Contacts of the helix formed by residues 143 - 165 (chain B) in PDB entry 5TWF
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 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 4.1 7.7 - - - +
141B PRO* 3.0 28.8 - - - +
142B LYS* 1.3 75.7 + - - +
144B PHE* 1.3 61.1 + - - +
145B MET 3.5 1.8 - - - -
146B SER* 2.0 37.4 + - - +
147B VAL* 3.2 23.8 + - - +
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASN* 3.3 45.5 - - + +
57B ILE* 4.6 3.1 - - + -
58B ALA* 3.9 14.6 - - + -
131B LEU* 3.4 32.5 - - + -
132B PHE* 3.7 36.8 - + - -
140B PHE* 3.6 16.6 - + + -
141B PRO* 2.7 28.2 + - + +
142B LYS 3.2 2.0 + - - -
143B ASN* 1.3 74.4 + - - +
145B MET* 1.3 69.5 + - + +
147B VAL* 2.9 19.8 + - + +
148B ALA* 2.9 29.3 + - + -
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.8 14.8 - - + -
54B ASN* 3.3 25.1 + - - +
57B ILE* 4.2 21.1 - - + -
142B LYS 5.0 1.8 + - - +
143B ASN 3.5 0.6 - - - -
144B PHE* 1.3 80.1 - - + +
146B SER* 1.3 64.4 + - - +
148B ALA* 3.1 1.8 + - - +
149B LYS* 2.9 52.8 + - + +
193B PHE* 4.9 4.7 - - - +
195B LEU* 3.3 31.0 - - - -
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASN* 2.0 42.0 + - - +
145B MET* 1.3 79.0 - - - +
147B VAL* 1.3 60.9 + - - +
149B LYS* 3.3 11.4 + - - +
150B THR* 2.7 34.5 + - - -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TRP* 5.1 2.0 - - + -
125B GLN* 3.8 26.7 - - + +
131B LEU* 3.7 26.7 - - + -
132B PHE* 5.2 4.7 - - + -
143B ASN* 3.3 35.4 - - - +
144B PHE* 2.9 13.0 + - + +
146B SER* 1.3 80.8 + - - +
148B ALA* 1.3 61.5 + - - +
150B THR* 3.5 6.6 + - - -
151B ILE* 3.2 32.1 + - + +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.7 29.4 - - + -
61B THR* 4.5 8.7 - - + +
132B PHE* 5.4 1.3 - - + -
144B PHE* 2.9 32.4 + - + +
145B MET* 3.8 4.0 - - - +
147B VAL* 1.3 75.8 - - - +
149B LYS* 1.3 66.1 + - + +
151B ILE* 3.2 10.3 + - - +
152B LEU* 3.0 30.7 + - - +
195B LEU* 5.4 0.2 - - + -
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B MET* 2.9 47.7 + - + +
146B SER* 3.7 8.5 - - - +
148B ALA* 1.3 75.4 - - - +
150B THR* 1.3 62.1 + - - +
152B LEU* 3.6 0.6 + - - -
153B LYS* 3.2 23.8 + - - +
193B PHE 5.2 0.7 - - - -
194B ASN* 3.4 23.1 - - - +
195B LEU* 3.2 44.0 - - + +
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TRP* 4.3 9.6 - - + -
146B SER* 2.7 24.5 + - - -
147B VAL* 3.7 8.0 - - - -
149B LYS* 1.3 74.5 - - - +
151B ILE* 1.3 64.9 + - - +
153B LYS* 3.2 30.0 + - - +
154B ARG* 3.0 51.3 - - - +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 4.1 18.4 - - + -
121B TRP* 3.7 23.8 - - + -
122B VAL* 3.6 33.0 - - + +
125B GLN* 3.7 27.4 - - + -
126B LEU* 4.8 0.7 - - + -
132B PHE* 4.1 24.0 - - + -
147B VAL* 3.2 18.9 + - + +
148B ALA* 3.2 7.6 + - - +
150B THR* 1.3 77.9 - - - +
152B LEU* 1.3 58.4 + - - +
154B ARG* 3.1 5.7 + - - +
155B LEU* 2.9 34.3 + - + +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.7 0.7 - - + -
