Contacts of the helix formed by residues 113 - 135 (chain A) in PDB entry 3P1Q
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 ASP 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLY* 1.3 81.8 - - - +
114A ALA* 1.3 66.3 + - - +
115A GLU* 3.2 13.7 - - + +
116A SER* 3.0 12.8 + - - +
117A ARG* 2.9 21.2 + - - +
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY 3.8 2.2 + - - -
113A ASP* 1.3 73.5 - - - +
115A GLU* 1.3 67.0 + - - +
117A ARG* 4.4 2.2 - - - -
118A VAL* 2.8 40.0 + - + +
157A ILE* 4.0 16.4 - - + -
161A GLU* 3.4 36.1 - - + +
162A MET* 4.0 6.7 - - + -
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 5.5 1.3 - - - +
41A ARG* 4.1 16.6 + - - +
113A ASP* 3.2 9.9 - - + +
114A ALA* 1.3 82.4 + - - +
116A SER* 1.3 58.6 + - - +
119A PHE* 3.1 25.5 + - - +
161A GLU 4.7 4.5 - - - +
162A MET* 3.7 25.7 - - + +
166A HIS* 3.9 25.3 + - + +
168A ILE* 3.6 12.0 - - + +
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 3.6 36.0 - - - +
111A ALA* 3.4 20.9 - - - +
112A GLY 4.0 0.2 + - - -
113A ASP* 3.0 21.3 + - - +
115A GLU* 1.3 80.3 - - - +
117A ARG* 1.3 67.2 + - - +
119A PHE* 3.4 1.6 + - - +
120A TYR* 3.0 34.9 + - - -
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Residues in contact with ARG 117 (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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108A ILE* 2.8 48.3 + - + +
109A LYS* 4.7 4.4 + - - +
111A ALA* 2.9 29.0 + - - +
112A GLY* 5.2 4.3 - - - -
113A ASP 2.9 18.6 + - - +
114A ALA* 3.9 4.5 - - - +
116A SER* 1.3 77.5 + - - +
118A VAL* 1.3 59.5 + - - +
120A TYR* 3.3 2.7 + - - +
121A LEU* 2.9 35.1 + - + +
153A GLU* 3.7 26.9 + - - -
157A ILE* 3.6 24.3 - - + +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA* 2.8 25.4 + - + +
117A ARG* 1.3 69.6 - - - +
119A PHE* 1.3 61.1 + - - +
121A LEU* 3.9 1.6 - - - +
122A LYS* 2.8 28.8 + - - +
154A ALA* 3.8 13.4 - - + +
157A ILE* 3.5 34.5 - - + -
158A SER* 3.8 13.7 - - - +
162A MET* 3.8 13.9 - - + -
168A ILE* 3.7 19.5 - - + +
172A LEU* 3.8 28.7 - - + -
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 5.7 1.8 - - - -
41A ARG* 3.3 45.3 - - + -
42A ASN* 3.3 20.2 - - - -
44A LEU* 5.8 0.2 - - + -
45A SER* 3.2 23.3 - - - -
115A GLU 3.1 20.3 + - - +
116A SER* 3.5 6.3 - - - +
117A ARG 3.3 0.2 - - - -
118A VAL* 1.3 80.7 - - - +
120A TYR* 1.3 64.9 + + - +
122A LYS* 3.3 5.4 + - - +
123A MET* 2.9 55.0 + - - +
168A ILE* 4.0 27.5 - - + +
249A FSC 3.6 31.0 - - + +
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Residues in contact with TYR 120 (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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36A LEU* 3.5 23.9 + - - +
41A ARG* 3.2 38.5 - - + +
44A LEU* 4.5 9.0 - - + -
103A LEU* 3.7 23.7 - - + +
107A LEU* 3.7 43.0 - - + +
108A ILE* 3.6 19.8 - - + +
111A ALA* 3.6 21.3 - - + -
116A SER* 3.0 28.0 + - - +
117A ARG* 4.0 2.5 - - - +
119A PHE* 1.3 85.0 - + - +
121A LEU* 1.3 58.9 + - - +
123A MET* 3.3 7.7 + - - +
124A LYS* 2.8 27.5 + - - +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE* 4.1 28.3 - - + -
117A ARG* 2.9 28.9 + - + +
120A TYR* 1.3 75.6 - - - +
122A LYS* 1.3 60.3 + - - +
124A LYS* 3.2 15.3 + - + +
125A GLY* 2.9 24.6 + - - -
150A ALA* 3.6 20.3 - - - +
153A GLU* 3.6 42.4 - - + +
154A ALA* 3.6 22.4 - - + +
157A ILE* 3.7 17.3 - - + -
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Residues in contact with LYS 122 (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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49A LYS* 4.8 1.4 - - - +
