Contacts of the helix formed by residues 108 - 137 (chain A) in PDB entry 4HYJ
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 GLY 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PRO* 3.5 23.5 - - - +
101A LEU* 5.7 5.6 - - - -
102A GLY 3.7 22.8 + - - -
107A LEU* 1.3 77.0 - - - +
109A ARG* 1.3 63.0 + - - +
110A PRO* 3.5 2.2 - - - -
111A LEU* 3.6 8.8 + - - +
112A LEU* 3.3 17.3 + - - +
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Residues in contact with ARG 109 (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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106A ARG* 4.6 12.3 - - - +
107A LEU 4.0 0.2 - - - +
108A GLY* 1.3 76.4 - - - +
110A PRO* 1.3 70.5 - - + +
111A LEU 3.3 0.2 - - - -
112A LEU* 4.2 14.1 - - - -
113A THR* 3.2 32.9 + - - +
80B GLU* 3.3 33.0 + - - +
127B TYR* 4.7 0.2 - - - -
131B SER* 4.9 8.1 - - - +
134B ASN* 5.9 4.3 - - + +
135B ILE* 3.9 24.6 - - + +
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Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG 4.0 9.0 - - - +
107A LEU* 4.0 15.0 - - - +
108A GLY 3.6 3.1 - - - -
109A ARG* 1.3 93.4 - - + +
111A LEU* 1.3 61.9 + - - +
113A THR* 3.4 6.9 + - - +
114A LYS* 3.2 37.8 + - - +
306A LFA 5.4 3.2 - - + +
135B ILE* 3.7 23.3 - - + -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PRO* 4.1 20.4 - - + -
101A LEU* 3.8 22.4 - - + -
107A LEU 5.7 0.9 - - - +
108A GLY* 3.6 10.7 + - - +
110A PRO* 1.3 79.5 - - - +
112A LEU* 1.3 63.0 + - - +
114A LYS* 3.2 9.4 + - - +
115A LEU* 2.9 38.5 + - + +
160A LEU* 4.3 13.7 - - + -
164A ASN* 3.8 37.8 - - + +
165A VAL* 3.6 30.7 - - + -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 3.5 46.0 - - + +
98A PRO* 4.0 15.7 - - + -
108A GLY 3.3 14.7 + - - +
109A ARG* 3.7 16.8 - - - +
110A PRO 3.3 0.4 - - - -
111A LEU* 1.3 79.7 - - - +
113A THR* 1.3 64.0 + - - +
115A LEU* 3.1 7.9 + - + +
116A VAL* 3.0 43.5 + - + +
80B GLU* 3.9 18.6 - - + -
127B TYR* 3.7 20.2 - - - +
302B LFA 4.2 2.0 - - + -
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Residues in contact with THR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG 3.2 15.8 + - - -
110A PRO* 3.6 7.0 - - - -
111A LEU 3.3 0.2 - - - -
112A LEU* 1.3 78.9 - - - +
114A LYS* 1.3 61.6 + - - +
116A VAL* 3.5 1.2 + - - +
117A ILE* 3.1 45.2 + - + +
306A LFA 3.9 22.2 - - + -
127B TYR* 3.5 21.0 + - + -
128B ILE* 4.0 10.3 - - + -
131B SER* 3.4 28.7 + - - -
135B ILE* 5.5 0.3 - - - +
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Residues in contact with LYS 114 (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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110A PRO* 3.2 26.6 + - - +
111A LEU* 3.6 9.0 - - - +
113A THR* 1.3 76.3 - - - +
115A LEU* 1.3 64.2 + - - +
116A VAL 3.3 0.2 + - - -
117A ILE* 4.0 7.4 - - - +
118A ALA* 3.2 24.3 + - - +
156A TYR* 3.6 20.4 - - - +
160A LEU* 3.6 25.4 - - + -
164A ASN* 5.6 6.5 - - - +
306A LFA 3.5 36.5 - - + +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.9 40.9 - - + +
97A PHE* 4.6 0.4 - - + -