61B THR* 4.0 30.7 - - + +
64B PHE* 4.0 21.8 - - + -
148B ALA 3.0 18.6 + - - +
149B LYS 4.2 1.8 - - - +
150B THR 3.3 0.2 - - - -
151B ILE* 1.3 76.5 - - - +
153B LYS* 1.3 65.4 + - - +
155B LEU* 3.2 8.0 + - + -
156B PHE 3.0 19.4 + - - -
186B PHE* 3.3 29.7 - - + -
189B PHE* 4.9 3.1 - - + -
190B VAL* 4.3 5.6 - - + -
195B LEU* 3.5 37.7 - - + -
196B ILE* 3.4 17.3 - - + +
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS 3.2 13.1 + - - +
150B THR* 3.2 38.5 + - - +
152B LEU* 1.3 76.9 - - - +
154B ARG* 1.3 74.0 + - + +
156B PHE* 3.5 15.2 - - - +
157B ARG* 3.7 33.9 + - - +
195B LEU 5.2 0.4 - - - +
196B ILE* 3.7 22.3 - - + +
200B GLU* 4.2 35.3 + - + +
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TRP* 3.3 42.4 - - - -
98B ALA 3.3 19.6 + - - -
99B ASP 3.9 17.0 + - - -
118B LEU* 3.5 25.6 - - + +
121B TRP* 4.1 20.9 - - + -
122B VAL* 5.5 1.1 - - + -
150B THR* 3.0 39.9 - - - +
151B ILE* 3.1 7.1 + - - +
153B LYS* 1.3 86.1 - - + +
155B LEU* 1.3 61.7 + - + +
156B PHE 3.1 1.3 - - - -
157B ARG* 3.0 49.0 + - - +
158B VAL* 3.8 2.1 + - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR 4.6 2.5 - - - +
64B PHE* 4.0 11.2 - - + +
65B PHE* 3.6 45.3 - - + +
68B ILE* 4.1 18.3 - - + +
118B LEU* 3.9 15.0 - - + -
119B MET* 4.3 4.5 - - - -
122B VAL* 3.9 27.1 - - + -
151B ILE* 2.9 24.3 + - + +
152B LEU* 3.2 11.6 + - + +
154B ARG* 1.3 76.7 - - - +
156B PHE* 1.3 62.3 + - - +
158B VAL* 3.3 16.2 + - + +
159B TYR* 3.5 13.0 + - - -
186B PHE* 4.4 9.4 - - + -
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Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B TYR* 5.4 1.6 - - - -
152B LEU 3.0 12.7 + - - +
153B LYS 3.5 13.7 - - - +
154B ARG 3.1 0.4 - - - -
155B LEU* 1.3 78.3 - - - +
157B ARG* 1.3 63.3 + - + +
159B TYR* 3.1 8.3 - - + +
160B ALA* 2.9 37.2 + - + -
183B PHE* 3.7 26.0 - + - -
186B PHE* 3.8 22.8 - + + -
187B ILE* 4.1 5.8 - - + -
196B ILE* 4.2 1.3 - - + -
200B GLU* 3.6 23.6 - - + -
201B LEU* 3.5 37.0 - - + -
203B PRO* 4.3 8.7 - - + -
204B LEU* 3.7 27.1 - - + -
208B ILE* 4.6 0.2 - - + -
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET* 4.1 12.1 - - + +
95B TYR* 3.6 48.2 + - + +
96B HIS 5.7 1.8 + - - -
114B TYR* 2.6 41.7 + - + +
115B ILE* 6.0 0.4 - - + -
153B LYS* 3.7 36.7 + - - +
154B ARG* 3.0 41.4 + - - +
156B PHE* 1.3 79.2 - - + +
158B VAL* 1.3 60.7 + - + +
160B ALA* 3.4 7.9 - - - +
161B HIS* 2.8 31.2 + - - +
200B GLU* 4.8 11.9 + - - +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 3.5 29.2 - - + -
72B TYR* 3.9 34.1 - - + -
115B ILE* 4.1 29.6 - - + -
118B LEU* 4.2 19.1 - - + -
119B MET* 4.8 4.0 - - + -
154B ARG 4.1 8.7 - - - +
155B LEU* 3.6 9.2 - - - +
156B PHE 3.2 0.4 - - - -
157B ARG* 1.3 72.6 - - - +
159B TYR* 1.3 65.9 + - - +
161B HIS* 3.4 2.6 + - - +
162B ILE* 3.1 32.0 + - + +
