Contacts of the helix formed by residues 120 - 145 (chain A) in PDB entry 3E5X
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 GLU 120 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE 3.5 12.4 + - - +
119A ASP* 1.3 73.6 - - - +
121A ASP* 1.3 62.5 + - - +
122A MET 3.1 1.2 + - - -
123A ILE* 3.2 37.4 + - + +
124A PHE* 3.6 8.1 - - + -
113B ARG* 2.7 36.4 + - - +
116B PHE* 5.6 1.5 - - + +
117B ARG* 2.8 54.4 + - - +
167C ARG* 2.8 25.3 + - + +
168C VAL* 5.4 0.2 - - - -
169C GLY 4.3 6.4 + - - +
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 5.7 2.0 + - - +
119A ASP* 3.1 12.6 + - - +
120A GLU* 1.3 77.2 - - - +
122A MET* 1.3 72.0 + - + +
123A ILE 3.2 0.2 - - - -
124A PHE* 3.2 16.6 + - - +
125A GLU* 3.3 18.4 + - + +
113B ARG* 2.9 34.7 + - - +
167C ARG* 3.4 13.8 + - - +
172C TYR* 2.4 36.0 + - - -
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Residues in contact with MET 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.3 11.9 - - - -
24A LYS* 3.6 36.1 - - + -
25A LEU* 4.2 17.7 - - + -
28A TYR* 3.6 28.3 - - + -
115A VAL* 3.9 22.9 - - + -
116A PHE* 3.9 6.7 - - + -
119A ASP* 3.2 30.8 + - - +
120A GLU 3.1 1.0 - - - -
121A ASP* 1.3 89.5 - - + +
123A ILE* 1.3 62.1 + - - +
125A GLU* 3.5 12.7 + - + +
126A ILE* 3.1 27.6 + - + +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 3.6 36.9 - - + +
120A GLU* 3.2 34.1 + - + +
122A MET* 1.3 78.6 - - - +
124A PHE* 1.3 60.1 + - + +
126A ILE* 3.3 4.3 + - - +
127A PHE* 3.0 59.4 + - + -
116B PHE* 3.8 26.0 - - + -
123B ILE* 3.5 32.8 - - + -
127B PHE* 4.2 1.1 - - + -
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 3.6 20.6 - - + -
121A ASP 3.2 7.0 + - - +
123A ILE* 1.3 75.4 - - + +
125A GLU* 1.3 60.9 + - - +
127A PHE* 3.4 21.3 + + - +
128A LYS* 3.0 35.7 + - - +
87B LEU* 4.1 3.6 - - + -
88B TYR* 3.4 23.9 - - - +
109B GLU* 3.6 21.8 - - + +
112B LEU* 4.0 8.3 - - + -
113B ARG* 3.6 55.6 - - + +
116B PHE* 3.5 36.6 - + - -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.3 24.6 - - - -
21A PRO 5.2 0.5 - - - +
22A ILE* 3.5 38.2 - - + +
24A LYS* 6.0 0.7 - - + -
121A ASP* 3.3 15.7 + - + +
122A MET* 3.8 19.5 - - + +
124A PHE* 1.3 74.3 - - - +
126A ILE* 1.3 58.7 + - - +
128A LYS* 2.7 36.3 + - - +
129A ASN* 3.0 27.7 + - - +
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.0 9.6 - - + -
25A LEU* 4.9 11.4 - - + -
53A MET* 3.7 31.9 - - + -
83A LEU* 3.8 19.7 - - + -
112A LEU* 4.4 8.7 - - + -
116A PHE* 3.7 27.6 - - + -
122A MET* 3.1 19.6 + - + +
123A ILE 3.7 7.0 - - - +
125A GLU* 1.3 73.8 - - - +
127A PHE* 1.3 59.3 + - - +
129A ASN* 3.2 4.2 + - - +
130A TYR* 2.9 36.5 + - + -
127B PHE* 3.5 21.3 - - + -
