Contacts of the helix formed by residues 108 - 137 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 4.3 6.1 - - - +
101B LEU* 6.6 0.2 - - - -
102B GLY 5.3 1.3 - - - -
103B LEU* 3.6 17.4 - - - +
106B ARG 3.1 2.6 + - - -
107B LEU* 1.3 71.4 - - - +
109B ARG* 1.3 64.0 + - - +
110B PRO* 3.5 5.8 - - - +
111B LEU* 3.8 11.2 + - - +
112B LEU* 3.4 16.8 + - - +
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 4.3 0.8 + - - -
127A TYR* 2.8 35.5 + - - -
128A ILE* 6.0 0.8 - - - +
131A SER* 3.0 31.4 + - - -
132A SER* 6.5 0.4 - - - -
135A ILE* 4.4 18.1 - - + +
103B LEU* 4.4 6.8 - - - +
105B GLY 3.6 20.9 - - - +
106B ARG* 3.2 13.5 + - + +
107B LEU 3.2 2.4 + - - -
108B GLY* 1.3 76.7 - - - +
110B PRO* 1.4 68.6 - - + +
112B LEU* 3.2 20.0 + - - +
113B THR* 2.9 41.8 + - - +
309B LFA 3.3 36.0 - - - +
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Residues in contact with PRO 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 3.5 14.6 - - + +
108B GLY* 3.8 4.3 - - - +
109B ARG* 1.4 90.9 - - + +
111B LEU* 1.3 66.0 + - - +
113B THR* 3.3 6.2 + - - -
114B LYS* 3.0 47.3 + - - +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 4.3 18.4 - - + -
101B LEU* 3.7 20.2 - - + -
108B GLY* 3.8 11.4 + - - +
109B ARG 3.3 0.4 - - - -
110B PRO* 1.3 79.9 - - - +
112B LEU* 1.3 65.3 + - - +
114B LYS* 3.2 8.5 + - + +
115B LEU* 2.9 45.3 + - + +
160B LEU* 4.4 18.4 - - + -
164B ASN* 3.7 31.6 - - - +
165B VAL* 3.7 30.3 - - + -
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 4.6 8.1 - - + +
128A ILE* 6.5 0.2 - - + -
95B VAL* 4.2 13.5 - - + -
98B PRO* 4.1 20.9 - - + -
103B LEU* 3.5 34.5 - - + -
108B GLY 3.4 9.6 + - - +
109B ARG* 3.2 35.1 + - - +
111B LEU* 1.3 79.8 - - - +
113B THR* 1.3 66.3 + - - +
115B LEU* 3.2 6.1 + - - +
116B VAL* 3.0 43.9 + - + +
309B LFA 4.2 19.5 - - + -
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 3.8 27.7 - - + +
142A LEU* 6.0 2.2 - - + -
109B ARG* 2.9 32.6 + - - +
110B PRO* 3.7 7.2 - - - +
111B LEU 3.3 0.2 - - - -
112B LEU* 1.3 79.1 - - - +
114B LYS* 1.3 65.3 + - + +
116B VAL* 3.3 4.6 + - - +
117B ILE* 3.0 45.0 + - + +
315B LFA 6.0 0.9 - - + -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO* 3.0 37.9 + - - +
111B LEU* 3.5 6.9 - - + +
113B THR* 1.3 76.2 - - + +
115B LEU* 1.3 65.8 + - - +
117B ILE* 4.1 0.5 - - - +
118B ALA* 3.0 27.2 + - - +
156B TYR* 3.5 23.6 - - - +
160B LEU* 3.8 27.3 - - + +
164B ASN* 5.5 7.5 - - - +
315B LFA 3.8 24.7 - - + +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 3.9 39.8 - - + +
95B VAL* 5.4 1.1 - - + +
97B PHE* 4.8 4.5 - - + -
98B PRO* 3.9 13.2 - - + -
111B LEU* 2.9 44.4 + - + +
112B LEU* 3.6 6.5 - - - +
114B LYS* 1.3 78.3 - - - +
116B VAL* 1.3 59.5 + - + +
