Contacts of the helix formed by residues 122 - 153 (chain B) in PDB entry 6P1A
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 122 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B HIS* 3.6 5.2 - - - -
120B LYS 3.6 3.1 + - - -
121B PRO* 1.3 77.0 - - - +
123B LEU* 1.3 64.7 + - - +
124B ALA* 3.7 6.2 + - - +
125B THR* 3.3 13.7 + - - -
126B CYS* 3.2 19.1 + - - -
7D G 2.4 68.0 + - - +
8D A 4.1 7.2 - - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B HIS* 4.3 21.5 - - + +
98B ALA* 3.7 36.3 - - + +
99B SER* 3.8 13.9 - - - +
102B HIS* 3.5 27.5 + - + +
122B SER* 1.3 71.0 - - - +
124B ALA* 1.3 60.2 + - - +
126B CYS* 3.2 2.0 + - + -
127B ARG* 2.9 37.8 + - + +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B SER* 3.2 9.6 + - - +
123B LEU* 1.3 77.7 - - - +
125B THR* 1.3 57.0 + - - +
127B ARG* 3.3 13.7 + - - +
128B ARG* 3.0 51.3 + - - +
7D G 4.0 3.4 - - + +
8D A 3.5 33.2 - - + +
9D G 5.5 3.1 - - - +
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 4.5 7.6 - - - +
110B MET* 5.3 3.6 - - - -
121B PRO* 4.7 4.5 - - + -
122B SER* 3.3 8.6 + - - -
123B LEU 3.3 0.6 - - - -
124B ALA* 1.3 78.1 - - - +
126B CYS* 1.3 58.6 + - - +
128B ARG* 3.3 13.7 + - + +
129B GLU* 2.9 50.3 + - + +
6D T 3.4 36.6 + - - +
7D G 2.7 26.8 + - - +
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Residues in contact with CYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 3.7 22.0 - - + +
101B TYR* 4.5 7.9 - - + -
102B HIS* 4.0 28.5 - - - -
105B ALA* 5.4 0.2 - - - -
108B ARG* 5.5 1.8 - - - -
121B PRO* 4.2 20.0 - - - -
122B SER 3.2 18.3 + - - +
123B LEU* 3.2 8.9 + - - +
125B THR* 1.3 77.9 - - - +
127B ARG* 1.3 61.8 + - - +
129B GLU* 3.3 13.6 + - - +
130B VAL* 2.9 29.0 + - + +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS 5.7 0.7 - - - -
95B HIS* 4.2 21.2 - - + +
98B ALA* 3.7 20.6 - - + -
123B LEU* 2.9 31.2 + - + +
124B ALA* 3.5 13.4 - - - +
126B CYS* 1.3 75.7 - - - +
128B ARG* 1.3 63.2 + - + +
130B VAL* 3.2 3.0 + - - +
131B ASP* 2.9 35.1 + - - +
9D G 3.3 19.2 + - - -
10D C 4.5 3.4 - - - +
11E T 3.6 24.9 - - - +
12E G 2.8 49.7 + - - -
13E C 4.3 3.7 - - - +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ALA* 3.0 36.9 + - - +
125B THR* 3.3 15.2 + - + +
127B ARG* 1.3 74.9 - - + +
129B GLU* 1.3 58.7 + - + +
131B ASP* 3.3 8.5 + - - +
132B GLU* 2.8 48.5 + - + +
6D T 3.9 35.0 + - - +
7D G 3.0 43.8 + - - -
8D A 3.7 12.3 - - - +
13E C 5.6 1.0 - - - +
14E T 4.0 6.7 + - - -
15E C 4.7 1.4 - - - +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS* 5.9 3.1 - - - -
108B ARG* 2.8 38.7 + - - -
125B THR* 2.9 33.1 + - + +
126B CYS* 3.7 10.8 - - - +
128B ARG* 1.3 76.1 - - + +
130B VAL* 1.3 56.9 - - + +
132B GLU* 3.2 14.1 + - - +
133B ILE* 2.8 45.3 + - + +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 4.6 11.9 - - + -
94B LYS* 4.1 33.0 - - + +
97B ILE* 3.9 28.7 - - + +
98B ALA* 4.0 13.9 - - - -
101B TYR* 5.3 4.7 - - + -
126B CYS* 2.9 20.7 + - + +
127B ARG* 3.6 6.1 - - - +
129B GLU* 1.3 74.9 - - + +
131B ASP* 1.3 65.9 + - - +
133B ILE* 3.3 8.1 + - + +
134B LEU* 3.0 34.1 + - + +
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 3.5 45.5 + - - +
127B ARG* 2.9 22.1 + - - +
128B ARG* 3.6 9.6 - - - +
130B VAL* 1.3 75.9 - - - +
132B GLU* 1.3 65.1 + - + +
134B LEU* 3.4 1.6 + - - +
135B ASN* 3.0 35.4 + - - +
201B EDO 4.9 0.2 - - - -
12E G 4.2 5.4 + - - -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 2.8 39.6 + - - +
