Contacts of the helix formed by residues 125 - 149 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER 3.0 27.7 - - - +
121A TYR 3.8 5.1 - - - +
122A LYS 3.7 6.2 + - - +
123A ALA* 3.2 4.6 - - - +
124A PRO* 1.3 85.1 - - + +
126A GLU* 1.3 63.9 + - - +
127A VAL 3.5 1.1 - - - -
128A THR* 3.5 13.1 - - - +
129A TRP* 3.3 18.9 + - - +
219A THR* 3.9 14.1 + - - +
220A GLY 2.4 32.1 + - - -
221A ASN 3.1 9.5 + - - -
222A ASN* 3.2 33.0 + - - +
228A GLU* 2.7 40.6 + - - -
355A ARG* 4.6 9.3 - - - +
501A HEM 3.0 28.1 + - - +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR 3.9 13.5 - - - +
123A ALA* 2.9 36.9 - - - +
124A PRO 2.9 3.7 + - - -
125A ARG* 1.3 75.1 - - - +
127A VAL* 1.3 67.2 + - - +
129A TRP* 3.0 7.8 + - - +
130A ILE* 3.0 24.6 + - + +
347A PRO* 4.1 16.1 - - + +
348A TRP* 4.4 15.9 + - + -
18D TRP* 3.8 26.5 + - + -
22D ARG* 2.6 36.8 + - - +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO 4.5 0.2 + - - -
125A ARG 3.5 0.2 - - - -
126A GLU* 1.3 74.8 - - - +
128A THR* 1.3 69.4 + - - +
130A ILE* 3.0 12.9 + - + +
131A VAL* 2.9 34.6 + - + +
215A ALA* 4.7 7.0 - - + -
18D TRP* 4.5 9.9 - - + -
19D LEU* 4.5 19.5 - - + -
22D ARG* 3.8 34.9 - - + +
23D LEU* 4.2 25.8 - - + -
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 3.5 21.4 + - - +
126A GLU 3.2 0.2 - - - -
127A VAL* 1.3 79.5 - - - +
129A TRP* 1.3 65.6 + - - +
131A VAL* 3.0 4.9 + - - +
132A GLY* 2.8 22.0 + - - -
212A HIS* 3.6 30.0 + - + +
215A ALA* 3.9 21.7 + - - +
216A PHE* 3.9 17.6 + - + +
219A THR* 4.8 2.6 + - - +
501A HEM 3.6 33.6 + - + -
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Residues in contact with TRP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 4.0 27.8 - - + -
115A GLY* 4.5 7.0 - - - -
116A LEU* 3.8 21.8 - - + -
121A TYR* 3.4 31.2 - + + -
125A ARG 3.3 8.8 + - - +
126A GLU* 3.0 10.9 + - - +
128A THR* 1.3 79.7 - - - +
130A ILE* 1.3 68.1 + - + +
132A GLY 3.1 2.1 + - - -
133A MET* 2.9 26.8 + - + +
343A MET* 3.2 37.1 + - + -
344A ALA* 3.6 20.6 + - - +
346A VAL* 3.4 12.0 - - + +
347A PRO* 3.7 11.0 - - + -
501A HEM 3.1 56.8 - - + +
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Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLU* 3.0 23.0 + - + +
127A VAL* 3.0 11.4 + - + +
129A TRP* 1.3 78.7 - - + +
131A VAL* 1.3 67.6 + - + +
133A MET* 2.8 22.1 + - + +
134A LEU* 3.0 25.6 + - + +
344A ALA* 5.2 3.6 - - + +
348A TRP* 3.8 32.5 - - + -
18D TRP* 4.9 8.1 - - + -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 2.9 32.3 + - + +
128A THR* 3.4 7.9 - - - +
130A ILE* 1.3 72.9 - - + +
132A GLY* 1.3 66.3 + - - +
134A LEU* 2.7 29.6 + - + +
135A ILE* 2.9 15.0 + - + +
208A LEU* 4.0 20.4 - - + +
211A ILE* 4.2 18.2 - - + -
212A HIS* 3.9 33.9 - - + +
215A ALA* 5.7 0.9 - - + -
23D LEU* 5.6 0.4 - - + -
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR 2.8 17.5 + - - -
129A TRP 3.4 4.0 - - - -
131A VAL* 1.3 73.9 - - - +
133A MET* 1.3 61.0 + - - +
135A ILE* 3.2 7.3 + - - +
136A TYR 2.9 8.3 + - - -
212A HIS* 4.0 6.3 - - - -
501A HEM 2.9 51.5 - - - +
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Residues in contact with MET 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 6.1 1.1 - - - -
129A TRP* 2.9 37.2 + - + +
130A ILE* 2.8 19.2 + - + +
132A GLY* 1.3 69.2 - - - +
134A LEU* 1.3 66.2 + - + +
136A TYR* 3.0 15.4 + - + +
137A LEU* 2.9 22.9 + - - +
340A ILE* 3.8 30.7 - - + +
343A MET* 3.9 20.6 - - + -
