Contacts of the helix formed by residues 119 - 142 (chain D) in PDB entry 4GCK
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 ASP 119 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C SER 4.9 2.4 - - - +
29C SER* 3.2 36.2 + - - +
30C GLN* 4.9 11.7 + - - +
114D LEU 5.5 1.7 - - - +
117D GLU 3.5 6.0 + - - +
118D GLN* 1.3 85.0 + - - +
120D ARG* 1.3 63.5 + - - +
121D LEU 3.1 0.2 - - - -
122D GLN* 3.1 20.3 + - + +
123D GLY* 3.5 6.4 + - - -
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Residues in contact with ARG 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D THR* 2.9 35.2 - - - +
57D ARG* 2.7 21.6 - - - +
60D ASP* 2.5 29.2 + - - -
118D GLN* 2.4 46.2 + - + +
119D ASP* 1.3 67.9 - - - +
121D LEU* 1.3 70.0 + - - +
123D GLY* 3.1 5.3 + - - +
124D ARG* 3.0 29.7 + - - +
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D THR* 3.7 26.7 - - + +
59D PHE* 3.8 12.6 - - + -
60D ASP* 3.6 35.2 - - - +
63D ILE* 3.7 13.1 - - + +
114D LEU* 3.9 17.3 - - + -
117D GLU* 3.5 37.5 - - + -
118D GLN 3.6 9.2 - - - +
119D ASP 3.1 0.8 - - - -
120D ARG* 1.3 90.1 - - - +
122D GLN* 1.3 61.6 + - - +
124D ARG* 3.0 16.4 + - - +
125D ILE* 3.1 15.4 + - - +
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Residues in contact with GLN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C HIS* 5.6 1.4 - - - -
175C ARG* 4.0 24.6 - - - +
109D LEU 5.3 0.3 - - - +
110D THR 5.5 0.5 - - - -
111D GLY* 3.2 35.9 + - - -
114D LEU* 3.7 20.8 - - + +
115D MET* 6.2 0.4 - - - -
118D GLN 4.4 0.6 + - - -
119D ASP* 3.1 13.7 + - + +
121D LEU* 1.3 76.3 - - - +
123D GLY* 1.3 58.4 + - - +
125D ILE* 2.9 16.1 + - - +
126D ASN* 2.8 53.5 + - - +
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Residues in contact with GLY 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ASP 3.5 5.2 + - - -
120D ARG* 3.1 9.6 + - - -
122D GLN* 1.3 80.0 - - - +
124D ARG* 1.3 55.4 + - - +
126D ASN* 3.1 14.9 + - - +
127D GLN* 2.9 33.4 + - - +
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ASP* 2.8 58.6 + - - +
63D ILE* 3.9 21.9 - - + +
64D GLU* 2.9 38.3 + - - +
67D GLU* 3.9 19.7 + - - +
120D ARG* 3.0 18.6 + - - +
121D LEU* 3.0 13.9 + - - +
123D GLY* 1.3 75.7 - - - +
125D ILE* 1.3 63.2 + - - +
127D GLN* 3.1 27.9 + - - +
128D LEU* 3.2 12.3 + - - +
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Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ILE* 3.9 30.3 - - + -
66D ILE* 5.0 4.3 - - + -
108D ILE* 4.1 13.2 - - + +
109D LEU* 3.6 28.5 - - + +
114D LEU* 3.7 18.8 - - + -
121D LEU 3.1 11.6 + - - +
122D GLN* 2.9 21.6 + - - +
124D ARG* 1.3 75.6 - - - +
126D ASN* 1.3 66.7 + - - +
128D LEU* 3.0 13.0 + - + +
129D PHE* 3.0 46.9 + - + -
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Residues in contact with ASN 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ARG* 2.8 66.8 + - - +
176C SER* 4.4 4.7 - - - +
122D GLN* 2.8 26.4 + - - +
123D GLY* 3.1 15.1 + - - +
125D ILE* 1.3 77.3 - - - +
127D GLN* 1.3 61.4 + - + +
129D PHE* 3.5 1.6 + - - +
130D GLU* 3.0 32.2 + - + +
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Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D GLU* 6.6 0.2 - - - -
123D GLY 2.9 15.7 + - - +
124D ARG* 3.4 30.9 + - + +