129B GLU* 3.7 13.9 - - - +
131B ASP* 1.3 79.1 - - + +
133B ILE* 1.3 62.1 + - + +
135B ASN* 4.0 5.0 - - - +
136B ALA* 3.1 24.9 + - - +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP* 6.0 1.1 - - - +
79B LYS* 4.7 16.8 - - + -
80B ALA* 3.5 36.1 - - + +
83B ILE* 3.8 29.4 - - + -
129B GLU* 2.8 31.8 + - + +
130B VAL* 3.8 5.4 - - + +
132B GLU* 1.3 76.1 - - + +
134B LEU* 1.3 61.3 + - + +
136B ALA* 3.4 5.3 + - - +
137B SER* 2.9 35.0 + - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA 5.9 0.2 - - - +
83B ILE* 3.9 23.6 - - + -
84B LEU* 4.2 28.9 - - + -
87B TYR* 4.0 24.5 - - + -
88B TYR* 4.9 3.6 - - + -
94B LYS* 3.6 36.8 - - + -
97B ILE* 5.5 0.2 - - + -
130B VAL* 3.0 23.1 + - + +
131B ASP 4.0 0.9 - - - +
133B ILE* 1.3 75.9 - - + +
135B ASN* 1.3 66.1 + - - +
137B SER* 3.3 3.2 + - - +
138B LEU* 3.0 32.5 + - + +
201B EDO 3.7 20.0 - - - +
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Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN* 4.4 28.7 + - - +
13B HIS* 5.3 5.5 + - - -
131B ASP* 3.0 19.4 + - - +
132B GLU* 4.0 5.1 - - - +
134B LEU* 1.3 76.9 - - - +
136B ALA* 1.3 58.0 + - - +
138B LEU* 3.4 6.1 + - - +
139B PHE* 2.9 29.9 + - - +
201B EDO 2.6 31.7 + - - -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU 3.1 18.6 + - - +
133B ILE* 3.8 5.2 - - - +
135B ASN* 1.3 72.5 - - - +
137B SER* 1.3 67.5 + - - +
139B PHE* 3.3 7.7 + - - +
140B MET* 2.9 37.9 + - + +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B MET* 3.3 31.5 - - - +
80B ALA* 4.0 9.0 + - - +
84B LEU* 4.5 16.1 - - - +
133B ILE* 2.9 19.8 + - - +
134B LEU* 3.3 7.7 + - - +
136B ALA* 1.3 77.2 - - - +
138B LEU* 1.3 58.6 + - - +
140B MET* 3.3 13.7 + - - +
141B ILE* 2.9 35.1 + - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.7 6.9 - - + +
13B HIS* 3.4 36.6 - - + +
16B LEU* 3.2 31.8 - - + +
17B ASN* 4.9 3.6 - - + +
20B LEU* 3.5 23.8 - - + -
84B LEU* 4.0 16.6 - - + -
88B TYR* 3.4 21.1 - - + +
134B LEU* 3.0 23.8 + - + +
135B ASN* 3.9 4.7 - - - +
137B SER* 1.3 76.9 - - - +
139B PHE* 1.3 63.1 + - - +
141B ILE* 4.4 2.0 - - + +
142B TYR* 3.0 23.4 + - - +
201B EDO 4.3 4.7 - - - +
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Residues in contact with PHE 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN* 4.0 43.5 - - - +
8B LEU* 4.2 21.2 - - + +
135B ASN 2.9 18.1 + - - +
136B ALA* 3.7 6.7 - - - +
138B LEU* 1.3 75.6 - - - +
140B MET* 1.3 70.1 + - + +
142B TYR* 4.3 1.0 - - - +
143B PRO* 3.4 19.1 - - - +
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 3.9 21.7 - - + +
74B MET* 4.4 14.6 - - + -
76B ILE* 6.0 4.7 - - + -
77B ASP* 6.4 2.7 - - + -
136B ALA* 2.9 28.8 + - + +
137B SER* 3.8 14.8 - - - +
139B PHE* 1.3 85.4 - - + +
141B ILE* 1.3 63.1 + - - +
143B PRO* 3.7 10.3 - - - +
144B VAL* 3.8 14.4 - - - +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.9 21.5 - - + -
20B LEU* 4.9 11.9 - - + -
69B VAL* 4.5 8.7 - - + -
70B VAL* 4.2 17.3 - - + -
73B VAL* 3.7 26.0 - - + -
74B MET* 4.1 11.4 - - + -
84B LEU* 3.9 28.3 - - + -
137B SER 2.9 25.1 + - - +
138B LEU* 3.9 5.2 - - - +
140B MET* 1.3 77.1 - - - +
142B TYR* 1.3 67.9 + - - +
143B PRO 3.4 0.2 - - - -
144B VAL* 3.2 4.7 + - - +
145B LEU* 3.1 24.5 + - + -
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Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.8 23.6 - - + -
12B GLN* 3.4 57.9 + - + +
15B TRP* 3.3 39.6 - + - -
16B LEU* 3.8 15.0 - - + -
