Contacts of the helix formed by residues 136 - 157 (chain A) in PDB entry 4BPK
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 ASN 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL* 1.3 76.9 - - - +
137A TRP* 1.3 63.7 + - + +
138A GLY* 3.1 6.1 + - - -
139A ARG* 2.8 50.1 + - - +
140A ILE* 3.1 22.6 + - - +
181A TRP* 3.8 14.8 - - + -
14C ASP* 3.1 23.9 + - - +
17C ASN* 3.3 29.5 - - - +
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Residues in contact with TRP 137 (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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136A ASN* 1.3 75.6 - - - +
138A GLY* 1.3 63.4 + - - +
140A ILE* 3.1 26.1 + - + +
141A VAL* 3.0 26.3 + - - +
181A TRP* 3.6 26.0 - + - -
182A ILE* 3.6 28.7 - - + -
185A ASN* 4.5 10.3 + - + +
187A GLY 3.7 17.5 - - - -
188A TRP* 3.9 19.3 - + - -
190A THR* 4.0 16.6 - - + +
191A PHE* 3.5 42.4 - + + -
194A LEU* 3.4 30.7 - - + +
17C ASN* 3.5 2.9 + - - +
20C TYR* 3.7 22.7 - - + -
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASN* 3.1 7.4 + - - -
137A TRP* 1.3 79.2 - - - +
139A ARG* 1.3 60.4 + - - +
141A VAL* 3.3 4.3 + - - +
142A ALA* 3.1 18.5 + - - +
13C ALA* 3.6 25.7 - - - +
16C LEU* 4.0 12.4 - - - +
17C ASN* 3.3 11.2 + - - -
20C TYR* 3.6 10.4 - - - -
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Residues in contact with ARG 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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130A LEU* 3.6 26.9 + - + +
131A PHE* 3.4 20.5 - - + -
133A ASP* 2.6 35.0 + - - +
134A GLY 2.9 36.6 + - - +
136A ASN* 2.8 33.2 + - - +
138A GLY* 1.3 76.5 - - - +
140A ILE* 1.3 57.3 + - - +
142A ALA* 3.4 1.0 + - - +
143A PHE* 2.8 28.6 + - - +
10C ARG* 3.3 14.5 - - + +
11C HR7 3.4 7.9 + - - -
13C ALA* 3.6 15.5 - - + -
14C ASP* 2.9 38.0 + - - +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 5.0 1.8 - - + -
131A PHE* 4.2 6.7 - - + -
135A VAL* 3.8 16.8 - - + -
136A ASN 3.1 9.2 + - - +
137A TRP* 3.1 33.0 + - + +
139A ARG* 1.3 78.4 - - - +
141A VAL* 1.3 62.2 + - + +
143A PHE* 3.2 11.1 + - + +
144A PHE* 3.1 34.0 + - + -
174A LEU* 6.3 0.4 - - + -
178A LEU* 4.8 9.0 - - + -
181A TRP* 3.8 20.0 - - + -
182A ILE* 3.9 19.5 - - + -
188A TRP* 3.8 28.5 - - + -
191A PHE* 6.2 0.2 - - + -
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Residues in contact with VAL 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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90A LEU* 4.5 12.1 - - + +
93A ALA* 3.6 48.2 - - + +
94A GLY* 3.9 6.3 - - - +
97A PHE* 3.9 9.0 - - + -
137A TRP 3.0 18.2 + - - +
138A GLY 3.7 0.7 - - - +
140A ILE* 1.3 78.2 - - + +
142A ALA* 1.3 57.7 + - - +
144A PHE* 3.1 5.6 + - + +
145A SER* 2.9 25.6 + - - -
191A PHE* 3.9 19.1 - - + -
12B PHE* 6.2 0.2 - - + -
16C LEU* 3.7 22.0 - - + -
20C TYR* 4.0 6.5 - - - +
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Residues in contact with ALA 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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97A PHE* 3.6 34.2 - - + -
130A LEU* 4.3 11.9 - - + -
138A GLY 3.1 13.2 + - - +
139A ARG* 3.6 7.6 - - - +
141A VAL* 1.3 76.0 - - - +
143A PHE* 1.3 57.9 + - - +
145A SER* 3.7 1.0 - - - -
146A PHE* 2.8 31.5 + - - +
9C AHP 4.4 10.0 - - + +
13C ALA* 3.9 14.4 - - + -
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Residues in contact with PHE 143 (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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123A PHE* 4.0 22.6 - + - -
