Contacts of the helix formed by residues 141 - 164 (chain A) in PDB entry 1F33
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.7 12.9 - - + +
25A GLU* 3.4 9.5 + - - +
29A THR* 3.8 16.7 + - - +
83A ARG* 2.6 35.3 + - - -
87A LEU* 4.1 6.8 - - + +
139A ALA* 3.6 1.3 - - - +
140A LYS* 1.3 78.0 - - - +
142A ASP* 1.3 68.3 + - - +
143A ASP* 3.9 3.5 + - - +
144A THR* 2.7 31.9 + - - +
145A ALA* 2.9 21.2 + - - +
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Residues in contact with ASP 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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140A LYS 3.3 8.3 + - - +
141A ASP* 1.3 73.7 + - - +
143A ASP* 1.3 69.8 + - - +
145A ALA* 3.0 10.5 + - - +
146A ASP* 2.9 22.1 + - - +
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Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 3.3 39.4 + - - +
141A ASP* 3.3 3.0 + - - -
142A ASP* 1.3 81.8 - - - +
144A THR* 1.3 57.2 + - - +
146A ASP* 3.1 9.9 + - - +
147A ILE* 3.0 33.4 + - + +
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Residues in contact with THR 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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29A THR* 3.2 22.2 - - + +
32A LEU* 5.0 4.3 - - + -
33A LEU* 3.6 28.5 - - + -
83A ARG* 3.6 10.9 - - - +
139A ALA* 4.4 7.9 - - + -
141A ASP* 2.7 33.2 + - - -
143A ASP* 1.3 75.8 - - - +
145A ALA* 1.3 67.3 + - - +
147A ILE* 3.2 9.6 + - - +
148A LEU* 2.9 35.5 + - + +
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Residues in contact with ALA 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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136A ILE* 4.0 23.1 - - + +
139A ALA* 4.0 16.3 - - + +
141A ASP 2.9 11.4 + - - +
142A ASP* 3.0 12.5 + - - +
144A THR* 1.3 76.6 - - - +
146A ASP* 1.3 54.2 + - - +
148A LEU* 3.4 5.1 + - - +
149A THR* 2.6 39.0 + - - +
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Residues in contact with ASP 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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142A ASP 2.9 11.9 + - - +
143A ASP* 3.2 12.6 - - - +
145A ALA* 1.3 74.0 - - - +
147A ILE* 1.3 69.1 + - + +
149A THR* 2.9 19.3 + - - -
150A ALA* 2.9 16.5 + - - +
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Residues in contact with ILE 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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33A LEU* 5.2 2.0 - - + -
76A HIS* 4.7 3.8 + - - +
79A THR* 3.8 31.0 - - + -
80A MET* 3.6 30.7 - - + -
83A ARG* 3.6 40.8 - - + -
143A ASP* 3.0 19.8 + - + +
144A THR* 3.2 8.9 + - + +
146A ASP* 1.3 79.5 - - + +
148A LEU* 1.3 64.9 + - + +
150A ALA* 3.3 7.0 + - - +
151A ALA* 3.1 20.7 + - + +
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Residues in contact with LEU 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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32A LEU* 4.2 8.1 - - + -
33A LEU* 4.6 7.9 - - + -
36A GLN* 3.9 11.4 - - + -
80A MET* 3.9 27.1 - - + -
132A VAL* 3.9 19.7 - - + +
135A ALA* 3.8 34.5 - - + +
136A ILE* 3.9 13.0 - - + -
139A ALA* 4.1 7.4 - - + -
144A THR* 2.9 35.8 + - + +
145A ALA 3.8 3.4 - - - +
147A ILE* 1.3 73.0 - - - +
149A THR* 1.3 55.6 + - - +
151A ALA* 3.3 4.5 + - - +
152A SER* 2.7 36.4 + - - -
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Residues in contact with THR 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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136A ILE* 3.4 30.0 - - + +
145A ALA 2.6 24.1 + - - -
146A ASP* 2.9 13.3 + - - -