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.0 33.8 + - + -
124A PHE* 3.4 29.4 + + - +
126A ILE* 1.3 74.0 - - - +
128A LYS* 1.3 52.0 + - - +
130A TYR* 3.4 3.4 + - - +
131A LEU* 2.8 37.4 + - - +
53B MET* 3.6 19.5 - - + -
87B LEU* 4.1 2.9 - - + -
88B TYR* 4.4 7.4 - - + -
112B LEU* 4.6 0.9 - - + -
116B PHE* 3.6 28.0 - + - -
123B ILE* 4.3 3.1 - - - -
126B ILE* 3.6 26.5 - - + -
127B PHE* 3.5 28.5 - + - -
130B TYR* 3.8 26.9 - + + +
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Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP* 2.8 32.2 + - - +
11A CYS* 3.5 14.3 - - - -
20A PHE* 3.5 33.2 - - + -
124A PHE* 3.0 17.5 + - - +
125A GLU* 2.7 36.2 + - - +
126A ILE 3.3 0.2 - - - -
127A PHE* 1.3 74.7 - - - +
129A ASN* 1.3 56.6 + - - +
131A LEU* 4.5 0.2 - - - -
132A THR* 2.9 33.9 + - - -
88B TYR* 3.4 43.3 - - + -
109B GLU* 4.6 3.6 + - - -
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Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE 3.5 14.5 + - - -
20A PHE* 2.9 35.7 + - - +
22A ILE* 4.1 7.6 - - + +
83A LEU* 3.8 32.9 + - + +
85A GLY* 5.7 0.5 - - - -
125A GLU 3.0 13.5 + - - +
126A ILE* 3.4 9.4 - - - +
128A LYS* 1.3 74.1 - - - +
130A TYR* 1.3 65.9 + - - +
132A THR* 3.5 3.8 + - - -
133A LYS* 3.2 54.3 + - - +
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Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 3.5 13.7 - - + +
85A GLY* 2.7 26.3 + - - -
87A LEU* 4.5 2.6 - - - +
126A ILE* 2.9 40.1 + - + +
127A PHE 3.7 1.8 - - - +
129A ASN* 1.3 74.3 - - - +
131A LEU* 1.3 64.8 + - - +
133A LYS* 3.0 8.9 + - + +
134A VAL* 2.9 24.8 + - - +
501A 3C4 3.6 29.2 - - + -
127B PHE* 3.6 41.7 + + + +
130B TYR* 3.5 35.0 - + + -
131B LEU* 3.8 20.3 - - + +
134B VAL* 3.9 8.5 - - + +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A CYS* 4.1 6.3 - - + -
127A PHE 2.8 22.5 + - - +
128A LYS 3.9 3.8 - - - +
129A ASN 3.3 0.2 - - - -
130A TYR* 1.3 73.4 - - - +
132A THR* 1.3 55.7 + - - +
134A VAL* 3.3 1.6 + - - +
135A ALA* 2.9 29.1 + - - +
85B GLY 3.6 22.4 - - - +
86B LYS* 4.5 1.6 - - - -
87B LEU 4.1 1.6 - - - +
88B TYR* 3.5 51.8 - - + +
90B THR* 3.9 18.2 - - + -
130B TYR* 3.8 11.6 - - + +
504B 3C4 3.6 31.2 - - + -
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Residues in contact with THR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A CYS* 3.3 32.9 - - - +
12A GLY 3.9 6.5 - - - +
13A ALA* 3.9 16.4 + - + +
19A PHE* 3.8 23.1 - - + -
20A PHE* 3.5 25.0 - - + +
128A LYS 2.9 20.6 + - - -
129A ASN 3.8 5.4 - - - -
130A TYR 3.2 0.2 - - - -
131A LEU* 1.3 75.4 - - - +
133A LYS* 1.3 63.2 + - - +
135A ALA* 3.9 1.4 - - - +
136A TYR* 3.1 23.6 + - - +