98A PRO* 4.2 9.9 - - + -
111A LEU* 2.9 38.2 + - + +
112A LEU* 3.1 9.2 + - + +
114A LYS* 1.3 77.8 - - - +
116A VAL* 1.3 57.9 + - + +
118A ALA* 3.5 4.9 + - - +
119A ASP* 3.0 28.4 + - - +
157A ILE* 4.1 25.2 - - + +
160A LEU* 3.6 28.7 - - + -
161A LEU* 4.2 17.7 - - + -
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO* 4.5 19.1 - - + +
94A LEU* 5.4 1.6 - - + -
95A VAL* 4.9 0.2 - - + -
112A LEU* 3.0 33.6 + - + +
113A THR 3.8 5.2 - - - +
115A LEU* 1.3 77.3 - - + +
117A ILE* 1.3 65.1 + - + +
119A ASP* 3.7 6.6 - - - +
120A VAL* 2.8 36.3 + - + +
127B TYR* 3.8 22.0 - - + -
302B LFA 3.7 45.5 - - + -
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Residues in contact with ILE 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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113A THR* 3.1 19.4 + - + +
114A LYS 4.0 1.8 - - - +
116A VAL* 1.3 80.6 - - + +
118A ALA* 1.3 66.3 + - - +
120A VAL* 3.2 7.3 + - - +
121A ILE* 3.0 39.7 + - + +
306A LFA 3.5 39.7 - - + -
311A LFA 5.6 1.8 - - + -
312A LFA 4.5 13.2 - - + -
124B VAL* 5.0 22.2 - - + -
127B TYR* 5.5 2.7 - - + -
128B ILE* 3.3 34.5 - - + -
302B LFA 6.1 0.2 - - + -
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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
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114A LYS 3.2 15.6 + - - +
115A LEU 3.6 4.3 - - - +
117A ILE* 1.3 79.5 - - - +
119A ASP* 1.3 62.5 + - - +
121A ILE* 3.1 3.7 + - - +
122A MET* 2.9 19.8 + - - +
153A ALA* 3.2 20.7 - - - +
156A TYR* 3.6 27.4 - - + -
157A ILE* 3.6 14.4 - - + -
306A LFA 4.2 12.7 - - + +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.9 0.5 - - - +
90A THR* 2.5 41.2 + - - -
91A PRO* 3.5 17.0 - - + +
94A LEU* 3.5 22.7 - - + +
115A LEU 3.0 18.7 + - - +
116A VAL* 3.7 7.6 - - + +
118A ALA* 1.3 76.7 - - - +
120A VAL* 1.3 58.5 + - + +
122A MET* 3.2 18.6 + - - +
123A ILE* 2.9 31.2 + - - +
157A ILE* 3.8 7.9 - - + +
191A TRP* 3.8 1.9 - - - -
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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
----------------------------------------------------------
87A LEU* 4.8 3.6 - - + -
91A PRO* 5.1 2.9 - - + -
116A VAL* 2.8 24.4 + - + +
117A ILE 3.7 4.0 - - - +
119A ASP* 1.3 82.5 - - - +
121A ILE* 1.3 62.6 + - - +
123A ILE* 4.6 3.6 - - - +
124A VAL* 3.0 31.4 + - + +
311A LFA 5.0 2.5 - - + -
87B LEU* 3.8 38.6 - - + -
120B VAL* 3.5 31.9 - - + -
124B VAL* 4.1 9.4 - - + -
302B LFA 4.6 9.9 - - + -
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.0 34.8 + - + +
118A ALA 3.5 5.8 - - - +
120A VAL* 1.3 75.7 - - + +
122A MET* 1.3 63.1 + - - +
124A VAL* 4.1 6.0 - - - +
125A GLY* 2.9 24.4 + - - -
149A ILE* 3.8 28.7 - - + +
150A GLY* 4.7 1.0 - - - -
153A ALA* 4.0 11.0 - - + -
306A LFA 4.2 22.2 - - + -
311A LFA 3.7 34.3 - - + +
312A LFA 4.2 22.2 - - + -
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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
----------------------------------------------------------
