Contacts of the helix formed by residues 125 - 149 (chain J) in PDB entry 2QJK
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 ARG 125 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J GLY 4.6 0.6 + - - -
120J SER 3.0 26.8 - - - +
121J TYR 3.8 6.0 - - - +
122J LYS 3.7 5.1 + - - +
123J ALA 3.1 3.8 - - - -
124J PRO* 1.3 82.3 - - + +
126J GLU* 1.3 64.7 + - - +
127J VAL 3.5 1.3 - - - -
128J THR* 3.5 15.9 - - - +
129J TRP* 3.3 18.9 + - - +
219J THR* 4.2 12.7 + - - +
220J GLY 3.8 6.7 + - - -
221J ASN 3.3 9.9 + - - -
222J ASN* 2.9 49.8 + - - +
223J ASN* 5.3 0.2 - - - +
228J GLU* 3.2 25.3 + - - -
355J ARG* 3.4 30.5 - - - +
501J HEM 3.0 30.0 + - - +
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Residues in contact with GLU 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G TRP* 3.7 26.8 + - + -
22G ARG* 2.6 35.8 + - - +
121J TYR 3.9 14.1 - - - +
123J ALA* 2.9 37.1 - - - +
124J PRO 2.9 3.3 + - - -
125J ARG* 1.3 73.2 - - - +
127J VAL* 1.3 65.7 + - - +
129J TRP* 3.0 7.9 + - - +
130J ILE* 2.9 26.0 + - + +
347J PRO* 4.1 16.3 - - + +
348J TRP* 4.4 17.1 + - + -
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Residues in contact with VAL 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G TRP* 4.4 10.5 - - + -
19G LEU* 4.4 19.3 - - + -
22G ARG* 4.0 31.2 - - + -
23G LEU* 4.2 26.7 - - + -
124J PRO 4.5 0.6 + - - -
125J ARG 3.5 0.2 - - - -
126J GLU* 1.3 75.9 - - - +
128J THR* 1.3 69.6 + - - +
130J ILE* 3.1 13.2 + - + +
131J VAL* 2.9 35.3 + - + +
215J ALA* 4.7 5.8 - - + -
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Residues in contact with THR 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125J ARG* 3.5 22.0 + - - +
127J VAL* 1.3 82.8 - - - +
129J TRP* 1.3 64.2 + - - +
131J VAL* 3.1 4.3 + - - +
132J GLY* 2.8 19.2 + - - -
212J HIS* 3.6 30.6 + - + +
215J ALA* 3.9 22.6 + - - +
216J PHE* 3.9 17.6 + - + +
219J THR* 4.8 3.3 + - - +
501J HEM 3.8 31.8 + - + -
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Residues in contact with TRP 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ILE* 4.3 19.5 - - + -
115J GLY* 4.6 5.4 - - - -
116J LEU* 3.8 25.8 - - + -
121J TYR* 3.4 30.7 - + + -
125J ARG 3.3 9.5 + - - +
126J GLU* 3.0 10.2 + - - +
128J THR* 1.3 78.7 - - - +
130J ILE* 1.3 67.5 + - + +
132J GLY 3.2 2.1 + - - +
133J MET* 3.0 30.6 + - + +
343J MET* 3.2 37.4 + - + -
344J ALA* 3.6 21.3 + - - +
346J VAL* 3.4 11.8 - - + +
347J PRO* 3.7 11.4 - - + -
501J HEM 3.3 58.0 - - + +
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Residues in contact with ILE 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G TRP* 5.0 7.0 - - + -
126J GLU* 2.9 24.9 + - + +
127J VAL* 3.1 11.2 + - + +
129J TRP* 1.3 76.8 - - + +
131J VAL* 1.3 67.1 + - + +
133J MET* 2.9 20.1 + - + +
134J LEU* 3.0 25.3 + - + +
344J ALA* 5.2 2.9 - - + +
348J TRP* 3.8 32.8 - - + -
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Residues in contact with VAL 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 5.8 0.2 - - + -
127J VAL* 2.9 33.4 + - + +
128J THR* 3.5 7.6 - - - +
130J ILE* 1.3 72.7 - - + +
132J GLY* 1.3 65.6 + - - +
134J LEU* 2.8 29.7 + - + +
135J ILE* 2.9 16.4 + - + +
208J LEU* 4.0 18.4 - - + +
211J ILE* 4.2 19.3 - - + -
212J HIS* 3.9 33.9 - - + +
215J ALA* 5.7 1.1 - - + -
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Residues in contact with GLY 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J THR 2.8 13.4 + - - -
129J TRP 3.2 0.9 + - - -
131J VAL* 1.3 77.0 - - - +
133J MET* 1.3 56.8 + - - +
135J ILE* 3.1 7.4 + - - +
136J TYR 2.9 13.7 + - - -
212J HIS* 4.0 6.4 + - - -
501J HEM 2.8 53.6 - - - +
