Contacts of the helix formed by residues 145 - 159 (chain A) in PDB entry 1XHU
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 ALA 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ILE 3.3 3.0 + - - -
144A SER* 1.3 72.5 - - - +
146A TYR* 1.3 57.9 + - - +
149A ALA 2.8 14.7 + - - -
200A ILE* 3.4 31.4 - - + -
206A MET* 2.9 24.9 + - + +
208A ILE* 3.8 8.1 - - + -
230A TYR* 2.6 28.6 + - - +
234A PHE* 3.1 19.1 - - + -
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Residues in contact with TYR 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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144A SER* 3.0 2.1 + - - +
145A ALA* 1.3 76.0 - - - +
147A LYS* 1.3 60.6 + - - +
148A LEU 3.0 1.7 + - - -
149A ALA* 3.1 1.6 + - + +
150A GLN* 2.9 76.5 + - + +
206A MET* 3.7 18.0 + - + +
234A PHE* 3.5 14.0 - + + -
248B LYS* 3.7 39.2 + - - +
249B PHE* 3.6 28.7 - + - -
253B PHE* 4.1 12.1 - + - -
5G G 4.0 13.7 - - - -
6G T 3.5 21.3 - - - +
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.7 18.5 - - + -
88A LEU* 4.3 9.2 - - + -
110A ASN 4.0 5.3 + - - -
112A THR* 3.3 30.9 + - + +
143A ILE* 4.7 10.8 - - + -
144A SER* 3.0 19.2 + - - +
146A TYR* 1.3 77.5 - - - +
148A LEU* 1.3 53.1 + - - +
150A GLN* 3.8 11.0 - - - +
151A THR* 2.6 40.0 + - - +
6G T 3.3 26.2 + - - +
7G C 2.4 40.2 + - - +
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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
----------------------------------------------------------
143A ILE* 4.3 26.9 - - + +
144A SER 2.8 17.7 + - - +
145A ALA* 4.1 0.4 - - - -
146A TYR 3.0 0.2 - - - -
147A LYS* 1.3 76.3 - - - +
149A ALA* 1.3 55.2 + - - +
151A THR* 3.1 13.0 + - + +
152A CYS* 2.8 38.1 + - - -
166A ILE* 5.6 2.2 - - + -
190A LEU* 4.2 20.2 - - + -
191A PHE* 4.6 7.2 - - + -
198A LEU* 4.2 7.6 - - + -
208A ILE* 4.6 4.5 - - + -
226A TRP* 4.0 23.8 - - + -
230A TYR* 3.2 39.3 - - + +
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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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145A ALA 2.8 17.3 + - - +
146A TYR 3.5 4.3 - - - +
148A LEU* 1.3 73.1 - - - +
150A GLN* 1.3 65.5 + - - +
152A CYS 3.2 0.7 + - - -
153A ALA 3.1 11.6 + - - -
230A TYR* 3.4 4.6 - - - -
231A LEU* 3.0 33.1 - - + +
234A PHE* 3.8 31.6 - - + -
253B PHE* 3.5 14.9 - - + -
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Residues in contact with GLN 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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87A PHE* 3.7 33.9 - - + -
146A TYR* 2.9 71.6 + - + +
147A LYS* 3.8 0.8 - - - +
149A ALA* 1.3 69.1 - - - +
151A THR* 1.3 67.0 + - - +
153A ALA* 3.2 3.8 + - - +
154A LYS* 3.0 38.0 + - + +
253B PHE* 4.0 12.8 - - + -
6G T 3.6 13.3 + - - -
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Residues in contact with THR 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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84A THR* 3.9 9.9 - - + -
87A PHE* 3.5 8.5 - - - -
88A LEU* 3.2 29.3 - - + +
147A LYS* 2.6 21.6 + - - +
148A LEU* 3.1 18.8 + - + +
150A GLN* 1.3 77.4 - - - +
152A CYS* 1.3 64.7 + - - +
154A LYS* 3.3 5.9 + - - +
155A MET* 3.0 22.2 + - + +
164A PHE* 3.4 35.4 - - + -
191A PHE* 5.7 0.7 - - + -
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Residues in contact with CYS 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 LEU* 2.8 15.9 + - - +