118B ALA* 4.0 3.2 - - - +
119B ASP* 2.9 31.7 + - - +
157B ILE* 4.0 27.5 - - + +
160B LEU* 4.1 17.9 - - + -
161B LEU* 4.4 13.7 - - + -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 5.3 6.5 - - + -
127A TYR* 5.3 3.6 - - + -
128A ILE* 5.0 12.8 - - + -
91B PRO* 4.5 19.5 - - + +
94B LEU* 6.4 0.2 - - + -
95B VAL* 4.5 11.7 - - + -
112B LEU* 3.0 38.2 + - + +
113B THR* 3.7 5.8 - - - +
114B LYS 3.2 0.2 - - - -
115B LEU* 1.3 76.1 - - + +
117B ILE* 1.3 62.9 + - + +
119B ASP* 3.2 5.7 + - - +
120B VAL* 2.9 44.8 + - + +
309B LFA 4.7 26.0 - - + -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 5.7 2.0 - - + -
128A ILE* 4.4 16.6 - - + -
311A LFA 4.3 38.1 - - + -
113B THR* 3.0 35.0 + - + +
114B LYS 4.1 2.0 - - - +
116B VAL* 1.3 78.3 - - + +
118B ALA* 1.3 63.4 + - - +
120B VAL* 3.4 5.9 + - - +
121B ILE* 3.0 40.8 + - + +
315B LFA 3.9 26.0 - - + -
317B LFA 4.0 18.4 - - + -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS 3.0 19.4 + - - +
115B LEU 4.0 0.2 - - - +
117B ILE* 1.3 76.4 - - - +
119B ASP* 1.3 58.5 + - - +
121B ILE* 3.1 5.4 + - - -
122B MET* 2.7 26.0 + - - +
153B ALA* 3.4 14.9 - - - +
156B TYR* 3.6 23.1 - - + -
157B ILE* 3.6 25.1 - - + -
315B LFA 4.4 10.7 - - + +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU 5.0 0.2 - - - +
90B THR* 2.6 40.7 + - - -
91B PRO* 3.2 20.3 - - + +
94B LEU* 3.3 21.8 - - + +
115B LEU 2.9 20.4 + - - +
116B VAL* 3.6 4.9 - - - +
118B ALA* 1.3 76.8 - - - +
120B VAL* 1.3 60.0 + - - +
122B MET* 3.1 18.1 + - - +
123B ILE* 2.8 29.3 + - - +
157B ILE* 3.6 8.0 - - - +
191B TRP* 3.6 1.2 - - - -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 5.9 1.6 - - + -
120A VAL* 3.5 28.5 - - + -
124A VAL* 4.2 19.1 - - + -
311A LFA 3.9 23.1 - - + -
87B LEU* 4.8 13.2 - - + +
91B PRO* 5.1 9.2 - - + -
116B VAL* 2.9 29.3 + - + +
117B ILE* 3.8 6.1 - - - +
119B ASP* 1.3 79.2 - - - +
121B ILE* 1.3 59.3 + - - +
123B ILE* 3.1 5.8 + - - +
124B VAL* 2.8 32.9 + - + +
309B LFA 6.4 0.4 - - + -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LFA 3.8 21.3 - - + -
117B ILE* 3.0 26.7 + - + +
118B ALA 3.1 6.7 + - - +
120B VAL* 1.3 74.8 - - - +
122B MET* 1.3 64.6 + - - +
124B VAL* 3.8 7.6 - - + +
125B GLY* 2.9 23.4 + - - -
149B ILE* 4.3 21.3 - - + +
150B GLY* 4.7 1.2 - - - -
153B ALA* 4.0 13.5 - - + -
315B LFA 4.5 22.2 - - + -
317B LFA 3.6 31.9 - - + -
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Residues in contact with MET 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 4.6 0.7 - - - +
118B ALA 2.7 16.9 + - - +
119B ASP* 3.3 33.9 - - - +
121B ILE* 1.3 74.2 - - - +
123B ILE* 1.3 81.1 + - + +
125B GLY* 3.5 1.2 + - - -
126B GLY* 3.1 18.4 + - - -
150B GLY* 3.5 29.7 - - - +