118A VAL* 2.8 18.1 + - + +
119A PHE* 3.4 5.4 - - - +
121A LEU* 1.3 74.0 - - - +
123A MET* 1.4 61.5 + - - +
125A GLY* 3.1 3.1 + - - -
126A ASP* 2.7 50.6 + - - +
151A TYR* 3.7 4.1 - - + -
154A ALA* 4.1 1.4 - - - +
168A ILE* 4.6 3.6 - - + +
171A GLY 3.4 24.7 - - - -
172A LEU* 3.6 41.7 - - + +
175A ASN* 3.4 10.1 - - - +
249A FSC 2.7 41.3 + - + +
374P VAL* 2.8 24.3 + - - -
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Residues in contact with MET 123 (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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44A LEU* 4.2 26.0 - - + +
45A SER* 4.0 21.1 - - - -
48A TYR* 5.3 2.0 - - + -
99A VAL* 3.8 25.1 - - + -
103A LEU* 3.8 17.3 - - + -
119A PHE* 2.9 35.3 + - - +
120A TYR* 3.3 9.2 + - - +
122A LYS* 1.4 75.8 - - - +
124A LYS* 1.3 63.0 + - - +
126A ASP* 3.1 10.0 + - - +
127A TYR* 2.9 42.7 + - + +
249A FSC 3.4 21.5 - - - -
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Residues in contact with LYS 124 (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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100A LEU* 3.7 11.1 - - + +
103A LEU* 3.5 16.1 - - + +
104A ASP* 5.0 9.9 + - - +
108A ILE* 3.9 21.4 - - + +
120A TYR 2.8 13.7 + - - +
121A LEU* 3.2 15.9 + - + +
123A MET* 1.3 76.3 - - - +
125A GLY* 1.4 61.4 + - - +
127A TYR 3.4 0.2 + - - -
128A TYR* 3.0 57.6 + - + -
146A SER* 5.3 2.0 - - - -
150A ALA* 3.7 17.7 - - + -
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Residues in contact with GLY 125 (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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121A LEU 2.9 13.2 + - - -
122A LYS 3.1 3.8 + - - -
124A LYS* 1.4 74.8 - - - +
126A ASP* 1.3 57.1 + - - +
129A ARG* 2.8 29.5 + - - +
147A ALA* 3.6 19.0 - - - +
150A ALA* 3.6 4.3 - - - +
151A TYR* 3.3 26.6 + - - -
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Residues in contact with ASP 126 (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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49A LYS* 4.2 6.6 - - - +
122A LYS* 2.7 45.4 + - - +
123A MET* 3.1 10.5 + - - +
125A GLY* 1.3 73.6 - - - +
127A TYR* 1.3 63.3 + - + +
129A ARG* 3.1 9.1 + - - +
130A TYR* 2.8 50.8 + - + +
151A TYR* 2.5 31.9 + - - -
175A ASN* 2.8 22.9 + - - +
249A FSC 4.8 1.0 - - - +
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Residues in contact with TYR 127 (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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45A SER* 4.4 1.2 + - - -
48A TYR* 3.2 35.0 + - + +
49A LYS* 3.2 15.1 + - + +
52A VAL* 3.7 24.7 - - + -
95A VAL* 4.9 1.1 - - + -
96A CYS* 3.7 27.7 - - + +
99A VAL* 3.6 31.9 - - + -
100A LEU* 4.0 24.5 - - + -
123A MET* 2.9 44.5 + - + +
126A ASP* 1.3 77.6 - - + +
128A TYR* 1.3 65.5 + - - +
130A TYR* 3.4 19.1 + + - -
131A LEU* 3.1 26.3 + - - +
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Residues in contact with TYR 128 (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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100A LEU* 3.7 36.1 - - + +
124A LYS* 3.0 51.0 + - + +
127A TYR* 1.3 75.3 - - - +
129A ARG* 1.3 58.4 + - - +
131A LEU* 3.2 10.9 + - + -
132A ALA* 2.8 25.5 + - - +
143A ILE* 3.3 29.9 - - + +
146A SER* 3.6 36.5 + - - -
147A ALA* 3.6 22.2 - - + +
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Residues in contact with ARG 129 (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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56A ARG* 4.0 1.4 - - - +