149A ALA 3.6 7.6 - - - +
150A GLN 3.2 0.4 - - - -
151A THR* 1.3 76.3 - - - +
153A ALA* 1.3 55.8 + - - +
155A MET* 2.7 34.4 + - - +
156A ILE* 2.9 17.8 + - - +
191A PHE* 5.5 1.6 - - - -
226A TRP* 4.3 11.4 - - - -
227A ALA* 3.5 39.0 - - - +
230A TYR* 3.6 25.6 - - - -
231A LEU* 3.8 8.3 - - + -
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Residues in contact with ALA 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 ALA 3.1 5.3 + - - -
150A GLN* 3.2 8.9 + - - +
152A CYS* 1.3 76.7 - - - +
154A LYS* 1.3 63.9 + - + +
156A ILE* 3.4 0.7 + - - +
157A ASP* 3.0 32.6 + - - +
231A LEU* 3.9 5.5 - - + +
253B PHE* 3.7 21.3 - - + -
256B TYR* 3.4 36.2 + - + +
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Residues in contact with LYS 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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83A PRO* 4.7 4.2 + - + -
84A THR* 3.0 33.7 + - + +
87A PHE* 3.3 41.0 - - + +
150A GLN* 3.0 31.8 + - - +
151A THR* 3.5 7.9 - - - +
153A ALA* 1.3 78.1 - - + +
155A MET* 1.3 63.3 + - - +
157A ASP* 4.6 3.8 - - - +
158A ASN* 3.0 41.7 + - - +
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Residues in contact with MET 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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84A THR* 3.4 6.7 + - + -
151A THR* 3.0 17.8 + - - +
152A CYS* 2.7 20.5 + - - +
154A LYS* 1.3 72.7 - - - +
156A ILE* 1.3 52.9 + - - +
159A LYS* 2.5 39.3 + - - -
160A GLU 3.2 29.8 + - - +
161A PHE* 3.9 16.1 - - + -
163A LEU 6.2 0.2 - - - +
164A PHE* 4.0 32.8 - - + -
191A PHE* 4.9 7.4 - - + -
223A ARG* 3.4 39.0 - - + +
226A TRP* 6.4 0.2 - - - -
227A ALA* 4.2 17.7 - - + -
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Residues in contact with ILE 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 CYS 2.9 17.7 + - - +
153A ALA 3.8 3.4 - - - +
155A MET* 1.3 74.8 - - - +
157A ASP* 1.3 74.5 + - - +
159A LYS* 2.7 10.6 + - - +
161A PHE* 3.9 17.3 - - + -
224A GLU* 5.2 2.9 - - + +
227A ALA* 4.1 24.5 - - + -
228A LYS* 4.3 10.5 - - + +
231A LEU* 3.5 31.2 - - + -
256B TYR* 3.7 27.4 - - + +
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Residues in contact with ASP 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 ALA* 3.0 17.9 + - - +
154A LYS* 4.0 4.4 + - - +
156A ILE* 1.3 83.0 - - - +
158A ASN* 1.3 63.1 + - - +
159A LYS* 2.7 12.3 + - - +
256B TYR* 2.5 37.2 + - - -
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Residues in contact with ASN 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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83A PRO* 2.8 43.3 - - + +
154A LYS* 3.0 27.4 + - - +
157A ASP* 1.3 78.5 - - - +
159A LYS* 1.3 67.7 + - - +
160A GLU* 3.4 23.4 + - + +
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Residues in contact with LYS 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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155A MET 2.5 18.9 + - - -
156A ILE 3.2 8.7 - - - +
157A ASP 2.7 8.7 + - - +
158A ASN* 1.3 72.2 - - - +
160A GLU* 1.3 57.6 + - - +
161A PHE* 3.6 27.2 + - + -
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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
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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