Contacts of the helix formed by residues 106 - 135 (chain L) in PDB entry 3GHG
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 SER 106 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165K LEU* 4.6 10.3 - - - +
169K ARG* 3.0 27.7 + - - -
101L LEU 4.6 0.2 + - - -
102L THR 3.1 23.9 + - - -
103L HIS* 3.0 12.1 + - - -
105L SER* 1.3 74.9 - - - +
107L ILE* 1.3 59.9 + - - +
108L ARG* 3.5 14.9 + - - +
109L TYR* 3.8 15.9 - - - +
110L LEU* 4.3 4.5 + - - +
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Residues in contact with ILE 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J LYS* 4.7 10.5 - - + -
132J HIS* 3.1 54.1 - - + +
133J ILE* 4.8 9.4 - - + -
136J LEU* 4.4 13.3 - - + +
165K LEU* 5.8 2.9 - - - -
103L HIS 3.8 1.5 + - - +
104L ASP 3.1 21.4 + - - +
105L SER* 2.9 7.0 - - - +
106L SER* 1.3 75.3 - - - +
108L ARG* 1.3 69.8 + - + +
109L TYR 3.2 6.2 + - - -
110L LEU* 3.8 4.1 + - - +
111L GLN* 3.3 23.9 + - + +
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Residues in contact with ARG 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L SER* 2.7 35.5 + - - +
106L SER* 3.7 15.0 + - - +
107L ILE* 1.3 81.9 - - + +
109L TYR* 1.3 83.1 + - - +
111L GLN* 4.0 7.4 - - - -
112L GLU* 3.1 24.6 + - - +
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Residues in contact with TYR 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K ARG* 3.3 41.7 - - - -
173K GLU* 2.6 33.8 + - - -
176K ARG* 6.0 2.9 - - - -
106L SER* 3.8 12.3 + - - +
107L ILE 3.2 0.2 - - - -
108L ARG* 1.3 93.6 - - - +
110L LEU* 1.3 85.1 + - + +
112L GLU* 3.1 5.0 + - - +
113L ILE* 3.0 33.6 + - + +
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Residues in contact with LEU 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J LEU* 5.8 4.7 - - + -
165K LEU* 5.4 13.2 - - + +
168K LEU* 3.2 35.7 - - + +
169K ARG* 3.3 35.4 - - + +
172K LEU* 3.7 27.9 - - + +
173K GLU* 5.6 0.7 - - - +
106L SER 4.3 3.1 + - - +
107L ILE* 3.8 5.8 + - - +
109L TYR* 1.3 108.3 - - + +
111L GLN* 1.3 59.7 + - - +
113L ILE* 3.0 21.3 - - + +
114L TYR* 3.1 14.6 + - - +
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Residues in contact with GLN 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J HIS* 6.4 1.3 - - + -
136J LEU* 3.4 40.7 - - + +
139J ASN* 5.9 0.8 - - - +
107L ILE* 3.3 21.7 + - + +
108L ARG* 4.2 6.7 - - - +
109L TYR 3.1 0.6 - - - -
110L LEU* 1.3 77.0 - - - +
112L GLU* 1.3 59.6 + - - +
114L TYR* 3.4 16.9 - - - +
115L ASN* 2.9 42.5 + - - +
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Residues in contact with GLU 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L ARG 3.1 20.1 + - - +
109L TYR* 3.1 3.6 + - - +
111L GLN* 1.3 74.1 - - - +
113L ILE* 1.3 56.6 + - - +
114L TYR 3.1 1.3 - - - -
115L ASN* 3.1 9.9 + - - +
116L SER* 2.7 51.9 + - - -
119L GLN* 4.5 8.9 + - - +
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Residues in contact with ILE 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K ARG* 6.4 0.2 - - + -
172K LEU* 3.1 39.5 - - + +
173K GLU* 3.5 31.9 - - + +