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.8 36.6 - - + -
76A TYR* 4.1 7.9 - - + -
83A LEU 2.8 22.6 + - - -
85A GLY* 3.6 4.2 - - - +
129A ASN* 3.2 30.7 + - - +
130A TYR* 3.0 9.9 + - - +
132A THR* 1.3 73.8 - - - +
134A VAL* 1.3 65.1 + - - +
136A TYR* 3.4 5.0 + - - +
137A TYR* 3.1 35.4 + - + -
501A 3C4 2.6 52.2 + - + +
134B VAL* 3.8 16.8 - - + -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR 2.9 16.2 + - - +
131A LEU 3.9 5.2 - - - +
133A LYS* 1.3 71.2 - - - +
135A ALA* 1.3 56.3 + - - +
137A TYR* 4.4 1.3 - - - +
138A ALA* 2.9 38.5 + - + +
76B TYR* 6.1 0.4 - - + -
130B TYR* 3.6 16.2 - - + +
133B LYS* 3.6 30.1 - - + -
134B VAL* 3.5 28.7 - - + +
137B TYR* 4.4 15.2 - - + -
504B 3C4 3.5 35.2 - - + -
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A CYS 3.9 7.9 - - - +
12A GLY* 5.6 0.9 - - - -
13A ALA 6.3 0.2 - - - +
131A LEU 2.9 18.5 + - - +
132A THR 3.9 3.4 - - - +
134A VAL* 1.3 77.3 - - - +
136A TYR* 1.3 61.9 + - - +
138A ALA* 4.8 0.2 - - - -
139A ARG* 3.2 15.8 + - - +
90B THR* 3.7 19.1 - - + +
92B ASN* 3.0 33.3 + - - +
504B 3C4 3.5 18.1 - - - +
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 3.7 23.8 - - + +
14A ILE 3.6 23.3 - - - -
16A PRO* 3.5 28.1 - - + +
19A PHE* 3.8 26.5 - + + -
132A THR 3.1 17.3 + - - +
133A LYS 3.7 3.6 - - - +
134A VAL 3.3 0.2 - - - -
135A ALA* 1.3 75.5 - - - +
137A TYR* 1.3 80.0 + + - +
139A ARG* 3.7 6.5 - - - +
140A GLN* 3.1 58.2 + - + +
186A ILE* 3.4 27.5 - - - +
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.6 18.7 - + - -
74A LEU 5.8 0.2 - - - -
75A LEU* 2.8 40.0 + - + +
76A TYR* 3.4 18.8 - + - +
133A LYS* 3.1 32.6 + - + +
134A VAL* 5.2 0.4 - - - -
136A TYR* 1.3 94.0 - + - +
138A ALA* 1.3 59.5 + - - +
140A GLN* 3.3 15.2 + - - +
141A VAL* 2.9 33.6 + - - +
134B VAL* 4.4 11.0 - - + +
137B TYR* 3.5 22.0 - - + -
138B ALA* 3.7 35.0 - - + +
141B VAL* 3.7 6.1 - - + +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 2.9 23.6 + - + +
135A ALA* 4.5 2.2 - - - +
137A TYR* 1.3 74.5 - - - +
139A ARG* 1.3 64.3 + - - +
141A VAL* 3.4 3.5 + - - +
142A ALA* 3.2 16.5 + - - +
75B LEU* 3.6 36.9 - - + +
92B ASN* 5.8 0.2 - - - +
137B TYR* 3.7 31.1 - - + +
504B 3C4 5.2 1.6 - - + -
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Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 5.7 5.8 - - - -
135A ALA 3.2 20.4 + - - +
136A TYR* 3.7 6.7 - - - +
138A ALA* 1.3 79.0 - - - +
140A GLN* 1.3 53.8 + - - +
142A ALA* 3.3 3.0 + - - +
143A GLU* 2.8 42.0 + - + +
155A ARG* 3.3 17.2 - - - +
159A GLU* 3.5 16.0 + - - -
65B ILE* 3.9 23.7 - - + +
66B ILE 5.7 1.8 + - - -
67B PHE* 4.0 13.8 - - + +