127A VAL* 3.9 16.6 - - + -
130A LEU* 3.7 7.1 - - - +
131A PHE* 3.7 24.5 - + + -
139A ARG 2.8 15.1 + - - +
140A ILE* 3.3 7.2 - - + +
141A VAL 3.2 0.2 - - - -
142A ALA* 1.3 75.9 - - - +
144A PHE* 1.3 89.5 + + - +
146A PHE* 3.7 5.7 - - - +
147A GLY* 3.0 19.8 + - - -
170A MET* 3.7 44.0 - - + +
173A TYR* 4.1 15.9 - + + -
174A LEU* 4.3 9.6 - - + -
178A LEU* 3.9 19.1 - - + -
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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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90A LEU* 3.5 40.4 - - + -
140A ILE* 3.1 41.1 + - + -
141A VAL 3.1 8.7 + - - +
143A PHE* 1.3 87.0 - + - +
145A SER* 1.3 57.0 + - - +
147A GLY* 3.2 2.3 + - - -
148A GLY 2.8 26.2 + - - -
170A MET* 3.9 17.6 - - + +
174A LEU* 3.6 24.0 - - + -
188A TRP* 4.0 7.4 - + - -
8B LEU* 4.0 10.3 - - + -
9B VAL* 4.0 28.7 - - + -
12B PHE* 3.2 37.6 - + + -
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Residues in contact with SER 145 (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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94A GLY* 3.8 14.2 - - - -
97A PHE* 3.4 30.4 - - - -
98A GLU* 3.0 29.2 + - - +
105A PHE* 4.2 7.1 - - - -
141A VAL 2.9 18.1 + - - -
142A ALA 3.7 2.7 - - - -
144A PHE* 1.3 76.5 - - - +
146A PHE* 1.3 55.5 + - - +
148A GLY* 3.3 1.7 + - - -
149A ALA* 2.9 29.5 + - - +
12B PHE* 3.8 5.3 - - - -
16B LYS* 5.7 0.2 - - - +
9C AHP 4.6 2.5 - - - -
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Residues in contact with PHE 146 (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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109A THR* 6.1 0.2 - - + -
112A LEU* 4.3 28.0 - - + -
122A SER 4.4 1.1 - - - -
123A PHE* 3.8 30.7 - + - -
126A VAL* 3.6 46.9 - - + -
127A VAL* 4.1 14.6 - - + -
130A LEU* 5.8 2.0 - - + -
142A ALA 2.8 20.8 + - - +
143A PHE* 3.7 7.2 - - - +
145A SER* 1.3 70.5 - - - +
147A GLY* 1.3 69.9 + - - +
149A ALA* 3.1 3.5 + - + +
150A LEU* 2.9 41.0 + - + +
5C ILE* 4.9 3.6 - - + -
9C AHP 3.8 31.1 - - + +
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Residues in contact with GLY 147 (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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123A PHE* 5.1 1.3 - - - -
143A PHE 3.0 12.3 + - - -
144A PHE 3.2 2.9 + - - -
146A PHE* 1.3 80.0 - - - +
148A GLY* 1.3 62.5 + - - +
150A LEU* 3.2 7.3 + - - +
151A CYS* 3.0 26.9 + - - -
166A ILE* 4.1 3.7 - - - +
170A MET* 3.6 25.6 - - - -
13B LEU* 3.8 6.7 - - - -
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Residues in contact with GLY 148 (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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144A PHE 2.8 16.9 + - - -
145A SER 3.6 3.6 - - - -
147A GLY* 1.3 73.4 - - - +
149A ALA* 1.3 55.8 + - - +
151A CYS* 3.2 4.6 + - - +
152A VAL* 3.0 35.0 + - - +
13B LEU* 3.6 17.0 - - - +
16B LYS* 4.2 23.7 - - - +
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Residues in contact with ALA 149 (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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105A PHE* 4.0 11.6 - - + -
109A THR* 3.7 32.1 - - + -
112A LEU* 4.7 6.5 - - + +
145A SER 2.9 16.1 + - - +
146A PHE* 3.1 7.6 + - + +
148A GLY* 1.3 76.0 - - - +
150A LEU* 1.3 58.1 + - - +
152A VAL* 3.4 7.3 + - - +
153A GLU* 2.9 30.5 + - - +
9C AHP 5.2 0.2 - - + -
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Residues in contact with LEU 150 (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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112A LEU* 3.9 26.6 - - + +