176K ARG* 4.2 26.2 - - - +
109L TYR* 3.0 26.0 + - + +
110L LEU* 3.0 35.7 - - + +
112L GLU* 1.3 75.5 - - - +
114L TYR* 1.3 54.9 + - - +
116L SER* 3.1 7.4 + - - +
117L ASN* 3.0 36.9 + - - +
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Residues in contact with TYR 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J LEU* 5.3 3.1 - - + -
139J ASN* 3.3 56.6 + - + +
140J VAL* 4.8 4.3 - - + -
142J ALA* 5.7 0.9 - - - +
143J GLN* 3.4 36.5 + - + +
172K LEU* 3.7 22.2 - - + -
110L LEU 3.1 20.2 + - - +
111L GLN* 3.4 16.6 - - - +
113L ILE* 1.3 75.5 - - - +
115L ASN* 1.3 91.1 + - - +
117L ASN* 2.7 28.4 + - - +
118L ASN* 3.1 26.6 + - - +
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Residues in contact with ASN 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L GLN* 2.9 42.9 + - - +
112L GLU* 3.1 11.9 + - - +
114L TYR* 1.3 98.5 - - - +
116L SER* 1.3 55.9 - - - +
118L ASN* 3.5 12.7 + - - +
119L GLN* 3.1 41.5 + - - +
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Residues in contact with SER 116 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176K ARG* 5.6 4.0 + - - -
112L GLU* 2.7 30.3 + - - -
113L ILE* 3.1 16.5 + - - +
115L ASN* 1.3 69.5 - - - +
117L ASN* 1.3 62.0 + - - +
118L ASN 3.0 1.8 - - - -
119L GLN* 3.3 15.3 + - - +
120L LYS* 2.7 43.4 + - - +
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Residues in contact with ASN 117 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J GLN* 3.2 18.5 + - - +
172K LEU* 3.8 11.6 - - - +
175K LEU* 3.9 9.5 - - - +
176K ARG* 3.6 46.4 + - - +
179K ILE* 3.7 9.2 - - + +
113L ILE* 3.0 19.4 + - - +
114L TYR* 2.7 18.0 + - - +
116L SER* 1.3 81.6 + - - +
118L ASN* 1.3 56.1 + - - -
120L LYS* 3.4 12.5 - - - +
121L ILE* 3.2 31.4 + - + +
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Residues in contact with ASN 118 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J GLN* 2.8 33.8 + - - +
114L TYR* 3.1 37.2 + - - -
115L ASN* 3.6 14.3 - - - +
116L SER 3.0 0.4 - - - -
117L ASN* 1.3 73.8 - - - +
119L GLN* 1.3 66.6 + - - +
120L LYS 2.9 1.1 - - - -
121L ILE* 2.8 18.8 + - - +
122L VAL* 3.1 14.7 + - - +
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Residues in contact with GLN 119 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L GLU* 4.5 8.2 + - - +
115L ASN* 3.1 26.3 + - - +
116L SER* 3.6 20.2 - - - +
118L ASN* 1.3 78.1 - - - +
120L LYS* 1.3 61.3 + - - +
122L VAL* 3.5 15.0 - - - +
123L ASN* 3.2 20.3 - - - +
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Residues in contact with LYS 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176K ARG* 6.0 2.2 - - + -
179K ILE* 3.4 34.4 + - + +
180K GLN* 5.1 3.0 - - - +
183K GLU* 2.3 41.9 + - - +
116L SER* 2.7 29.8 + - - +
117L ASN* 3.4 13.9 - - - +
118L ASN 2.9 0.2 - - - -
119L GLN* 1.3 74.3 - - + +
121L ILE* 1.3 57.9 + - - +
123L ASN* 3.0 29.5 + - + +
124L LEU* 3.1 6.8 + - - +
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Residues in contact with ILE 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J GLN* 5.0 10.3 - - + +