68B GLU* 2.8 31.5 + - - -
91B GLY 4.1 12.3 + - - -
92B ASN* 2.8 38.8 + - - +
93B ASN 5.3 0.8 - - - +
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Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.1 50.9 + - + +
137A TYR* 3.5 10.0 - - - +
138A ALA 3.2 0.2 - - - -
139A ARG* 1.3 75.2 - - - +
141A VAL* 1.3 66.1 + - - +
143A GLU* 3.4 15.0 + - - +
144A MET* 2.9 40.1 + - + +
186A ILE* 2.6 31.5 + - - +
187A THR* 4.8 1.8 - - - +
141B VAL* 3.5 27.9 - - + +
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR 2.9 19.7 + - - +
138A ALA 3.7 6.5 - - - +
139A ARG 3.4 0.2 - - - -
140A GLN* 1.3 75.9 - - - +
142A ALA* 1.3 62.9 + - - +
144A MET* 3.2 5.9 + - - +
145A ASN* 3.1 36.1 + - - +
74B LEU 5.8 3.1 - - - +
75B LEU* 6.1 1.3 - - + -
136B TYR* 6.2 0.2 - - + -
137B TYR* 3.6 28.3 - - + +
140B GLN* 3.9 23.6 - - + +
141B VAL* 3.6 19.5 - - + +
144B MET* 3.7 15.6 - - - +
186B ILE 5.5 2.9 - - - +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ALA 3.2 8.8 + - - +
139A ARG 3.7 3.8 - - - +
141A VAL* 1.3 77.2 - - - +
143A GLU* 1.3 61.3 + - - +
145A ASN* 3.1 13.9 + - - +
146A THR* 2.7 26.6 + - - -
65B ILE* 3.4 33.0 - - + -
67B PHE* 3.6 9.2 - - + -
73B LYS* 3.6 17.4 - - + +
74B LEU 5.2 1.3 - - - +
75B LEU* 4.4 4.0 - - + -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 2.8 28.9 + - + +
140A GLN* 3.5 17.5 + - - +
142A ALA* 1.3 73.3 - - - +
144A MET* 1.3 57.5 + - - +
146A THR 3.2 0.5 + - - -
147A TYR* 2.9 49.3 + - + +
152A ARG* 3.7 32.1 - - - +
155A ARG* 3.1 37.0 + - - +
159A GLU* 5.1 3.3 - - - +
67B PHE* 3.5 15.2 - - + -
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Residues in contact with MET 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 2.9 31.8 + - + +
141A VAL 3.6 4.9 - - - +
143A GLU* 1.3 75.7 - - - +
145A ASN* 1.3 60.9 + - - +
146A THR 3.3 0.8 + - - -
147A TYR 3.9 9.2 + - - +
152A ARG* 3.8 37.1 + - - +
187A THR 4.9 2.7 - - - +
141B VAL* 3.7 27.1 - - - +
144B MET* 3.6 35.1 - - + +
145B ASN* 3.1 40.4 - - - +
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Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 3.1 29.5 + - - +
142A ALA* 3.1 11.0 + - - +
144A MET* 1.3 77.1 - - - +
146A THR* 1.3 56.6 + - - +
73B LYS* 3.2 30.7 + - + +
144B MET* 3.1 19.6 - - - +
152B ARG* 5.2 0.9 + - - -
185B GLU 4.5 9.1 + - - -
186B ILE 5.2 1.4 + - - -
187B THR 5.2 0.6 - - - -
188B GLY* 3.3 34.9 - - - +
190B HIS* 5.8 2.3 + - - -
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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
------------------------------------------------------------
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