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Residues in contact with MET 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ILE* 5.3 1.3 - - - -
129J TRP* 3.0 38.2 + - + +
130J ILE* 2.9 12.6 + - + +
132J GLY* 1.3 71.2 - - - +
134J LEU* 1.3 67.8 + - + +
136J TYR* 3.0 15.3 + - + +
137J LEU* 2.9 28.2 + - + +
340J ILE* 3.8 40.4 - - + +
343J MET* 3.9 18.2 - - + -
344J ALA* 3.9 24.0 - - + +
501J HEM 3.0 18.3 - - + +
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Residues in contact with LEU 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J ILE* 3.0 19.6 + - + +
131J VAL* 2.8 30.6 + - + +
133J MET* 1.3 70.9 - - + +
135J ILE* 1.3 64.9 + - - +
137J LEU* 3.1 23.2 + - + +
138J ALA* 2.9 22.0 + - - +
208J LEU* 3.9 24.9 - - + -
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Residues in contact with ILE 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J VAL* 2.9 12.3 + - + +
132J GLY* 3.1 18.4 - - - +
134J LEU* 1.3 76.9 - - - +
136J TYR* 1.3 54.8 + - - +
138J ALA* 3.0 7.7 + - - +
139J MET* 2.7 50.9 + - + +
205J ILE* 4.3 6.5 - - + +
208J LEU* 3.8 20.9 - - + -
209J VAL* 4.0 24.0 - - + +
212J HIS* 4.1 18.4 - - + -
501J HEM 3.2 48.0 - - + -
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Residues in contact with TYR 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J PHE* 4.3 17.0 - + - -
108J VAL* 4.5 13.7 - - + -
109J TYR* 2.7 44.7 + + - -
112J ILE* 4.4 13.7 - - + -
132J GLY 2.9 6.8 + - - +
133J MET* 3.0 30.9 + - + +
135J ILE* 1.3 76.5 - - - +
137J LEU* 1.3 66.0 + - + +
139J MET* 3.5 6.3 - - - +
140J MET* 3.2 48.0 + - + +
301J PHE* 3.1 28.1 - + - -
340J ILE* 4.6 6.3 - - + -
343J MET* 4.4 11.0 - - + -
501J HEM 3.6 16.2 - - + -
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J MET* 2.9 13.4 + - + +
134J LEU* 3.2 29.2 - - + +
136J TYR* 1.3 76.6 - - + +
138J ALA* 1.3 64.7 + - - +
140J MET* 3.1 17.8 + - + +
141J ALA* 2.9 22.9 + - - +
337J PHE* 5.7 7.2 - - + -
340J ILE* 5.7 11.9 - - + -
503J SMA 3.9 24.7 - - - +
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Residues in contact with ALA 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J LEU 2.9 9.0 + - - +
135J ILE* 3.3 10.3 - - - +
137J LEU* 1.3 78.8 - - - +
139J MET* 1.3 65.4 + - - +
141J ALA* 3.1 9.1 + - - +
142J THR* 2.8 28.7 + - - -
201J LEU* 3.9 13.5 - - + +
204J VAL* 5.9 2.9 - - + -
205J ILE* 3.9 21.1 - - + +
208J LEU* 5.2 7.2 - - + -
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Residues in contact with MET 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J PHE* 3.5 52.5 - - + +
105J PHE* 4.0 21.3 - - + -
108J VAL* 3.9 34.8 - - + -
135J ILE* 2.7 44.2 + - + +
136J TYR* 3.5 9.0 - - - +
138J ALA* 1.3 73.5 - - - +
140J MET* 1.3 55.2 + - - +
142J THR* 3.0 3.4 + - - -
143J ALA* 2.8 34.0 + - - +
205J ILE* 3.8 18.6 - - + +
501J HEM 4.4 1.1 - - - -
502J HEM 4.9 3.7 - - + +
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Residues in contact with MET 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J PHE* 3.9 20.9 - - + -
109J TYR* 5.0 0.2 - - - -
136J TYR* 3.2 53.8 + - + +
137J LEU* 3.1 10.8 + - + +
139J MET* 1.3 75.7 - - - +
141J ALA* 1.3 72.7 + - - +
142J THR 3.0 0.3 + - - -
143J ALA* 3.5 2.4 - - - +
144J PHE* 2.9 22.0 + - - +
298J PHE* 3.7 33.4 - - + -
301J PHE* 4.8 4.3 - - - -
340J ILE* 3.9 10.5 - - + -
503J SMA 3.7 45.1 - - - +
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Residues in contact with ALA 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J LEU 2.9 16.0 + - - +
138J ALA* 3.3 11.0 - - - +
140J MET* 1.3 75.2 - - - +
142J THR* 1.3 67.0 + - - +
144J PHE* 3.1 14.9 + - - +
145J MET* 3.1 15.9 + - + +
201J LEU* 3.7 14.4 - - + -
503J SMA 4.1 33.0 + - + -