146J ASP* 4.9 15.5 - - - +
147J MET* 3.4 31.4 - - + -
150J LEU* 4.0 24.0 - - + -
179K ILE* 3.4 19.1 - - + -
117L ASN* 3.2 17.0 + - + +
118L ASN* 2.8 17.9 + - - +
120L LYS* 1.3 71.2 - - - +
122L VAL* 1.3 57.9 + - - +
123L ASN 3.0 1.8 - - - -
124L LEU* 2.7 25.3 + - + +
125L LYS* 2.8 23.2 + - + +
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Residues in contact with VAL 122 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L ASN 3.1 9.2 + - - +
119L GLN* 3.5 17.7 - - - +
121L ILE* 1.3 77.3 - - - +
123L ASN* 1.3 66.0 + - - +
125L LYS* 4.8 3.3 - - - +
126L GLU* 3.1 34.5 + - - +
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Residues in contact with ASN 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K GLU* 4.5 8.5 - - - +
119L GLN 3.2 15.0 + - - +
120L LYS* 3.0 18.0 + - + +
121L ILE 3.0 0.8 - - - -
122L VAL* 1.3 89.2 - - - +
124L LEU* 1.3 60.3 + - - +
126L GLU* 3.9 8.6 - - - +
127L LYS* 3.5 34.0 + - + +
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Residues in contact with LEU 124 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J MET* 5.5 1.6 - - + -
150J LEU* 3.8 24.7 - - + -
154J ILE* 4.6 11.0 - - + -
179K ILE* 4.6 17.9 - - + +
182K LEU* 4.7 17.0 - - + -
183K GLU* 3.8 46.2 - - + +
186K VAL* 4.8 13.4 - - + +
120L LYS 3.1 6.0 + - - +
121L ILE* 2.7 22.6 + - + +
123L ASN* 1.3 72.1 - - - +
125L LYS* 1.3 58.8 + - - +
127L LYS* 3.4 6.6 + - + +
128L VAL* 3.0 36.8 + - + +
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Residues in contact with LYS 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J LEU* 4.0 37.2 - - + -
153J ASP* 5.9 2.7 - - - +
428K LYS* 5.0 20.8 - - - +
121L ILE* 2.8 21.4 + - + +
122L VAL* 4.8 2.7 - - - +
124L LEU* 1.3 72.8 - - - +
126L GLU* 1.3 63.1 + - - +
128L VAL* 3.7 12.8 - - + +
129L ALA* 3.3 22.7 + - - +
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Residues in contact with GLU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L VAL* 3.1 25.2 + - - +
123L ASN* 3.9 10.2 - - - +
124L LEU 3.3 0.2 - - - -
125L LYS* 1.3 79.9 - - - +
127L LYS* 1.3 62.4 + - + +
129L ALA* 4.1 5.3 + - - +
130L GLN* 3.4 34.3 + - - +
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Residues in contact with LYS 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K GLU* 5.3 13.1 + - - +
186K VAL* 5.0 16.1 - - + +
187K SER* 4.8 9.9 + - - -
190K MET* 3.2 29.3 - - + +
123L ASN* 3.5 24.5 + - + +
124L LEU* 3.4 7.4 + - - +
125L LYS 3.3 0.4 - - - -
126L GLU* 1.3 84.8 - - + +
128L VAL* 1.3 55.5 + - - +
129L ALA 3.5 0.2 - - - -
130L GLN* 3.4 15.0 + - - +
131L LEU* 2.8 27.0 + - - +
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Residues in contact with VAL 128 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J LEU* 6.1 0.9 - - + -
153J ASP* 4.4 3.8 - - - +
154J ILE* 3.4 37.2 - - + -
157J LYS* 3.9 31.2 - - + +
186K VAL* 4.2 12.6 - - + -
124L LEU* 3.0 27.0 + - + +
125L LYS* 3.4 14.1 + - + +
127L LYS* 1.3 74.3 - - - +
129L ALA* 1.3 56.5 - - - +
130L GLN 3.2 0.2 - - - -
131L LEU* 3.0 11.2 + - + +
