Contacts of the helix formed by residues 141 - 164 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21H VAL* 4.7 12.8 - - + +
25H GLU* 3.4 9.6 + - - +
29H THR* 3.8 17.1 + - - +
83H ARG* 2.7 34.5 + - - -
87H LEU* 4.2 7.1 - - - +
139H ALA* 3.5 1.3 - - - +
140H LYS* 1.3 77.8 - - - +
142H ASP* 1.3 69.9 + - - +
143H ASP* 3.9 3.3 + - - +
144H THR* 2.6 33.4 + - - +
145H ALA* 2.9 21.8 + - - +
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Residues in contact with ASP 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H LYS 3.3 7.8 + - - +
141H ASP* 1.3 73.5 + - - +
143H ASP* 1.3 69.4 + - - +
145H ALA* 3.0 10.1 + - - +
146H ASP* 2.9 22.1 + - - +
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Residues in contact with ASP 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ARG* 3.3 39.5 + - - +
141H ASP* 3.3 2.5 + - - -
142H ASP* 1.3 82.9 - - - +
144H THR* 1.3 63.9 + - - +
146H ASP* 3.2 10.0 + - - +
147H ILE* 3.0 27.8 + - + +
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Residues in contact with THR 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H THR* 3.1 23.0 - - + +
32H LEU* 5.1 4.0 - - + -
33H LEU* 3.5 29.8 - - + -
83H ARG* 3.6 10.1 - - - +
139H ALA* 4.4 7.6 - - + -
141H ASP* 2.6 32.7 + - - -
143H ASP* 1.3 75.6 - - - +
145H ALA* 1.3 68.1 + - - +
147H ILE* 3.3 9.9 + - - +
148H LEU* 3.0 34.3 + - + +
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Residues in contact with ALA 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H ILE* 4.0 24.1 - - + +
139H ALA* 4.0 15.6 - - + +
141H ASP 2.9 12.3 + - - +
142H ASP* 3.0 13.2 + - - +
144H THR* 1.3 76.6 - - - +
146H ASP* 1.3 53.7 + - - +
148H LEU* 3.3 4.9 + - - +
149H THR* 2.7 38.5 + - - +
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Residues in contact with ASP 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H ASP 2.9 11.7 + - - +
143H ASP* 3.3 13.2 - - - +
145H ALA* 1.3 76.6 - - - +
147H ILE* 1.3 65.0 + - - +
149H THR* 2.9 10.4 + - - -
150H ALA* 2.9 24.9 + - - +
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Residues in contact with ILE 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU* 5.2 2.2 - - + -
76H HIS* 4.7 3.4 + - - +
79H THR* 3.8 31.0 - - + -
80H MET* 3.6 30.5 - - + -
83H ARG* 3.6 41.5 - - + -
143H ASP* 3.0 19.0 + - + +
144H THR* 3.5 8.7 - - + +
146H ASP* 1.3 79.4 - - + +
148H LEU* 1.3 63.5 + - + +
150H ALA* 3.3 7.1 + - - +
151H ALA* 3.1 21.8 + - + +
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Residues in contact with LEU 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU* 4.2 8.1 - - + -
33H LEU* 4.6 6.7 - - + -
36H GLN* 3.9 11.4 - - + -
80H MET* 3.8 27.8 - - + -
132H VAL* 3.8 20.4 - - + +
135H ALA* 3.7 33.4 - - + +
136H ILE* 3.9 12.9 - - + +
139H ALA* 4.1 7.2 - - + -
144H THR* 3.0 35.4 + - + +
145H ALA 3.7 3.8 - - - +
147H ILE* 1.3 73.2 - - + +
149H THR* 1.3 55.9 + - - +
151H ALA* 3.7 3.7 - - - +
152H SER* 2.7 35.5 + - - -
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Residues in contact with THR 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136H ILE* 3.5 31.1 - - + +
145H ALA* 2.7 21.8 + - - +
