Contacts of the helix formed by residues 113 - 140 (chain A) in PDB entry 4IVR
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 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.7 4.0 - - - +
112A ILE* 1.3 78.5 - - - +
114A ALA* 1.3 65.4 + - - +
115A GLY* 3.4 8.9 + - - -
116A ASP* 2.4 31.3 + - - -
117A ALA* 3.1 23.2 + - - +
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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
----------------------------------------------------------
107A LEU* 3.8 14.5 - - + +
113A SER* 1.3 75.2 - - - +
115A GLY* 1.3 54.3 + - - +
117A ALA* 3.1 3.6 + - - +
118A ALA* 2.7 37.0 + - - +
180A GLY 4.1 17.5 - - - +
181A SER 5.2 0.2 - - - -
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER* 3.4 6.2 + - - -
114A ALA* 1.3 78.7 - - - +
116A ASP* 1.3 60.8 + - - +
118A ALA* 3.6 6.7 + - - +
119A VAL* 3.2 28.8 + - - +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 4.3 13.0 - - + -
113A SER* 2.4 41.0 + - - +
114A ALA 3.1 0.6 - - - -
115A GLY* 1.3 73.8 - - - +
117A ALA* 1.3 67.0 + - - +
118A ALA 3.1 0.7 + - - -
119A VAL* 3.3 19.2 + - - +
120A VAL* 3.3 17.6 + - + +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR* 4.0 16.8 - - + +
107A LEU* 4.1 25.1 - - + -
112A ILE* 3.8 15.1 - - + +
113A SER 3.1 14.3 + - - +
114A ALA 3.1 4.6 + - - +
116A ASP* 1.3 79.6 - - - +
118A ALA* 1.3 56.4 + - - +
120A VAL* 3.3 2.4 + - - +
121A MET* 3.0 34.5 + - + +
181A SER* 3.7 10.5 - - - -
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA 2.7 20.6 + - - +
115A GLY* 3.6 11.0 - - - +
117A ALA* 1.3 73.1 - - - +
119A VAL* 1.3 54.2 + - + +
121A MET* 3.3 2.3 + - - +
122A THR* 2.5 39.3 + - - +
181A SER 3.2 15.2 + - - +
182A MET* 4.0 6.7 - - - +
183A THR* 4.3 23.8 - - + +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 3.2 16.6 - - - +
116A ASP* 3.3 13.2 + - - +
118A ALA* 1.3 74.4 - - + +
120A VAL* 1.3 75.8 + - + +
122A THR* 4.2 0.2 - - - -
123A SER* 3.2 14.9 + - - -
99B ASN* 6.1 2.9 - - - +
119B VAL* 4.0 10.6 - - + +
120B VAL* 4.3 26.7 - - + +
123B SER* 2.7 38.6 + - - +
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 4.0 24.0 + - - +
100A ILE* 5.7 0.9 - - - -
103A THR* 3.5 35.9 - - + +
112A ILE* 6.2 0.2 - - + -
116A ASP* 3.3 13.8 + - + +
117A ALA 3.7 6.3 - - - +
118A ALA 3.3 0.4 - - - -
119A VAL* 1.3 85.5 - - + +
121A MET* 1.3 64.2 + - + +
123A SER* 3.8 4.2 - - - -
124A ALA* 3.1 23.8 + - + +
119B VAL* 4.8 16.8 - - + +
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 3.3 44.6 - - - +
103A THR* 4.4 7.6 - - + -
104A GLN* 3.6 39.3 - - + +
117A ALA 3.0 21.1 + - - +
118A ALA 3.8 0.2 - - - +
119A VAL 3.3 0.2 - - - -
120A VAL* 1.3 78.3 - - + +
122A THR* 1.3 63.5 + - - +
124A ALA* 4.1 2.4 - - - +
125A GLN* 3.0 34.8 + - - +
176A ARG* 3.7 21.3 - - + +
181A SER* 3.4 26.9 - - - +
182A MET* 3.5 12.6 - - + -
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Residues in contact with THR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA* 2.5 22.2 + - - +
119A VAL* 4.2 0.3 - - - -
121A MET* 1.3 78.0 - - - +
123A SER* 1.3 60.8 + - - +
126A ILE* 3.2 21.7 + - - +
182A MET* 3.2 16.5 - - + +
186A ALA* 4.4 19.6 - - + +
190A PHE* 3.5 28.3 - - + -
122B THR* 5.4 0.4 - - - -
123B SER* 3.3 30.0 - - - +
126B ILE* 4.6 12.3 - - + -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL 3.2 10.7 + - - -
120A VAL 3.8 3.8 - - - -
122A THR* 1.3 76.8 - - - +
124A ALA* 1.3 65.5 + - - +
125A GLN 3.2 0.2 + - - -
126A ILE* 3.4 5.9 + - - +
127A THR* 3.2 22.2 + - - -
119B VAL* 2.8 48.5 + - - -
122B THR* 3.2 24.0 - - - +