125A GLY 2.8 14.0 + - - +
126A ASP* 3.2 14.8 + - - +
128A TYR* 1.3 76.7 - - - +
130A TYR* 1.3 74.0 + - + +
132A ALA* 3.0 9.3 + - - +
133A GLU* 2.9 30.1 + - - +
147A ALA* 3.8 6.7 - - + +
151A TYR* 2.9 20.5 + - + +
175A ASN* 3.3 33.0 + - - +
178A VAL* 3.8 8.9 - - - +
179A PHE* 3.9 31.2 - - + +
182A GLU* 4.8 0.4 + - - -
183A ILE* 3.9 18.3 - - + +
371P ARG* 3.6 11.3 - - - +
373P SEP 2.7 46.8 + - - -
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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
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49A LYS* 2.9 21.4 + - + -
52A VAL* 3.7 24.7 - - + -
56A ARG* 3.2 49.1 - - - -
92A LEU* 4.2 7.0 - - + +
96A CYS* 3.8 16.4 - - - -
126A ASP* 2.8 34.8 + - + +
127A TYR* 3.6 27.1 - + - -
128A TYR 3.3 0.2 - - - -
129A ARG* 1.3 90.8 + - - +
131A LEU* 1.3 60.9 + - - +
133A GLU* 3.3 22.7 + - - +
134A VAL* 3.7 10.7 + - - +
373P SEP 2.6 24.4 + - - -
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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
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92A LEU* 5.0 0.7 - - + -
93A GLN* 3.7 37.4 + - + +
96A CYS* 3.6 20.2 - - + -
97A ASP* 3.8 18.4 - - - +
100A LEU* 3.8 22.9 - - + -
127A TYR 3.1 15.2 + - - +
128A TYR* 3.2 20.4 + - + +
130A TYR* 1.3 75.0 - - - +
132A ALA* 1.3 63.9 + - - +
134A VAL* 3.3 9.1 + - - +
135A ALA* 3.0 22.9 + - - +
143A ILE* 3.7 19.4 - - + +
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Residues in contact with ALA 132 (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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128A TYR 2.8 15.9 + - - +
129A ARG* 3.0 11.8 + - - +
131A LEU* 1.3 73.9 - - - +
133A GLU* 1.3 64.3 + - - +
134A VAL 3.2 0.5 + - - -
135A ALA* 3.3 9.2 + - - -
140A LYS* 3.2 23.4 + - - +
143A ILE* 3.5 11.2 - - + +
144A ILE* 3.9 17.9 - - + -
183A ILE* 3.7 31.0 - - + +
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Residues in contact with GLU 133 (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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56A ARG* 2.8 51.9 + - - +
59A TRP* 3.7 18.8 - - + -
60A ARG* 4.9 4.0 + - - -
129A ARG* 2.9 24.9 + - - +
130A TYR* 3.5 14.3 - - - +
131A LEU 3.2 0.4 - - - -
132A ALA* 1.3 77.7 - - - +
134A VAL* 1.3 62.2 + - + +
135A ALA 5.0 0.7 - - - +
140A LYS* 5.5 0.5 + - - -
182A GLU* 3.7 16.5 - - - +
183A ILE* 3.9 17.5 - - + -
370P ARG* 5.0 3.2 + - - -
371P ARG* 3.8 1.6 + - - -
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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
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59A TRP* 3.4 45.3 - - + +
89A GLU* 3.9 28.8 - - + +
92A LEU* 4.2 15.9 - - + -
93A GLN* 3.9 31.3 + - + +
130A TYR 3.7 11.6 + - - +
131A LEU* 3.4 12.6 - - - +
133A GLU* 1.3 82.0 - - + +
135A ALA* 1.3 63.7 + - - +
136A THR* 3.6 12.7 + - - +
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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
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93A GLN* 5.6 3.1 - - - +
131A LEU 3.0 16.9 + - - +
132A ALA* 3.3 10.8 + - - +
133A GLU 5.0 0.9 - - - +
134A VAL* 1.3 79.3 - - - +
136A THR* 1.3 63.3 + - - +
137A GLY 3.8 0.4 - - - +
140A LYS* 3.1 41.7 + - + +
143A ILE* 3.9 24.0 - - + -
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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) + - + + + + + -
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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