146H ASP* 2.9 13.2 + - - +
148H LEU* 1.3 72.3 - - - +
150H ALA* 1.3 60.3 + - - +
152H SER* 3.2 1.4 + - - -
153H ARG* 2.8 42.7 + - - +
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Residues in contact with ALA 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H HIS* 3.4 19.6 + - + +
146H ASP* 2.9 13.2 + - - +
147H ILE* 3.6 11.0 - - - +
149H THR* 1.3 77.0 - - - +
151H ALA* 1.3 63.5 + - - +
153H ARG* 3.4 10.3 - - - +
154H ASP* 3.4 16.1 + - - +
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Residues in contact with ALA 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 3.9 22.2 - - + -
76H HIS* 3.4 30.5 - - + +
80H MET* 5.0 5.8 - - - -
132H VAL* 4.7 2.9 - - + -
147H ILE* 3.1 16.1 + - + +
148H LEU* 3.7 7.6 - - - +
150H ALA* 1.3 76.6 - - - +
152H SER* 1.3 65.8 - - - +
154H ASP* 3.1 4.0 + - - +
155H LEU* 3.0 28.0 + - - +
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Residues in contact with SER 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H VAL* 4.0 21.2 - - - +
133H ARG* 3.7 28.9 - - - +
136H ILE* 3.7 17.4 - - - +
148H LEU 2.7 21.3 + - - -
149H THR 3.5 4.5 - - - -
151H ALA* 1.3 73.0 - - - +
153H ARG* 1.3 64.4 + - - +
155H LEU* 3.1 1.9 + - - +
156H ASP* 2.9 32.8 + - - +
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Residues in contact with ARG 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H THR* 2.8 28.0 + - - +
150H ALA* 3.4 11.7 - - - +
152H SER* 1.3 78.1 - - - +
154H ASP* 1.3 63.9 + - - +
156H ASP* 3.7 5.0 + - - +
157H LYS* 3.3 19.2 + - - +
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Residues in contact with ASP 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ALA* 4.2 8.7 - - - +
76H HIS* 2.7 35.6 + - + +
150H ALA 3.4 3.9 + - - -
151H ALA 3.1 4.3 + - - +
153H ARG* 1.3 80.7 - - - +
155H LEU* 1.3 60.5 + - + +
157H LYS* 3.0 12.3 + - - +
158H PHE* 2.8 57.6 + - + -
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Residues in contact with LEU 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 3.2 39.5 - - + -
43H LEU* 3.8 20.2 - - + -
73H LEU* 4.2 14.6 - - + -
76H HIS* 5.4 1.1 - - + -
125H TYR* 4.2 10.5 - - + +
128H VAL* 3.5 26.9 - - + -
129H ALA* 3.8 25.3 - - + +
132H VAL* 4.8 2.5 - - + -
151H ALA* 3.0 22.8 + - - +
152H SER* 3.8 4.7 - - - +
154H ASP* 1.3 79.7 - - + +
156H ASP* 1.3 58.4 + - - +
158H PHE* 3.7 7.3 - - + +
159H LEU* 2.9 30.7 + - - +
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Residues in contact with ASP 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H ALA* 3.7 11.6 - - - +
133H ARG* 2.6 46.7 + - - -
152H SER* 2.9 23.1 + - - +
153H ARG* 4.0 6.0 - - - +
155H LEU* 1.3 76.5 - - - +
157H LYS* 1.3 61.7 + - - +
159H LEU* 3.8 9.3 - - - +
160H TRP* 3.1 23.2 + - - +
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Residues in contact with LYS 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H ARG 3.3 12.2 + - - +
154H ASP* 3.0 17.3 + - - +
156H ASP* 1.3 78.2 - - - +
158H PHE* 1.3 72.9 + - + +
160H TRP* 3.3 24.8 + - + +
161H PHE* 2.9 58.6 + - + +
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Residues in contact with PHE 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H GLY 5.3 0.2 - - - -