123B SER* 3.7 0.9 + - - -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR* 3.6 16.5 - - + +
99A ASN* 4.5 13.2 - - - +
100A ILE* 3.7 28.5 - - + -
120A VAL 3.1 15.6 + - - +
121A MET 4.1 2.2 - - - +
123A SER* 1.3 79.6 - - - +
125A GLN* 1.3 57.0 + - - +
127A THR* 3.3 7.9 - - - -
128A MET* 2.8 31.7 + - - +
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Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 4.5 13.9 - - + +
121A MET* 3.0 23.1 + - - +
124A ALA* 1.3 74.5 - - - +
126A ILE* 1.3 66.7 + - - +
127A THR 3.1 0.9 - - - -
128A MET* 3.1 11.8 + - - +
129A GLY* 3.1 11.8 + - - -
168A ALA* 4.5 3.7 - - - +
172A TYR* 3.4 13.1 + - - +
173A PRO* 3.4 27.5 - - - +
176A ARG* 3.6 16.7 - - - +
182A MET* 3.2 27.5 - - - +
190A PHE* 3.9 15.4 - - + -
501A N50 3.5 30.5 + - - +
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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
----------------------------------------------------------
122A THR 3.2 12.8 + - - +
123A SER 3.6 8.7 - - - +
125A GLN* 1.3 75.0 - - - +
127A THR* 1.3 64.7 + - - +
129A GLY* 3.3 7.4 + - - -
130A MET* 3.4 13.3 + - - +
169A LEU* 5.0 4.9 - - + -
190A PHE* 3.7 31.5 - - + -
193A LEU* 5.5 0.2 - - + -
122B THR* 4.7 8.7 - - + -
126B ILE* 4.2 15.0 - - + -
186B ALA* 4.9 4.0 - - + +
189B ALA* 3.6 23.9 - - + +
190B PHE* 3.9 24.2 - - + -
193B LEU* 3.9 28.6 - - + +
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 3.2 38.0 + - + +
88A TRP* 5.4 1.3 - - + -
92A GLY* 4.6 18.2 + - - -
93A ALA* 4.7 5.3 - - + +
96A THR* 4.0 23.1 - - + +
123A SER 3.2 9.7 + - - -
124A ALA* 3.3 11.4 - - - +
125A GLN 3.1 0.2 - - - -
126A ILE* 1.3 78.8 - - - +
128A MET* 1.3 66.7 + - - +
129A GLY 3.1 2.9 + - - -
130A MET* 3.4 9.1 + - - +
185B GLN* 5.4 2.1 - - - +
186B ALA* 5.2 11.4 + - - +
189B ALA* 5.0 2.0 - - - +
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Residues in contact with MET 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 2.9 56.7 + - + +
96A THR* 3.7 25.4 - - + -
97A ILE* 3.6 24.9 - - + -
100A ILE* 4.1 8.1 - - + -
124A ALA 2.8 30.3 + - - +
125A GLN* 3.1 10.7 + - - +
127A THR* 1.3 73.2 - - - +
129A GLY* 1.3 57.6 + - - +
131A PRO* 3.8 5.5 - - - +
132A TYR* 4.2 5.4 - - - -
168A ALA* 4.5 0.4 - - - -
501A N50 3.5 56.8 - - + +
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN 3.1 8.6 + - - -
126A ILE 3.3 3.8 + - - -
127A THR 3.1 1.0 - - - -
128A MET* 1.3 77.0 - - - +
130A MET* 1.3 64.2 + - - +
131A PRO* 3.4 3.4 - - - -
132A TYR* 3.1 20.8 + - - +
133A ALA* 3.2 13.2 + - - +
168A ALA* 3.5 25.4 - - - -
169A LEU* 6.0 5.3 - - - +
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Residues in contact with MET 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 3.7 24.7 - - - +
126A ILE 3.4 5.1 + - - +
127A THR 3.8 6.1 - - - +
129A GLY* 1.3 74.3 - - - +
131A PRO* 1.3 68.5 - - + +
133A ALA* 3.2 8.2 + - - +
134A VAL* 3.0 38.8 + - + +
188B LEU* 4.3 9.4 - - + +
189B ALA* 3.6 35.2 - - + +
192B ALA* 4.7 2.9 - - + -
307B VAL* 3.5 45.3 - - + +
308B PHE* 4.1 16.8 - - + -
311B ALA* 4.0 12.6 - - + -
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Residues in contact with PRO 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PRO* 4.0 22.7 - - + -
87A TYR* 3.7 35.4 - - + -
128A MET 3.8 11.2 - - - +
129A GLY 3.5 3.6 - - - -
130A MET* 1.3 93.0 - - + +
132A TYR* 1.3 61.3 + - + +
134A VAL* 3.3 10.0 - - + +
135A THR* 2.7 34.6 + - - -
368A PHE* 3.8 25.1 - - + -
372A MET* 4.3 4.5 - - - -
307B VAL* 4.3 1.8 - - + -