125D ILE 3.1 0.6 - - - -
126D ASN* 1.3 75.2 - - + +
128D LEU* 1.3 59.8 + - - +
130D GLU* 3.2 7.5 + - - +
131D ARG* 2.8 29.7 + - - +
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ILE* 5.5 2.7 - - + +
66D ILE* 3.9 28.7 - - + -
67D GLU* 3.7 43.0 - - + +
70D LEU* 4.2 9.6 - - + -
71D ILE* 4.3 13.5 - - + -
109D LEU* 4.2 16.2 - - + -
124D ARG 3.2 10.7 + - - +
125D ILE* 3.0 17.4 + - + +
127D GLN* 1.3 74.5 - - - +
129D PHE* 1.3 58.8 + - + +
131D ARG* 3.0 9.8 + - + +
132D ILE* 2.8 47.4 + - + +
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Residues in contact with PHE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ARG* 3.6 43.5 - - - +
95D ILE* 6.0 4.7 - - + -
109D LEU* 3.5 46.4 - - + -
125D ILE* 3.0 30.0 + - + -
126D ASN 3.7 6.7 - - - +
128D LEU* 1.3 80.7 - - + +
130D GLU* 1.3 52.3 + - - +
132D ILE* 3.3 13.1 + - + +
133D GLU* 2.7 36.3 + - - +
163D LEU* 3.7 29.1 - - + +
166D CYS* 6.1 0.7 - - + -
167D GLU* 4.0 24.0 - - + -
170D LEU* 5.3 9.2 - - + -
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ARG* 5.0 0.2 + - - -
175C ARG* 4.7 7.8 + - - -
180C TYR* 2.4 37.2 + - - -
126D ASN* 3.0 25.5 + - + +
127D GLN* 3.6 7.4 - - - +
129D PHE* 1.3 75.5 - - - +
131D ARG* 1.3 59.0 + - - +
133D GLU* 3.2 14.7 + - - +
134D VAL* 2.8 40.2 + - + +
137D ARG* 5.0 11.4 + - - -
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Residues in contact with ARG 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLU* 4.1 20.4 + - - +
71D ILE* 3.7 50.0 - - + +
127D GLN 2.8 14.1 + - - +
128D LEU* 3.0 13.9 + - + +
130D GLU* 1.3 78.3 - - - +
132D ILE* 1.3 62.1 + - - +
134D VAL* 3.3 7.4 + - - +
135D GLN* 3.1 27.3 + - + +
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Residues in contact with ILE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 4.1 23.8 - - + -
71D ILE* 4.4 11.7 - - + -
74D ILE* 5.5 7.9 - - + -
91D ILE* 4.9 4.7 - - + -
95D ILE* 3.9 30.3 - - + -
109D LEU* 6.2 0.2 - - + -
128D LEU* 2.8 45.6 + - + +
129D PHE* 3.7 16.4 - - + +
131D ARG* 1.3 73.4 - - - +
133D GLU* 1.3 64.4 + - - +
135D GLN* 3.2 9.2 + - + +
136D LEU* 3.0 32.8 + - + +
163D LEU* 4.4 12.6 - - + -
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Residues in contact with GLU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ARG* 3.2 29.6 + - - -
175C ARG* 4.9 0.5 + - - -
129D PHE 2.7 19.0 + - - +
130D GLU* 3.2 17.0 + - - +
132D ILE* 1.3 74.7 - - - +
134D VAL* 1.3 56.6 + - - +
136D LEU* 3.3 10.8 + - - +
137D ARG* 2.9 48.7 + - - +
156D THR* 4.4 4.7 - - - +
159D ALA* 3.9 17.9 - - + +
160D SER* 3.4 19.6 + - - -
163D LEU* 3.1 26.2 - - + +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D GLU* 2.8 35.2 + - + +
131D ARG* 3.6 7.9 - - - +
132D ILE 3.3 0.2 - - - -
133D GLU* 1.3 72.8 - - - +
135D GLN* 1.3 57.4 + - - +
137D ARG* 2.8 35.8 - - + +
138D GLN* 2.9 28.8 + - + +
141D ARG* 4.7 3.9 + - - +
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Residues in contact with GLN 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ILE* 5.7 7.0 - - + -
74D ILE* 4.2 17.4 - - + +
75D ASN* 4.1 11.9 + - - -
78D LEU* 3.5 32.2 - - - +
91D ILE* 5.5 3.6 - - + -
131D ARG* 3.1 17.2 + - + +
132D ILE* 3.2 12.3 + - + +
134D VAL* 1.3 73.1 - - - +
136D LEU* 1.3 68.4 + - + +