90A THR* 4.9 0.2 - - + -
118A ALA 2.9 13.1 + - - +
119A ASP* 3.2 30.0 + - - +
121A ILE* 1.3 76.9 - - - +
123A ILE* 1.3 77.9 + - + +
125A GLY* 3.9 0.3 - - - -
126A GLY* 2.9 26.3 + - - -
150A GLY* 3.5 27.3 - - - +
153A ALA* 3.7 3.1 - - + +
154A TRP* 3.6 35.7 - - - -
157A ILE* 4.4 4.3 - - + -
191A TRP* 4.0 8.1 - - + -
301A RET 3.7 48.1 - - + +
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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
----------------------------------------------------------
83A TYR* 3.3 30.0 - - + +
86A TRP* 4.0 27.1 - - + +
87A LEU* 3.9 36.1 - - + +
90A THR* 3.5 26.5 - - + +
119A ASP* 2.9 23.8 + - - +
120A VAL* 4.1 2.2 - - - +
122A MET* 1.3 91.8 - - + +
124A VAL* 1.3 60.6 + - + +
126A GLY 3.1 1.9 + - - -
127A TYR 2.9 22.7 + - - -
301A RET 4.3 9.0 - - + -
309B LFA 5.3 2.5 - - + -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.2 17.3 - - + -
120A VAL* 3.0 31.7 + - + +
121A ILE 4.1 0.4 - - - +
123A ILE* 1.3 73.4 - - - +
125A GLY* 1.3 69.6 + - - +
127A TYR* 3.0 7.0 + - + +
128A ILE* 2.9 33.5 + - + +
311A LFA 3.4 38.8 - - + -
116B VAL* 5.3 7.2 - - + -
117B ILE* 5.7 2.5 - - + -
120B VAL* 4.2 19.1 - - + -
309B LFA 4.7 11.9 - - + -
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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
----------------------------------------------------------
121A ILE 2.9 18.4 + - - -
122A MET 3.9 0.4 - - - -
124A VAL* 1.3 79.7 - - - +
126A GLY* 1.3 62.2 + - - +
128A ILE* 3.3 2.3 + - - +
129A GLY 2.9 18.7 + - - -
146A SER* 3.3 27.2 - - - -
150A GLY* 5.3 0.9 - - - -
311A LFA 3.9 20.2 - - - -
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Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 3.3 21.9 + - - -
122A MET 2.9 11.9 + - - -
123A ILE 3.1 4.2 + - - -
125A GLY* 1.3 74.8 - - - +
127A TYR* 1.3 57.3 + - - +
129A GLY* 3.2 1.0 + - - -
130A GLU* 2.8 28.9 + - - +
146A SER* 5.4 0.7 - - - -
198A TYR* 3.7 4.4 - - - -
301A RET 3.7 25.8 - - - +
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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
----------------------------------------------------------
79A THR* 4.4 7.9 - - + -
80A GLU* 2.7 39.7 + - + -
83A TYR* 3.3 40.8 - + + -
123A ILE 2.9 9.1 + - - +
124A VAL* 3.0 6.5 + - - +
126A GLY* 1.3 76.2 - - - +
128A ILE* 1.3 72.2 + - + +
130A GLU* 3.9 0.5 - - - +
131A SER* 2.8 48.1 + - - -
109B ARG* 2.8 26.2 + - - -
112B LEU* 4.6 7.4 - - + -
116B VAL* 5.3 4.9 - - + -
309B LFA 3.7 53.4 - - + +
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Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 2.9 23.8 + - + +
125A GLY 3.6 5.4 - - - +
127A TYR* 1.3 91.0 - - + +
129A GLY* 1.3 62.2 + - - +
131A SER* 3.9 4.6 - - - -
132A SER* 3.1 23.0 + - - -
142A LEU* 3.8 23.7 - - + +
146A SER* 3.8 12.6 - - - +
311A LFA 4.3 20.2 - - + -
109B ARG* 6.1 0.7 - - - +
112B LEU* 6.5 0.2 - - + -
113B THR* 3.8 37.5 - - + +
116B VAL* 5.0 9.2 - - + -
117B ILE* 4.4 13.2 - - + -