344A ALA* 3.9 33.7 - - + +
501A HEM 3.1 17.7 - - + +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 3.0 24.6 + - + +
131A VAL* 2.7 26.6 + - + +
133A MET* 1.3 72.2 - - + +
135A ILE* 1.3 62.5 + - - +
137A LEU* 3.1 17.6 + - + +
138A ALA* 2.9 22.7 + - - +
208A LEU* 3.9 26.0 - - + +
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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 VAL* 2.9 11.4 + - + +
132A GLY* 3.2 18.2 - - - +
134A LEU* 1.3 76.3 - - - +
136A TYR* 1.3 53.9 + - - +
138A ALA* 3.0 7.7 + - - +
139A MET* 2.7 50.2 + - + +
205A ILE* 4.4 7.2 - - + +
208A LEU* 3.8 22.2 - - + +
209A VAL* 4.0 32.5 - - + +
212A HIS* 4.1 18.6 - - + -
501A HEM 3.3 40.4 - - + -
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 4.3 17.5 - + - -
108A VAL* 4.1 18.8 - - + -
109A TYR* 2.7 42.9 + + - -
112A ILE* 4.4 7.4 - - + -
132A GLY 2.9 6.4 + - - +
133A MET* 3.0 23.1 + - + +
135A ILE* 1.3 77.5 - - - +
137A LEU* 1.3 65.8 + - + +
139A MET* 3.5 5.6 - - - +
140A MET* 3.2 46.7 + - + +
301A PHE* 3.1 28.0 - + - -
340A ILE* 4.5 14.4 - - + -
343A MET* 4.4 11.7 - - + -
501A HEM 3.7 17.3 - - + -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 4.0 25.3 - - - +
133A MET 2.9 10.8 + - - +
134A LEU* 3.4 19.3 - - + +
136A TYR* 1.3 77.5 - - + +
138A ALA* 1.3 64.2 + - - +
140A MET* 3.1 20.5 + - + +
141A ALA* 2.8 24.0 + - + +
337A PHE* 5.6 4.9 - - + -
340A ILE* 5.0 15.9 - - + -
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Residues in contact with ALA 138 (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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134A LEU 2.9 13.0 + - - +
135A ILE* 3.3 10.3 - - - +
137A LEU* 1.3 75.0 - - - +
139A MET* 1.3 65.8 + - - +
141A ALA* 3.0 10.6 + - - +
142A THR* 2.8 27.7 + - - -
201A LEU* 4.0 12.7 - - + +
204A VAL* 5.9 2.7 - - + -
205A ILE* 3.9 23.8 - - + +
208A LEU* 5.2 5.6 - - + -
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Residues in contact with MET 139 (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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104A PHE* 3.4 61.7 - - + +
105A PHE* 4.1 26.5 - - + -
108A VAL* 4.5 13.7 - - + -
135A ILE* 2.7 43.9 + - + +
136A TYR* 3.5 12.1 - - - +
138A ALA* 1.3 73.3 - - - +
140A MET* 1.3 64.9 + - - +
142A THR* 3.0 3.4 + - - -
143A ALA* 2.8 23.7 + - - +
205A ILE* 3.9 18.8 - - + +
501A HEM 4.3 5.4 - - - -
502A HEM 5.1 4.4 - - + +
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Residues in contact with MET 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 4.0 29.4 - - - +
105A PHE* 3.9 21.1 - - + -
109A TYR* 5.0 0.4 - - - -
136A TYR* 3.2 52.9 + - + +
137A LEU* 3.1 18.2 + - + +
139A MET* 1.3 78.3 - - - +
141A ALA* 1.3 68.4 + - - +
142A THR 3.0 0.2 + - - -
143A ALA* 3.1 2.9 + - - +
144A PHE* 2.9 23.2 + - - +
298A PHE* 3.7 33.4 - - + -
301A PHE* 4.8 3.8 - - - -
340A ILE* 3.9 20.9 - - + -
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Residues in contact with ALA 141 (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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1A SMA 4.1 31.1 + - + +
137A LEU* 2.8 16.3 + - + +
138A ALA* 3.1 14.4 - - - +
140A MET* 1.3 73.6 - - - +
142A THR* 1.3 64.9 + - - +
144A PHE* 3.3 14.4 - - - +
145A MET* 3.0 18.1 - - + +
201A LEU* 3.6 14.8 - - + -
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Residues in contact with THR 142 (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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138A ALA 2.8 19.9 + - - -