132L GLU* 2.7 33.1 + - - +
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Residues in contact with ALA 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J LYS* 5.2 1.8 - - - +
125L LYS 3.3 13.0 + - - +
126L GLU* 4.3 5.6 - - - +
127L LYS 3.5 0.2 - - - -
128L VAL* 1.3 78.7 - - - +
130L GLN* 1.3 60.7 + - + +
132L GLU* 3.7 20.7 - - - +
133L ALA* 3.3 23.7 + - - +
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Residues in contact with GLN 130 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K MET* 4.6 8.6 - - + +
126L GLU* 3.4 30.3 - - - +
127L LYS* 3.4 20.1 + - - +
128L VAL 3.2 0.6 - - - -
129L ALA* 1.3 78.7 - - + +
131L LEU* 1.3 57.9 + - - +
133L ALA* 3.8 6.1 - - - +
134L GLN* 3.2 31.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 131 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J ILE* 5.9 2.5 - - + -
157J LYS* 4.8 14.6 - - + +
158J ILE* 4.3 23.1 - - + +
161J CYS* 4.2 14.8 - - - -
186K VAL* 4.2 19.5 - - + +
189K GLN* 4.1 21.8 - - + -
190K MET* 4.1 26.7 - - + +
193K CYS* 5.1 1.3 - - - -
127L LYS 2.8 14.4 + - - +
128L VAL* 3.0 17.8 + - + +
130L GLN* 1.3 72.8 - - - +
132L GLU* 1.3 60.0 + - - +
133L ALA 3.0 1.3 - - - -
134L GLN* 2.7 40.1 + - + +
135L CYS* 3.4 5.0 + - - -
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Residues in contact with GLU 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J LYS* 2.8 44.6 + - + +
161J CYS* 5.9 0.4 - - - -
261K ASP* 3.8 21.7 - - - +
263K GLY 5.7 1.0 - - - +
128L VAL 2.7 17.9 + - - +
129L ALA* 3.7 17.8 - - - +
131L LEU* 1.3 75.4 - - - +
133L ALA* 1.3 55.4 + - - +
135L CYS* 2.9 36.5 + - - +
136L GLN* 3.5 11.7 - - - +
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Residues in contact with ALA 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L ALA 3.3 16.2 + - - +
130L GLN* 3.8 9.6 - - - +
131L LEU 2.9 0.4 + - - -
132L GLU* 1.3 81.1 - - - +
134L GLN* 1.3 65.9 + - - +
136L GLN* 4.0 19.1 + - - +
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Residues in contact with GLN 134 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J SER* 5.1 2.8 - - - +
165J CYS* 5.2 3.3 - - - -
190K MET* 4.7 17.7 + - - +
193K CYS* 4.6 17.9 + - + +
130L GLN* 3.2 21.1 + - - +
131L LEU* 2.7 26.7 + - + +
133L ALA* 1.3 77.0 - - - +
135L CYS* 1.3 63.6 + - - +
136L GLN 3.4 3.6 + - - -
137L GLU* 4.4 11.1 + - - +
----------------------------------------------------------
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Residues in contact with CYS 135 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J LYS 5.4 0.9 - - - +
160J SER* 3.5 19.5 - - - +
161J CYS* 2.0 52.9 - - - -
164J SER* 4.1 12.2 + - - -
165J CYS* 4.0 3.4 - - - -
193K CYS* 3.7 16.4 - - - -
261K ASP* 4.5 5.7 + - - +
264K ARG* 4.9 1.2 + - - -
131L LEU* 4.1 8.3 - - - +
132L GLU* 2.9 13.8 + - - +
134L GLN* 1.3 78.6 - - - +
136L GLN* 1.3 68.8 + - - +
137L GLU 3.7 0.9 - - - -
----------------------------------------------------------
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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