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Residues in contact with TYR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PHE* 5.0 1.4 - - - -
68B ILE* 3.1 31.4 - - + +
71B LEU* 4.5 10.1 - - + -
155B LEU 3.5 7.7 + - - -
156B PHE* 3.1 8.9 + - + +
158B VAL* 1.3 78.1 - - - +
160B ALA* 1.3 56.9 + - - +
162B ILE* 3.3 6.3 + - + +
163B TYR* 2.9 40.2 + + - -
179B LEU* 4.2 11.4 - - + -
182B SER* 2.7 38.4 + - - -
183B PHE* 3.2 52.0 - + + -
186B PHE* 3.3 43.8 - + + +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ALA* 3.8 24.9 - - + -
95B TYR* 5.2 4.7 - - + +
156B PHE* 2.9 31.0 + - + +
157B ARG* 3.1 13.2 + - - +
159B TYR* 1.3 74.1 - - - +
161B HIS* 1.3 66.7 + - - +
163B TYR* 3.1 4.8 + - - +
164B HIS* 3.1 33.0 + - + +
203B PRO* 4.7 4.0 - - + -
204B LEU* 6.4 0.9 - - - -
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Residues in contact with HIS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 4.5 13.5 - + - -
79B CYS* 4.2 4.5 - - - -
84B CYS* 3.4 12.0 - - + +
86B VAL 4.7 6.3 - - - -
87B MET* 4.0 20.8 - - + +
88B SER 3.5 23.2 + - - -
111B ALA* 3.6 15.9 - - + +
115B ILE* 5.2 2.0 - - + -
157B ARG 2.8 18.5 + - - +
158B VAL* 3.8 6.1 - - + +
160B ALA* 1.3 72.0 - - - +
162B ILE* 1.3 63.9 + - + +
165B GLN* 3.0 52.7 + - + +
166B HIS* 3.2 6.6 + + - -
301B ZN 2.1 35.8 - - - -
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 5.5 1.6 - - + +
71B LEU* 4.6 4.5 - - + +
72B TYR* 4.0 36.1 - - + +
75B ILE* 3.6 35.2 - - + -
158B VAL* 3.1 21.6 + - + +
159B TYR* 3.7 5.4 - - + +
161B HIS* 1.3 80.6 - - + +
163B TYR* 1.3 63.5 + - - +
166B HIS* 3.6 3.5 + - - +
167B PHE* 3.1 26.4 + - + +
170B VAL* 3.9 12.6 - - + -
179B LEU* 3.4 36.3 - - + -
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Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 2.9 29.2 + + - +
160B ALA* 3.1 4.9 + - - +
162B ILE* 1.3 79.4 - - - +
164B HIS* 1.3 69.8 + - + +
167B PHE* 3.4 40.8 - + - +
179B LEU* 3.3 29.1 + - + -
180B ASN* 3.0 45.5 + - - +
183B PHE* 3.8 32.7 - + - +
204B LEU* 6.5 0.7 - - + -
207B LEU* 3.2 36.1 - - + +
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Residues in contact with HIS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 2.7 41.3 + - + +
90B GLY* 4.4 5.2 - - - +
160B ALA* 3.1 20.1 + - + +
163B TYR* 1.3 89.2 - - + +
165B GLN* 1.3 67.6 + - - +
167B PHE* 4.2 4.5 + - - +
203B PRO* 3.2 29.4 + - + +
204B LEU* 5.0 1.8 - - - -
207B LEU* 6.3 1.2 - - - +
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Residues in contact with GLN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B SER 4.4 12.7 + - - -
84B CYS* 4.0 4.8 - - + +
85B PRO* 5.6 2.8 - - - +
88B SER* 4.9 7.4 - - - +
90B GLY* 5.4 6.2 + - - +
161B HIS* 3.0 32.7 + - + +
164B HIS* 1.3 83.6 - - - +
166B HIS* 1.3 82.4 + - + +
167B PHE 3.8 0.2 + - - -
168B ASP* 4.4 5.0 - - - +
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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