139A MET* 3.0 10.3 + - - -
141A ALA* 1.3 68.3 - - - +
143A ALA* 1.3 55.0 + - - +
144A PHE 2.7 16.2 + - - -
145A MET* 2.7 28.3 + - - +
146A GLY 3.0 9.0 + - - -
198A HIS* 3.3 28.0 - - + +
201A LEU* 3.3 21.0 - - + +
202A PRO* 4.1 10.0 - - + +
205A ILE* 4.0 6.9 - - - +
502A HEM 3.8 25.8 - - + -
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 5.5 0.9 - - + -
105A PHE* 3.7 29.8 - - + -
139A MET 2.8 13.7 + - - +
140A MET* 3.5 5.2 - - - +
142A THR* 1.3 79.3 - - - +
144A PHE* 1.3 60.3 + - - +
146A GLY 3.7 1.1 + - - -
147A TYR* 3.2 22.5 + - - +
295A GLU* 5.2 0.3 - - - +
297A TYR* 4.0 16.3 + - + +
298A PHE* 4.6 1.3 - - + -
502A HEM 3.8 27.0 - - + +
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Residues in contact with PHE 144 (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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1A SMA 3.5 68.0 - - + -
140A MET 2.9 9.6 + - - +
141A ALA 3.3 11.0 - - - +
142A THR 2.7 4.9 + - - -
143A ALA* 1.3 73.0 - - - +
145A MET* 1.3 74.6 + - + +
147A TYR* 3.1 16.8 + - + +
148A VAL* 3.1 23.9 + - + +
158A GLY 4.2 1.8 - - - -
159A ALA* 3.8 16.4 - - - -
162A ILE* 3.6 38.1 - - + -
163A THR 5.0 1.3 - - - -
194A PHE* 3.6 25.1 - + - -
295A GLU* 5.2 1.6 - - - -
298A PHE* 4.5 8.9 - + + -
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Residues in contact with MET 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 4.2 22.0 - - + -
141A ALA* 3.0 33.4 - - + +
142A THR* 2.7 16.5 + - - +
144A PHE* 1.3 85.8 - - + +
146A GLY* 1.3 63.6 + - - +
148A VAL* 2.8 26.3 + - - +
149A LEU* 3.2 11.4 + - - +
194A PHE* 3.7 37.6 - - + +
197A LEU* 3.7 30.7 - - + -
198A HIS* 4.1 9.4 - - + +
201A LEU* 3.7 17.7 - - + -
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Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A THR 3.0 9.5 + - - -
143A ALA 4.0 0.4 - - - -
145A MET* 1.3 75.7 - - - +
147A TYR* 1.3 62.1 + - - +
149A LEU* 3.0 18.4 + - - +
150A PRO* 3.2 10.7 - - - +
198A HIS* 3.5 29.2 + - - -
502A HEM 3.4 22.0 - - - +
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Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 4.5 3.4 - - - -
143A ALA 3.2 13.8 + - - +
144A PHE* 3.1 10.6 + - + +
146A GLY* 1.3 74.2 - - - +
148A VAL* 1.3 59.0 + - + +
150A PRO* 3.3 6.6 - - - +
154A MET* 3.5 40.0 - - + +
155A SER* 2.7 24.3 + - - -
158A GLY* 6.2 0.4 - - - -
275A GLY* 6.4 0.9 - - - -
276A HIS* 3.6 24.9 + - - +
279A ASN* 3.5 22.9 + - + +
293A VAL 5.6 0.3 + - - -
295A GLU* 3.2 46.6 + - + +
297A TYR* 5.3 0.7 - - - -
502A HEM 3.7 34.0 - - + +
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 3.3 32.8 - - + +
145A MET* 2.8 11.5 + - - +
147A TYR* 1.3 78.7 - - + +
149A LEU* 1.3 50.8 + - - +
151A TRP* 2.8 54.9 + - + -
155A SER* 3.3 20.2 - - - +
159A ALA* 4.1 11.7 - - + +
190A THR* 6.5 0.2 - - + -
191A LEU* 4.3 8.3 - - + -
194A PHE* 3.7 30.5 - - + -
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 2.6 39.3 + - + +
76A ALA* 3.9 1.6 - - - +
145A MET 3.5 8.7 - - - +
146A GLY 3.0 7.2 + - - +
148A VAL* 1.3 71.2 - - - +
150A PRO* 1.3 60.0 - - + +
151A TRP* 2.6 24.3 + - - +
191A LEU* 3.8 17.3 - - + +
194A PHE* 4.5 4.0 - - + -
195A PHE* 4.0 34.5 - - + +
198A HIS* 3.5 37.5 - - + -
502A HEM 3.5 28.3 - - + -
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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