138D GLN* 3.0 26.1 + - - +
139D VAL* 2.8 27.4 + - - +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D LEU* 3.8 25.7 - - + +
91D ILE* 3.7 31.4 - - + -
92D VAL* 5.3 5.4 - - + -
95D ILE* 5.7 1.3 - - + -
132D ILE* 3.0 25.8 + - + +
133D GLU* 3.4 13.5 - - - +
135D GLN* 1.3 81.1 - - - +
137D ARG* 1.3 61.2 + - - +
139D VAL* 3.4 4.5 + - - +
140D MET* 3.0 31.9 + - + +
159D ALA* 3.9 27.1 - - + +
162D LEU* 4.1 19.7 - - + -
163D LEU* 4.5 9.4 - - + +
166D CYS* 6.2 0.9 - - - -
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Residues in contact with ARG 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D GLU* 5.0 6.9 + - - -
133D GLU* 2.9 40.2 + - - +
134D VAL* 2.8 48.6 - - - +
136D LEU* 1.3 73.6 - - - +
138D GLN* 1.3 54.8 + - - +
140D MET* 3.1 7.8 + - - +
141D ARG* 2.8 67.8 + - - +
155D GLU* 3.8 22.0 - - + +
156D THR* 3.8 34.3 + - - +
159D ALA* 4.1 6.2 - - - +
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Residues in contact with GLN 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D LEU* 4.7 6.4 - - - +
87D ARG* 4.9 2.8 + - - -
134D VAL* 2.9 15.4 + - + +
135D GLN* 3.0 33.2 + - - +
137D ARG* 1.3 72.5 - - - +
139D VAL* 1.3 78.4 + - - +
141D ARG* 3.1 23.5 + - - +
142D GLU* 3.2 44.7 + - + +
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Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D LEU* 3.5 31.6 - - + -
84D THR* 3.8 29.1 + - + +
87D ARG* 3.9 24.1 + - + +
88D LEU* 3.7 22.2 - - + -
91D ILE* 4.4 11.4 - - + -
135D GLN* 2.8 24.3 + - - +
136D LEU 3.6 7.9 - - - +
138D GLN* 1.3 78.8 - - - +
140D MET* 1.3 63.5 + - - +
142D GLU* 3.3 12.8 + - - +
143D LYS 3.7 5.5 + - - -
146D ARG* 5.8 0.2 - - - -
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Residues in contact with MET 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D THR* 4.5 2.0 - - - -
88D LEU* 4.0 18.2 - - + -
136D LEU* 3.0 17.4 + - + +
137D ARG 3.4 6.7 - - - +
139D VAL* 1.3 76.4 - - - +
141D ARG* 1.3 62.2 + - - +
143D LYS* 3.1 21.5 + - - +
144D LYS* 4.8 1.6 + - - +
150D GLY* 5.5 0.3 - - - -
151D TYR* 3.6 26.6 - - + -
155D GLU* 3.6 24.9 - - + +
158D LEU* 3.6 28.3 - - + -
159D ALA* 3.4 36.3 - - + +
162D LEU* 3.4 26.5 - - + -
197D LEU* 5.0 1.8 - - + -
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Residues in contact with ARG 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D VAL* 4.7 4.8 + - - +
137D ARG* 2.8 63.3 + - - +
138D GLN* 3.1 13.9 + - - +
140D MET* 1.3 72.4 - - - +
142D GLU* 1.3 61.1 + - + +
143D LYS 3.2 1.4 + - - -
144D LYS* 3.8 23.2 - - - +
145D MET* 4.6 4.9 - - - +
155D GLU* 3.8 27.8 + - + +
156D THR* 4.8 5.3 + - - -
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Residues in contact with GLU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ARG* 3.9 5.7 + - - -
138D GLN* 3.2 41.6 + - + +
139D VAL* 3.7 8.7 - - - +
140D MET 3.1 1.2 - - - -
141D ARG* 1.3 77.7 - - + +
143D LYS* 1.3 64.3 + - - +
144D LYS 3.3 1.6 - - - -
145D MET* 3.6 18.6 + - + +
146D ARG* 2.7 70.2 + - + +
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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) + - + + + + + -
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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