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Residues in contact with THR 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J ALA 2.8 20.9 + - - -
139J MET 3.0 9.4 - - - -
141J ALA* 1.3 70.4 - - - +
143J ALA* 1.3 54.9 + - - +
144J PHE 2.7 12.8 + - - -
145J MET* 2.7 29.4 + - - +
146J GLY 3.0 8.8 + - - -
198J HIS* 3.4 28.6 + - + +
201J LEU* 3.3 21.8 - - + +
202J PRO* 4.0 9.0 - - + -
205J ILE* 3.9 7.3 - - - +
502J HEM 3.4 28.0 - - + -
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Residues in contact with ALA 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J ALA* 5.5 0.2 - - + -
105J PHE* 3.7 28.3 - - + -
139J MET 2.8 17.8 + - - +
140J MET* 3.5 4.7 - - - +
142J THR* 1.3 73.9 - - - +
144J PHE* 1.3 60.0 + - - +
146J GLY 3.9 1.3 - - - -
147J TYR* 3.2 21.7 + - - +
295J GLU* 4.8 0.5 - - - +
297J TYR* 3.9 16.2 + - + +
298J PHE* 4.7 1.8 - - + -
502J HEM 3.7 30.2 - - + +
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Residues in contact with PHE 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J MET 2.9 9.2 + - - +
141J ALA 3.2 7.6 - - - +
142J THR 2.7 4.8 + - - -
143J ALA* 1.3 72.1 - - - +
145J MET* 1.3 72.4 + - + +
147J TYR* 3.1 16.2 + - + +
148J VAL* 3.2 16.6 + - + +
158J GLY 4.2 1.3 - - - -
159J ALA* 3.8 24.5 - - - -
162J ILE* 3.5 45.5 - - + -
163J THR* 5.0 1.1 - - + -
194J PHE* 3.6 32.8 - + - -
295J GLU* 5.1 2.2 - - - -
298J PHE* 4.5 9.1 - - + -
503J SMA 3.8 59.5 - - + -
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Residues in contact with MET 145 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J ALA 3.1 29.4 + - - +
142J THR* 2.7 18.1 + - - +
144J PHE* 1.3 85.6 - - + +
146J GLY* 1.3 63.3 + - - +
148J VAL* 2.9 25.4 + - - +
149J LEU* 3.2 12.2 + - - +
194J PHE* 3.7 37.6 - - + +
197J LEU* 3.7 34.3 - - + -
198J HIS* 4.2 9.2 - - + +
201J LEU* 3.7 17.3 - - + -
503J SMA 3.6 20.0 - - + -
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Residues in contact with GLY 146 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J THR 3.0 10.1 + - - -
143J ALA 4.1 0.2 - - - -
145J MET* 1.3 76.8 - - - +
147J TYR* 1.3 63.5 + - - +
148J VAL 2.9 1.6 + - - -
149J LEU* 3.0 16.0 + - - +
150J PRO* 3.2 10.6 - - - +
198J HIS* 3.5 29.5 + - - -
502J HEM 3.4 23.5 - - - +
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Residues in contact with TYR 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J ALA 3.2 13.8 + - - +
144J PHE* 3.1 10.6 + + + +
146J GLY* 1.3 75.0 - - - +
148J VAL* 1.3 52.9 + - + +
150J PRO* 3.4 5.8 - - - +
154J MET* 3.4 40.6 - - + +
155J SER* 2.7 29.4 + - - -
158J GLY* 6.2 0.4 - - - -
275J GLY* 6.4 0.7 - - - -
276J HIS* 3.6 25.4 + - - +
279J ASN* 3.5 23.8 + - + +
293J VAL 5.6 0.4 + - - -
295J GLU* 3.2 46.8 - - + +
297J TYR* 5.1 0.2 - - - +
502J HEM 3.7 33.2 - - + -
503J SMA 4.5 4.3 - - - -
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Residues in contact with VAL 148 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J PHE* 3.2 33.6 + - + +
145J MET 2.9 9.8 + - - +
147J TYR* 1.3 77.7 - - - +
149J LEU* 1.3 53.2 + - - +
151J TRP* 2.8 54.8 + - + -
155J SER* 3.3 20.6 - - - +
159J ALA* 4.1 11.7 - - + -
191J LEU* 4.3 8.5 - - + -
194J PHE* 3.7 31.6 - - + -
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Residues in contact with LEU 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J TYR* 2.7 38.6 + - + +
76J ALA* 3.9 1.7 - - - +
145J MET 3.4 8.5 - - - +
146J GLY 3.0 7.2 + - - +
148J VAL* 1.3 71.7 - - - +
150J PRO* 1.3 61.3 - - + +
151J TRP* 2.6 24.5 + - - +
191J LEU* 3.8 18.0 - - + +
194J PHE* 4.6 2.9 - - + -
195J PHE* 4.0 31.0 - - + +
198J HIS* 3.5 29.2 - - + -
502J HEM 3.5 37.5 - - + -
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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