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Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 6.4 2.0 - - + -
82A PRO 5.6 0.7 - - - -
83A GLU* 5.4 0.3 - - - +
84A PRO* 4.0 19.8 - - + +
88A TRP* 3.2 27.6 - + - -
128A MET 4.2 12.8 - - - -
129A GLY* 3.1 19.2 + - - +
131A PRO* 1.3 79.9 - - + +
133A ALA* 1.3 58.0 - - - +
135A THR* 3.6 5.7 + - - -
136A ASP* 3.0 29.6 + - - +
162A ASP* 3.5 22.0 + - - -
163A ARG* 3.4 33.8 - - + +
164A HIS 4.4 8.5 - - - -
165A PRO* 3.9 29.4 - - + +
167A ALA* 4.7 1.8 - - + -
168A ALA* 4.2 9.0 - - + -
368A PHE* 5.8 3.4 - + - -
501A N50 4.2 16.8 - - + +
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY 3.2 9.0 + - - +
130A MET* 3.6 10.3 - - - +
131A PRO 3.2 0.8 - - - -
132A TYR* 1.3 77.3 - - - +
134A VAL* 1.3 66.1 + - - +
136A ASP* 3.5 6.4 + - - +
137A ALA* 3.1 22.5 + - - +
165A PRO* 5.0 4.7 - - + -
169A LEU* 5.6 4.5 - - + -
195A PRO* 5.6 4.5 - - + +
192B ALA* 4.1 15.5 - - + +
193B LEU* 3.8 30.5 - - + -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A MET* 3.0 32.8 + - + +
131A PRO* 3.3 17.7 - - + +
133A ALA* 1.3 75.4 - - - +
135A THR* 1.3 57.6 + - - +
137A ALA* 2.9 7.7 + - - +
138A VAL* 2.9 33.8 + - - +
368A PHE* 5.4 0.2 - - + -
192B ALA* 3.4 24.5 - - + -
307B VAL* 4.0 13.9 - - + +
310B TRP* 4.3 17.5 - - + -
311B ALA* 3.8 28.9 - - - +
314B VAL* 4.8 2.5 - - + -
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 4.6 12.0 - - + +
131A PRO 2.7 22.5 + - - -
132A TYR* 3.6 6.7 - - - -
134A VAL* 1.3 77.1 - - - +
136A ASP* 1.3 63.6 + - - +
138A VAL* 3.5 10.7 - - + +
139A LEU* 3.1 46.0 + - + +
161A PHE* 3.8 20.4 - - + -
368A PHE* 3.3 25.2 - - + -
310B TRP* 5.6 2.1 - - - -
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Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 4.7 10.3 + - + -
132A TYR 3.0 15.1 + - - +
133A ALA 3.8 4.9 - - - +
134A VAL 3.3 0.2 - - - -
135A THR* 1.3 81.5 - - - +
137A ALA* 1.3 58.1 + - - +
139A LEU* 3.9 4.9 - - - +
140A ALA* 3.0 30.8 + - - +
164A HIS* 5.3 4.7 + - - -
165A PRO* 4.2 15.5 - - + +
195A PRO* 3.3 33.6 - - + +
196A PRO* 4.4 6.8 - - - +
198A LEU* 3.8 20.6 - - - +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA 3.1 13.4 + - - +
134A VAL* 2.9 10.1 + - - +
136A ASP* 1.3 77.7 - - - +
138A VAL* 1.3 65.5 + - - +
139A LEU 3.4 0.2 + - - -
140A ALA* 3.7 4.9 + - - +
141A PRO* 3.5 16.6 - - - +
192B ALA 4.4 8.1 - - - +
314B VAL* 3.7 23.6 - - + -
318B ARG* 4.0 23.8 + - - +
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL 2.9 22.2 + - - +
135A THR* 3.5 12.3 - - + +
137A ALA* 1.3 76.3 - - - +
139A LEU* 1.3 72.9 + - + +
141A PRO* 3.5 7.5 - - - +
142A HIS* 3.5 17.8 + - - -
364A LEU* 5.5 6.5 - - + -
310B TRP* 3.9 52.9 - - + +
313B ASP* 4.6 9.6 - - + +
314B VAL* 4.3 6.5 - - + -
----------------------------------------------------------
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 5.2 3.1 - - - -
53A TYR* 5.7 0.7 - - - +
81A VAL* 5.8 1.3 - - + -
135A THR* 3.1 31.4 + - + +
136A ASP* 3.9 4.7 - - - +
138A VAL* 1.3 89.4 - - + +
140A ALA* 1.3 55.2 + - - +
141A PRO 3.3 0.7 - - - -
142A HIS* 2.7 38.9 + - + +
143A ILE* 3.6 17.9 - - + +
159A LEU* 3.9 15.0 - - + -
161A PHE* 3.8 29.4 - - + -
198A LEU* 5.5 2.7 - - + -
361A ILE* 4.6 23.8 - - + -
364A LEU* 4.7 16.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP* 3.0 21.4 + - - +
137A ALA* 3.9 6.5 - - - +
139A LEU* 1.3 75.3 - - - +
141A PRO* 1.4 69.7 - - + +
142A HIS 3.1 1.0 + - - -
143A ILE* 3.1 19.2 + - - +
198A LEU* 3.6 32.6 - - + +
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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