69H PHE* 3.4 51.6 - + + -
72H ALA* 3.5 32.5 - - + -
73H LEU* 4.1 13.7 - - + -
76H HIS* 5.7 0.2 - + - -
125H TYR* 3.7 25.6 - + + -
154H ASP* 2.8 45.2 + - + +
155H LEU* 3.3 6.5 + - + +
157H LYS* 1.3 89.0 - - + +
159H LEU* 1.3 56.1 + - - +
161H PHE* 3.0 2.9 + + - +
162H ILE* 2.7 40.8 + - - +
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Residues in contact with LEU 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H ALA* 3.4 29.4 - - - +
125H TYR* 4.1 11.6 - - + -
126H ALA* 3.9 26.7 - - + +
129H ALA* 4.3 11.0 - - + -
130H ASN* 5.2 5.8 - - - +
133H ARG* 6.2 0.4 - - - +
155H LEU 2.9 18.0 + - - +
156H ASP* 3.8 8.5 - - - +
157H LYS 3.3 0.2 - - - -
158H PHE* 1.3 74.0 - - - +
160H TRP* 1.3 58.1 + - - +
162H ILE* 3.2 5.6 + - - +
163H GLU* 2.9 62.6 + - + +
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Residues in contact with TRP 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H ASP 3.1 11.9 + - - +
157H LYS* 3.4 24.7 - - + +
158H PHE 3.1 0.2 - - - -
159H LEU* 1.3 80.4 - - - +
161H PHE* 1.3 87.5 + + - +
163H GLU* 3.5 8.6 + - - +
164H SER* 2.7 64.7 + - - -
52L TRP* 3.8 28.8 + + - -
54L MET 5.2 2.0 + - - -
55L ARG* 4.1 21.4 - - - +
59L PHE* 4.4 12.5 - + - -
63L HIS* 4.0 15.9 - + - -
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Residues in contact with PHE 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H MET* 4.0 6.3 - - + -
69H PHE* 3.6 29.6 - + + -
157H LYS* 2.9 39.6 + - + +
158H PHE 3.0 6.9 + - - +
160H TRP* 1.3 116.1 - + - +
162H ILE* 1.3 58.1 + - - +
164H SER* 3.5 2.1 + - - -
165H ASN* 2.7 32.9 + - - -
59L PHE* 3.8 12.8 - + - -
60L ILE* 3.5 23.3 - - + -
63L HIS* 3.8 26.9 - + - -
64L GLU* 5.0 4.9 - - - -
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Residues in contact with ILE 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H MET* 4.5 9.9 - - + -
66H LEU* 4.8 5.8 - - + -
69H PHE* 3.7 15.5 - - + -
118H LEU* 3.3 39.8 - - + +
121H LEU* 4.1 9.4 - - + -
122H ALA* 3.9 12.1 - - + +
125H TYR* 3.5 54.1 - - + -
158H PHE 2.7 20.3 + - - +
159H LEU* 3.6 4.0 - - - +
161H PHE* 1.3 73.0 - - - +
163H GLU* 1.3 63.2 - - - +
165H ASN* 3.1 17.5 + - - +
166H ILE* 3.6 7.7 - - + +
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Residues in contact with GLU 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H ALA* 4.3 14.6 - - + +
126H ALA* 5.6 1.2 - - - +
159H LEU* 2.9 49.7 + - + +
160H TRP* 3.9 7.8 - - - +
162H ILE* 1.3 73.4 - - - +
164H SER* 1.3 57.7 + - - +
166H ILE* 2.9 40.5 + - + +
55L ARG* 4.6 17.8 + - - +
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Residues in contact with SER 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H TRP* 2.7 49.7 + - - -
161H PHE 3.9 0.4 - - - -
162H ILE 3.3 0.4 - - - -
163H GLU* 1.3 72.9 - - - +
165H ASN* 1.3 56.7 + - - +
166H ILE 3.4 0.2 - - - -
55L ARG* 3.7 23.3 + - - +
56L GLY 2.8 26.8 + - - -
59L PHE* 3.1 40.9 - - - +
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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
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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