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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 GLY 2.9 10.7 + - - -
126A GLY 3.7 1.1 - - - -
128A ILE* 1.3 74.7 - - - +
130A GLU* 1.3 65.3 + - - +
132A SER* 3.2 5.1 + - - -
133A ILE* 3.0 26.3 + - - +
142A LEU 4.4 0.4 - - - -
143A GLY* 4.0 8.0 - - - -
146A SER* 3.6 15.0 + - - -
198A TYR* 3.0 21.3 - - - -
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 4.1 15.0 + - + +
82A ARG* 2.9 32.2 + - - -
83A TYR* 2.8 31.0 + - + +
86A TRP* 4.7 0.9 - - - -
126A GLY 2.8 13.3 + - - +
127A TYR 4.0 2.0 - - - +
129A GLY* 1.3 71.3 - - - -
131A SER* 1.3 58.2 + - - +
133A ILE* 3.2 10.1 + - + +
134A ASN* 2.8 40.8 + - - +
198A TYR* 3.4 19.6 + - + -
201A THR* 5.0 4.1 - - + +
213A ARG* 2.8 37.8 + - - -
301A RET 5.2 0.3 - - - +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 4.9 1.8 - - - +
80A GLU* 4.6 1.6 + - - -
127A TYR* 2.8 37.5 + - - -
128A ILE* 3.9 5.2 - - - -
130A GLU* 1.3 76.3 - - - +
132A SER* 1.3 64.6 + - - +
134A ASN* 3.4 8.4 + - - +
135A ILE* 3.0 33.4 + - - +
109B ARG* 3.0 40.4 + - - -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE 3.1 18.3 + - - -
129A GLY 3.6 4.9 - - - -
131A SER* 1.3 76.8 - - - +
133A ILE* 1.3 62.3 + - - +
135A ILE* 3.9 5.7 - - - +
136A ALA* 3.0 25.6 + - - +
140A THR* 2.5 34.4 + - - +
142A LEU* 3.8 24.9 - - - +
109B ARG* 6.5 0.7 - - - -
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY 3.0 21.2 + - - +
130A GLU* 3.5 8.5 - - - +
132A SER* 1.3 76.4 - - - +
134A ASN* 1.3 54.8 + - - +
136A ALA 3.3 0.2 + - - -
137A GLY* 2.7 31.5 + - - -
138A GLY* 3.1 34.3 + - - +
140A THR* 4.3 2.9 - - - +
143A GLY* 4.1 7.2 - - - -
198A TYR* 3.5 27.4 - - + +
201A THR* 4.2 31.9 - - + +
202A LEU* 3.5 36.3 - - + +
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Residues in contact with ASN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.1 36.4 + - - +
130A GLU* 2.8 31.1 + - - +
131A SER* 3.7 6.8 - - - +
133A ILE* 1.3 75.5 - - - +
135A ILE* 1.3 71.1 + - + +
137A GLY* 3.1 13.1 + - - -
201A THR* 5.2 1.6 - - - +
210A GLN* 4.3 16.6 + - - -
309B LFA 6.4 0.7 - - + -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.0 29.0 + - - +
132A SER* 3.9 5.8 - - - +
134A ASN* 1.3 82.9 - - + +
136A ALA* 1.3 64.4 + - + +
137A GLY 3.5 0.2 + - - -
105B GLY* 3.6 28.9 - - - +
106B ARG* 3.9 31.0 - - + +
109B ARG* 4.4 20.6 - - + +
309B LFA 4.2 24.2 - - + -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER 3.0 16.8 + - - +
133A ILE 3.9 1.8 - - - +
135A ILE* 1.3 80.1 - - + +
137A GLY* 1.3 63.3 + - - +
138A GLY* 3.4 5.9 + - - +
139A PHE 4.8 1.8 - - - +
140A THR* 3.5 22.7 - - + -
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Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 2.7 10.1 + - - -
134A ASN* 3.1 12.0 + - - -
135A ILE 3.5 0.2 + - - -
136A ALA* 1.3 78.7 - - - +
138A GLY* 1.3 55.8 + - - +
205A PRO* 4.1 16.1 - - - +
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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).
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