153B ALA* 3.8 4.5 - - + +
154B TRP* 3.5 33.7 - - - +
157B ILE* 4.7 4.3 - - + -
191B TRP* 3.9 6.7 - - + -
301B RET 3.7 48.2 - - + +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 3.5 20.7 - - + -
86B TRP* 3.9 33.7 - - + +
87B LEU* 4.1 26.7 - - + +
90B THR* 3.6 18.6 - - - +
119B ASP* 2.8 24.4 + - - +
120B VAL* 3.1 6.3 + - - +
122B MET* 1.3 90.9 - - + +
124B VAL* 1.3 60.8 + - - +
126B GLY 3.2 1.2 + - - -
127B TYR* 3.0 22.7 + - - +
301B RET 4.2 11.7 - - + -
302B LFA 4.3 11.9 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 5.0 21.8 - - + -
120A VAL* 4.1 15.3 - - + -
311A LFA 3.9 22.0 - - + -
312A LFA 6.3 2.0 - - + -
87B LEU* 5.0 2.5 - - + -
120B VAL* 2.8 38.7 + - + +
121B ILE* 3.8 5.8 - - + +
123B ILE* 1.3 69.5 - - - +
125B GLY* 1.3 65.2 + - - +
127B TYR* 3.7 1.2 - - + +
128B ILE* 2.8 39.5 + - + +
302B LFA 3.7 25.8 - - + -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE 2.9 17.5 + - - -
122B MET 3.8 1.8 - - - -
124B VAL* 1.3 80.3 - - - +
126B GLY* 1.3 60.5 + - - +
128B ILE* 4.4 2.5 - - - -
129B GLY* 3.1 16.8 + - - -
146B SER* 3.3 38.0 + - - +
149B ILE* 5.7 4.0 - - - -
150B GLY* 4.9 2.2 - - - -
301B RET 4.7 0.2 - - - -
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Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 3.1 22.6 + - - -
122B MET 3.1 11.3 + - - -
123B ILE 3.2 3.3 + - - -
124B VAL 3.2 0.2 - - - -
125B GLY* 1.3 76.2 - - - +
127B TYR* 1.3 56.6 + - - +
129B GLY* 3.2 1.6 + - - -
130B GLU* 2.9 27.0 + - - +
147B TYR* 5.6 0.2 - - - -
198B TYR* 3.8 4.5 - - - -
301B RET 3.7 26.1 - - - +
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 4.7 1.0 - - - -
112A LEU* 3.7 14.6 - - - +
113A THR* 3.5 23.4 + - + -
116A VAL* 3.8 22.9 - - + -
117A ILE* 5.5 2.2 - - + -
79B THR* 4.4 8.3 - - + -
80B GLU* 2.9 44.5 + - + +
83B TYR* 3.3 39.8 - + + -
123B ILE 3.0 12.5 + - - +
124B VAL* 3.1 4.2 + - - +
126B GLY* 1.3 73.7 - - - +
128B ILE* 1.3 66.7 + - + +
130B GLU* 4.9 0.2 - - - -
131B SER* 2.7 51.1 + - - -
302B LFA 3.9 28.7 - - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A THR* 4.0 12.5 - - + +
117A ILE* 3.3 38.6 - - + -
306A LFA 4.5 9.9 - - + +
312A LFA 5.3 11.0 - - + -
124B VAL* 2.8 29.0 + - + +
125B GLY* 3.4 9.2 - - - +
127B TYR* 1.3 73.7 - - + +
129B GLY* 1.3 65.2 + - - +
131B SER* 3.6 4.4 - - - -
132B SER* 3.0 22.5 + - - -
142B LEU* 3.7 36.9 - - + +
146B SER* 3.8 9.0 - - - +
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY 3.1 8.0 + - - -
126B GLY 3.5 1.8 - - - -
127B TYR 3.2 0.4 - - - -
128B ILE* 1.3 83.6 - - - +
130B GLU* 1.3 62.5 + - - +
132B SER* 3.2 2.9 + - - -
133B ILE* 3.1 25.6 + - - +
143B GLY* 3.8 7.4 - - - -
146B SER* 3.3 14.4 - - - -