138B LEU 3.0 15.5 + - - +
141B ILE* 1.3 78.0 - - - +
143B PRO* 1.3 77.1 - - + +
145B LEU* 3.2 2.1 + - - +
146B ASP* 2.9 38.3 + - + +
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Residues in contact with PRO 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 5.6 0.7 - - + -
139B PHE* 3.4 16.2 - - + +
140B MET* 3.7 8.3 - - - +
141B ILE 3.5 2.7 - - - -
142B TYR* 1.3 105.0 - - + +
144B VAL* 1.3 65.6 + - + +
146B ASP* 3.3 5.1 + - + +
147B SER* 2.9 30.6 + - - +
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 3.5 24.0 - - + -
72B SER* 4.3 9.0 - - - +
73B VAL* 3.7 23.6 - - + -
140B MET 3.8 11.7 - - - +
141B ILE 3.2 6.0 + - - +
143B PRO* 1.3 79.5 - - + +
145B LEU* 1.3 58.3 + - - +
147B SER* 3.4 5.0 + - - -
148B ALA* 2.9 28.7 + - + +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 3.9 15.7 - - + -
16B LEU* 3.6 27.1 - - + -
19B TRP* 4.2 13.7 - - + -
20B LEU* 5.4 1.6 - - + -
65B LEU* 3.6 21.3 - - + -
66B ILE* 4.0 19.7 - - + -
69B VAL* 3.7 18.0 - - + +
141B ILE* 3.1 20.2 + - + +
142B TYR 3.8 2.9 - - - +
144B VAL* 1.3 73.9 - - - +
146B ASP* 1.3 66.5 + - - +
148B ALA 3.2 0.5 + - - -
149B PHE* 2.9 49.1 + - + +
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Residues in contact with ASP 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 4.2 18.7 - - + -
142B TYR* 2.9 35.1 + - + +
143B PRO* 3.6 7.6 - - + +
145B LEU* 1.3 76.4 - - - +
147B SER* 1.3 65.6 + - - +
149B PHE* 3.3 3.8 + - - +
150B LYS* 2.9 66.4 + - - +
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PRO* 2.9 18.1 + - - +
144B VAL* 3.8 5.4 - - - -
146B ASP* 1.3 79.6 + - - +
148B ALA* 1.3 58.5 + - - +
150B LYS* 3.4 7.2 + - - +
151B ASN* 2.9 47.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.6 27.3 - - + +
69B VAL* 3.7 13.7 - - + -
144B VAL* 2.9 18.1 + - + +
145B LEU 3.2 4.7 + - - +
147B SER* 1.3 76.8 - - - +
149B PHE* 1.3 62.9 + - - +
151B ASN* 3.8 4.5 - - - +
152B ARG* 3.0 26.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 3.8 17.9 - + + -
19B TRP* 3.6 52.3 - + - -
62B ASP* 4.5 9.0 - - + -
65B LEU* 4.0 19.1 - - + -
66B ILE* 4.3 7.9 - - + -
145B LEU* 2.9 44.7 + - + +
146B ASP* 3.8 4.5 - - - +
148B ALA* 1.3 77.0 - - - +
150B LYS* 1.3 64.2 + - + +
152B ARG* 3.6 41.2 + - - +
153B LYS* 4.1 5.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ASP* 2.9 51.7 + - - +
147B SER* 3.8 7.0 - - - +
149B PHE* 1.3 79.5 - - + +
151B ASN* 1.3 67.2 + - - +
152B ARG 3.5 0.3 + - - -
153B LYS* 3.6 15.9 + - - +
----------------------------------------------------------
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Residues in contact with ASN 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B SER* 2.9 33.2 + - - +
148B ALA* 4.1 4.0 - - - +
150B LYS* 1.3 79.3 - - - +
152B ARG* 1.3 65.7 + - - +
153B LYS 3.2 5.8 + - - -
----------------------------------------------------------
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASP* 4.1 13.4 - - - +
62B ASP* 2.5 43.9 + - - +
65B LEU* 3.7 18.3 - - + +
148B ALA 3.0 18.7 + - - +
149B PHE* 3.8 30.7 + - - +
150B LYS 3.3 0.6 - - - -
151B ASN* 1.3 78.2 - - - +
153B LYS* 1.3 63.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PHE 4.1 4.5 + - - +
150B LYS 3.6 12.4 + - - +
151B ASN 3.2 8.1 - - - -
152B ARG* 1.3 84.5 - - - +
----------------------------------------------------------
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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