - +
92A ARG* 1.3 75.1 - - - +
94A GLU* 1.3 58.1 + - - +
96A SER* 3.1 1.6 + - - -
97A ASN* 2.7 62.8 + - - +
97L ASN* 3.8 7.3 - - - +
100L SER* 3.4 33.7 + - - +
101L ASN* 5.5 1.7 - - - +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE* 3.0 24.1 + - + +
91A ALA* 3.2 5.1 + - - +
93A GLU* 1.3 80.7 - - - +
95A ALA* 1.3 56.5 + - - +
97A ASN* 3.6 4.5 + - - +
98A PHE* 3.2 24.8 + - - +
106A ILE* 4.1 7.1 - - + +
110A HIS* 5.4 1.3 - - + -
111A LEU* 4.0 11.9 - - + -
114A ARG* 2.7 64.3 + - + +
115A VAL* 4.8 3.1 - - + -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 4.7 6.3 - - + +
70A ASP* 3.9 19.1 - - + +
73A VAL* 5.9 0.2 - - + -
91A ALA 2.9 17.4 + - - +
92A ARG 3.9 2.5 - - - +
94A GLU* 1.3 74.3 - - - +
96A SER* 1.3 60.4 + - - +
98A PHE* 3.4 13.3 - - - +
99A ARG* 3.7 16.7 + - - +
106A ILE* 3.5 33.8 + - + +
111A LEU* 4.0 10.5 - - + +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ARG 3.0 16.8 + - - -
93A GLU 3.4 4.0 - - - -
95A ALA* 1.3 75.4 - - - +
97A ASN* 1.3 57.6 + - - +
98A PHE 3.0 4.3 - - - -
99A ARG* 2.7 29.0 + - - +
100A SER 3.1 3.8 + - - -
96L SER* 2.3 55.4 + - - -
99L ARG* 4.4 10.1 + - - +
100L SER* 3.6 18.6 + - - -
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Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLU* 2.7 45.6 + - - +
94A GLU* 4.0 4.5 - - - +
96A SER* 1.3 69.8 - - - +
98A PHE* 1.3 65.2 + - - +
100A SER* 4.0 7.7 + - - -
101A ASN* 3.1 23.8 + - - +
93L GLU* 3.8 11.0 - - - +
97L ASN* 3.0 24.0 + - - +
100L SER* 4.7 1.0 + - - -
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU 3.2 14.5 + - - +
95A ALA 3.4 13.0 - - - +
97A ASN* 1.3 77.4 - - - +
99A ARG* 1.3 56.4 + - + +
101A ASN* 2.6 32.2 + - - +
102A PHE* 3.0 54.7 + + + -
104A TYR* 3.8 19.1 - + - -
105A ASN 3.1 25.6 - - - -
106A ILE* 3.7 28.5 - - + -
107A PRO* 3.8 18.4 - - + -
102K PHE* 3.6 31.6 - + - -
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 2.8 36.1 + - - -
71A ARG* 3.1 25.9 - - - +
95A ALA 3.7 12.2 + - - +
96A SER* 2.7 16.7 + - - +
98A PHE* 1.3 77.4 - - - +
100A SER* 1.3 64.6 + - - +
101A ASN 3.3 0.3 + - - -
103A GLY* 3.4 25.6 + - - +
104A TYR* 3.3 21.1 + - - +
105A ASN* 2.7 28.7 + - - +
69L VAL 5.1 5.8 - - - +
70L ASP* 3.6 28.7 - - - +
71L ARG* 4.9 0.7 - - - +
92L ARG* 4.1 8.1 - - + +
96L SER* 4.6 4.0 + - - +
99L ARG* 4.1 16.4 - - - +
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A SER 3.1 7.0 + - - -
97A ASN* 4.0 13.5 + - - -
98A PHE 2.8 4.3 + - - -
99A ARG* 1.3 75.4 - - - +
101A ASN* 1.3 68.3 + - - +
89L ASP* 4.4 7.5 - - - +
92L ARG* 3.5 34.6 - - - +
93L GLU* 3.5 32.0 + - - -
96L SER* 3.3 24.7 + - - -
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASN* 3.1 22.6 + - - +
98A PHE* 2.6 10.4 + - - +
100A SER* 1.3 81.9 - - - +
102A PHE* 1.3 72.1 + - + +
103A GLY* 3.2 4.7 + - - -
110K HIS* 3.9 11.6 + - - -
114K ARG* 3.6 30.5 + - - +
89L ASP* 5.1 5.5 - - - +
92L ARG* 5.5 1.7 + - - -
93L GLU* 5.5 2.6 - - - +
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.0 54.5 + + + +
101A ASN* 1.3 85.1 - - + +
103A GLY* 1.3 57.9 + - - +
104A TYR* 2.9 48.2 - + - -
98K PHE* 2.7 44.9 - + - -
102K PHE* 4.3 23.8 - + - -
104K TYR* 5.5 4.0 - + - -
107K PRO* 5.0 2.9 - - + -
110K HIS* 3.3 40.5 - + - -
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Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 3.4 23.0 + - - +
101A ASN 3.2 5.1 - - - -
102A PHE* 1.3 78.3 - - - +
104A TYR* 1.3 61.9 + - - +
68L ASN* 5.7 2.4 - - - +
92L ARG* 5.0 15.3 + - - -
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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
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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