148A LEU* 1.3 77.0 - - - +
150A ALA* 1.3 54.3 + - - +
152A SER* 3.2 1.4 + - - -
153A ARG* 2.8 46.7 + - - +
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Residues in contact with ALA 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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76A HIS* 3.4 19.8 + - + +
146A ASP* 2.9 12.4 + - - +
147A ILE* 3.6 10.8 - - - +
149A THR* 1.3 76.8 - - - +
151A ALA* 1.3 62.3 + - - +
153A ARG* 3.4 11.1 - - - +
154A ASP* 3.3 17.5 + - - +
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Residues in contact with ALA 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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40A PHE* 3.9 22.7 - - + -
76A HIS* 3.4 32.4 - - + +
80A MET* 5.0 6.1 - - + -
132A VAL* 4.7 2.7 - - + -
147A ILE* 3.1 13.5 + - + +
148A LEU* 3.7 9.6 - - - +
150A ALA* 1.3 74.8 - - - +
152A SER* 1.3 65.8 + - - +
154A ASP* 3.1 4.2 + - - +
155A LEU* 2.9 28.4 + - - +
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Residues in contact with SER 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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132A VAL* 3.9 21.6 - - - +
133A ARG* 3.6 30.0 + - - +
136A ILE* 3.7 16.3 - - - +
148A LEU 2.7 21.8 + - - -
149A THR 3.5 4.3 - - - -
151A ALA* 1.3 72.7 - - - +
153A ARG* 1.3 66.1 + - - +
155A LEU* 3.1 1.8 + - - +
156A ASP* 2.9 31.1 + - - +
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Residues in contact with ARG 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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149A THR* 2.8 27.4 + - - +
150A ALA* 3.4 12.3 - - - +
151A ALA 3.2 0.2 - - - -
152A SER* 1.3 78.2 - - - +
154A ASP* 1.3 62.2 + - - +
156A ASP* 3.7 5.2 + - - +
157A LYS* 3.3 19.2 + - - +
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Residues in contact with ASP 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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72A ALA* 4.2 8.1 - - - +
76A HIS* 2.7 35.9 + - + +
150A ALA 3.3 3.5 + - - -
151A ALA 3.1 3.3 + - - +
152A SER 3.1 1.0 - - - -
153A ARG* 1.3 80.7 - - - +
155A LEU* 1.3 61.7 + - + +
157A LYS* 3.0 12.2 + - - +
158A PHE* 2.8 57.7 + - + -
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Residues in contact with LEU 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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40A PHE* 3.2 39.5 - - + -
43A LEU* 3.8 17.3 - - + -
73A LEU* 4.1 15.7 - - + -
76A HIS* 5.5 1.1 - - + -
125A TYR* 4.2 10.2 - - + +
128A VAL* 3.5 33.4 - - + -
129A ALA* 3.8 21.3 - - + +
132A VAL* 4.8 2.0 - - + -
151A ALA* 2.9 24.3 + - + +
152A SER* 3.1 5.4 + - - +
154A ASP* 1.3 78.8 - - + +
156A ASP* 1.3 58.6 + - - +
158A PHE* 3.1 7.6 + - + +
159A LEU* 2.8 31.4 + - - +
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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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129A ALA* 3.7 10.6 - - - +
133A ARG* 2.6 47.1 + - - -
152A SER* 2.9 22.7 + - - +
153A ARG* 4.0 6.4 - - - +
155A LEU* 1.3 76.0 - - - +
157A LYS* 1.3 62.1 + - - +
159A LEU* 3.5 9.3 + - - +
160A TRP* 3.1 23.4 + - - +
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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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153A ARG 3.3 12.0 + - - +
154A ASP* 3.0 17.8 + - - +
156A ASP* 1.3 80.5 - - - +
158A PHE* 1.3 71.2 + - + +
160A TRP* 3.2 25.1 + - + +
161A PHE* 2.9 57.0 + - + +