114A ILE* 3.5 30.3 - - + +
119A ALA* 4.7 7.2 - - + +
122A SER* 5.4 8.1 - - - -
123A PHE* 4.1 29.6 - - + -
146A PHE* 2.9 37.0 + - + +
147A GLY* 3.2 6.0 + - - +
149A ALA* 1.3 78.7 - - - +
151A CYS* 1.3 56.2 + - - +
153A GLU* 3.4 2.4 + - - -
154A SER* 2.8 32.7 + - - -
166A ILE* 3.8 25.1 - - + -
169A TRP* 4.8 0.4 - - + -
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Residues in contact with CYS 151 (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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147A GLY 3.0 17.2 + - - +
148A GLY* 3.2 7.8 + - - +
150A LEU* 1.3 74.3 - - - +
152A VAL* 1.3 59.2 + - - +
154A SER* 3.1 5.1 + - - -
155A VAL* 2.9 32.2 + - - +
163A VAL* 3.8 32.2 - - + +
166A ILE* 3.7 31.2 - - - -
13B LEU* 3.8 21.8 - - + -
17B LEU* 4.2 13.7 - - + -
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Residues in contact with VAL 152 (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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148A GLY 3.0 21.3 + - - +
149A ALA* 3.7 7.2 - - - +
151A CYS* 1.3 76.1 - - - +
153A GLU* 1.3 56.9 + - - +
155A VAL* 3.3 3.0 + - - +
156A ASP* 2.8 44.6 + - - +
16B LYS* 4.2 12.1 - - + +
17B LEU* 4.2 19.7 - - + +
20B LYS* 3.8 42.0 - - + -
22B TYR* 4.2 6.3 - - + -
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Residues in contact with GLU 153 (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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109A THR 4.7 4.2 - - - +
112A LEU* 3.6 30.5 - - + +
113A HIS* 5.2 1.2 - - - -
114A ILE* 3.6 24.5 - - + -
149A ALA 2.9 21.0 + - - +
150A LEU* 3.7 6.7 - - - +
152A VAL* 1.3 73.3 - - - +
154A SER* 1.3 62.7 + - - +
156A ASP* 3.2 14.7 - - - +
157A LYS* 3.0 46.2 + - + +
1199A CD 2.3 31.4 - - - -
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Residues in contact with SER 154 (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 ILE* 3.3 12.6 - - - +
150A LEU 2.8 18.4 + - - -
151A CYS* 3.3 11.2 - - - -
153A GLU* 1.3 77.4 - - - +
155A VAL* 1.3 56.3 + - - +
157A LYS 3.1 6.1 + - - -
159A MET* 2.7 61.9 + - - +
162A LEU* 3.7 13.2 - - - +
163A VAL* 4.4 4.7 - - - -
166A ILE* 3.5 13.4 - - - +
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Residues in contact with VAL 155 (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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151A CYS 2.9 18.6 + - - +
152A VAL 3.8 1.1 - - - +
154A SER* 1.3 72.4 - - - +
156A ASP* 1.3 66.1 + - - +
158A GLU* 3.0 13.0 + - - +
160A GLN* 3.5 37.9 + - + +
163A VAL* 3.7 19.5 - - + -
17B LEU* 3.9 16.2 - - + -
22B TYR* 3.6 44.2 + - + -
23B SER 6.1 0.9 - - - +
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Residues in contact with ASP 156 (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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152A VAL* 2.8 26.1 + - - +
153A GLU* 3.2 25.6 - - - +
155A VAL* 1.3 78.0 - - - +
157A LYS* 1.3 65.1 + - + +
158A GLU* 3.2 6.2 + - - +
22B TYR* 2.4 39.6 + - - -
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Residues in contact with LYS 157 (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 HIS* 5.9 6.9 + - - +
114A ILE 5.3 5.4 - - - +
153A GLU* 3.0 41.3 + - + +
154A SER 3.1 0.2 + - - -
155A VAL 3.1 0.6 - - - -
156A ASP* 1.3 79.7 - - - +
158A GLU* 1.3 69.6 + - - +
159A MET* 3.1 36.2 + - + +
1199A CD 4.0 6.1 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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