198B TYR* 3.1 22.7 - - - -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 3.9 20.5 + - + +
82B ARG* 2.8 33.9 + - - -
83B TYR* 2.7 32.0 + - + +
86B TRP* 4.6 1.0 - - - -
126B GLY 2.9 11.3 + - - +
127B TYR 4.4 1.1 - - - +
129B GLY* 1.3 72.3 - - - +
131B SER* 1.3 56.4 + - - +
133B ILE* 3.6 10.5 + - + +
134B ASN* 3.0 30.3 + - - +
198B TYR* 3.4 17.5 + - + -
201B THR* 5.4 2.1 - - + +
213B ARG* 2.9 34.8 + - - -
301B RET 5.1 0.3 - - - +
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 4.9 9.4 - - - +
113A THR* 3.4 19.6 + - - -
79B THR* 5.1 1.9 - - - +
80B GLU* 4.5 2.3 + - - -
127B TYR* 2.7 51.6 + - - -
128B ILE* 3.6 4.0 - - - -
130B GLU* 1.3 74.5 - - - +
132B SER* 1.3 59.9 + - - +
134B ASN* 3.3 5.1 + - - +
135B ILE* 2.9 40.1 + - - +
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE 3.0 13.7 + - - -
129B GLY 3.2 7.6 + - - -
131B SER* 1.3 76.5 - - - +
133B ILE* 1.3 63.9 + - - +
135B ILE* 3.4 10.1 + - - +
136B ALA* 3.1 23.9 + - - +
140B THR* 3.5 21.9 - - - +
142B LEU* 4.0 26.9 - - - -
143B GLY 4.3 0.4 - - - -
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY 3.1 17.1 + - - +
130B GLU* 3.7 10.5 - - + +
132B SER* 1.3 75.7 - - - +
134B ASN* 1.3 61.5 + - - +
136B ALA 3.1 2.1 + - - -
137B GLY* 2.9 26.0 + - - -
138B GLY* 3.3 33.8 + - - +
139B PHE* 5.2 0.2 - - - -
140B THR* 3.9 10.5 + - - +
143B GLY* 4.4 2.0 - - - -
198B TYR* 3.8 19.1 - - + +
201B THR* 5.2 19.7 - - + +
202B LEU* 3.6 36.6 - - + +
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Residues in contact with ASN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG* 5.1 1.4 - - - +
109A ARG* 5.9 5.4 - - + +
79B THR* 5.3 8.5 - - + +
130B GLU 3.0 18.9 + - - +
131B SER* 3.7 6.1 - - - +
132B SER 3.3 0.2 - - - -
133B ILE* 1.3 79.1 - - - +
135B ILE* 1.3 62.8 + - + +
136B ALA 3.3 0.5 + - - -
137B GLY* 3.4 11.2 + - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG* 3.6 37.2 - - + +
109A ARG* 3.9 24.2 - - + +
110A PRO* 3.7 39.3 - - + -
113A THR* 5.5 0.4 - - - +
131B SER* 2.9 27.3 + - - +
132B SER* 3.6 8.1 - - - +
134B ASN* 1.3 77.4 - - - +
136B ALA* 1.3 62.9 + - + +
137B GLY 3.7 0.3 + - - -
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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 SER 3.1 7.9 + - - +
133B ILE 3.8 2.2 - - - +
135B ILE* 1.3 79.9 - - + +
137B GLY* 1.3 61.8 + - - +
138B GLY 3.3 4.4 + - - +
139B PHE 4.8 1.8 - - - +
140B THR* 3.5 32.3 - - + -
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 2.9 8.1 + - - -
134B ASN* 3.4 10.0 + - - -
135B ILE 3.4 0.6 + - - -
136B ALA* 1.3 78.3 - - - +
138B GLY* 1.3 55.9 + - - +
205B PRO* 5.8 2.6 - - - +
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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