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Residues in contact with PHE 158 (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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68A GLY 5.3 0.4 - - - -
69A PHE* 3.4 61.0 - + + -
72A ALA* 3.5 33.9 - - + -
73A LEU* 4.1 14.4 - - + -
125A TYR* 3.7 19.1 - + + -
154A ASP* 2.8 43.6 + - + +
155A LEU* 3.1 5.8 + - - +
157A LYS* 1.3 91.4 - - + +
159A LEU* 1.3 56.3 + - - +
161A PHE* 2.9 2.3 + - - +
162A ILE* 2.7 39.8 + - - +
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Residues in contact with LEU 159 (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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122A ALA* 3.5 28.9 - - - +
125A TYR* 4.2 11.5 - - + -
126A ALA* 3.9 26.7 - - + +
129A ALA* 4.4 10.3 - - + -
130A ASN* 5.2 6.5 - - - +
133A ARG* 6.1 0.7 - - - +
155A LEU 2.8 20.3 + - - +
156A ASP* 3.7 9.2 - - - +
158A PHE* 1.3 71.7 - - - +
160A TRP* 1.3 60.1 + - - +
162A ILE* 3.2 5.5 + - - +
163A GLU* 2.9 62.6 + - + +
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Residues in contact with TRP 160 (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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156A ASP 3.1 11.9 + - - +
157A LYS* 3.3 25.8 - - + +
159A LEU* 1.3 80.4 - - - +
161A PHE* 1.3 87.8 + + - +
163A GLU* 3.9 8.1 - - - +
164A SER* 2.7 63.7 + - - -
52D TRP* 3.9 27.2 + + - -
54D MET 5.1 2.4 + - - -
55D ARG* 4.1 22.7 - - - +
59D PHE* 4.1 15.1 - + - -
63D HIS* 3.9 17.5 - + - -
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Residues in contact with PHE 161 (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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65A MET* 3.9 7.0 - - + -
69A PHE* 3.7 30.1 - + + -
157A LYS* 2.9 38.3 + - + +
158A PHE 2.9 6.5 + - - +
160A TRP* 1.3 113.6 - + - +
162A ILE* 1.3 66.3 + - - +
164A SER* 3.5 1.7 + - - -
165A ASN* 2.8 29.4 + - - -
59D PHE* 3.6 17.2 - + - -
60D ILE* 3.4 28.5 - - + -
63D HIS* 3.9 17.0 - + - -
64D GLU* 4.8 4.3 - - - -
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Residues in contact with ILE 162 (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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65A MET* 4.5 9.6 - - + -
66A LEU* 4.8 5.6 - - + -
69A PHE* 3.7 15.7 - - + -
118A LEU* 3.3 39.1 - - + +
121A LEU* 4.1 10.1 - - + -
122A ALA* 3.8 11.4 - - + +
125A TYR* 3.5 53.8 - - + -
158A PHE 2.7 21.4 + - - +
159A LEU* 3.6 4.5 - - - +
161A PHE* 1.3 73.1 - - - +
163A GLU* 1.3 65.0 + - - +
165A ASN* 3.0 19.0 + - - +
166A ILE* 3.6 7.7 + - + +
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Residues in contact with GLU 163 (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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122A ALA* 4.3 13.5 - - + +
126A ALA* 5.7 1.4 - - - +
159A LEU* 2.9 47.1 + - + +
160A TRP* 3.9 8.0 - - - +
162A ILE* 1.3 76.5 - - - +
164A SER* 1.3 57.9 + - - +
165A ASN 3.0 0.2 - - - -
166A ILE* 2.9 40.0 + - + +
55D ARG* 4.7 15.3 + - - +
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Residues in contact with SER 164 (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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160A TRP* 2.7 46.7 + - - -
161A PHE 3.9 0.4 - - - -
162A ILE 3.2 0.4 - - - -
163A GLU* 1.3 74.7 - - - +
165A ASN* 1.3 56.6 + - - +
166A ILE 3.3 0.7 - - - -
55D ARG* 3.6 21.0 + - - +
56D GLY 2.8 32.6 + - - +
59D PHE* 3.0 39.3 - - - +
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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
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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