Contacts of the helix formed by residues 145 - 159 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE 3.4 1.0 + - - -
144B SER* 1.3 72.5 - - - +
146B TYR* 1.3 53.8 + - - +
148B LEU 3.3 0.2 + - - -
149B ALA* 2.8 26.9 + - - +
200B ILE* 3.6 31.0 - - + -
202B TRP* 5.1 0.2 - - + -
206B MET* 2.6 22.7 + - + +
208B ILE* 4.2 8.7 - - + -
230B TYR* 2.7 30.9 + - - +
234B PHE* 3.6 12.3 - - + -
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Residues in contact with TYR 146 (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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248A LYS* 3.3 39.5 + - - +
249A PHE* 3.6 28.7 - + - -
253A PHE* 4.2 17.3 - + - -
144B SER* 3.1 7.8 + - - +
145B ALA* 1.3 77.8 - - - +
147B LYS* 1.3 65.7 + - - +
149B ALA* 3.0 3.4 + - - +
150B GLN* 2.8 64.2 + - + +
206B MET* 4.3 16.7 + - + +
234B PHE* 3.8 10.2 - + + -
5E G 4.0 14.6 - - - -
6E T 3.9 16.2 - - - +
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.7 20.0 - - + -
88B LEU* 4.3 7.2 - - + -
110B ASN* 4.2 4.6 + - - +
112B THR* 2.5 37.7 + - - +
143B ILE* 4.0 13.9 - - + -
144B SER* 3.1 15.2 + - - +
146B TYR* 1.3 80.1 - - - +
148B LEU* 1.3 55.2 + - - +
150B GLN* 3.4 10.6 + - - -
151B THR* 2.5 43.7 + - - +
6E T 3.6 30.4 + - - +
7E C 2.7 27.1 + - - +
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Residues in contact with LEU 148 (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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143B ILE* 4.4 12.8 - - + +
144B SER 3.1 16.5 + - - +
145B ALA 3.4 5.8 - - - +
146B TYR 3.1 0.6 - - - -
147B LYS* 1.3 77.0 - - - +
149B ALA* 1.3 60.4 + - - +
151B THR* 3.2 9.3 + - + -
152B CYS* 2.8 40.9 + - - -
155B MET* 5.8 0.2 - - + -
166B ILE* 5.3 5.2 - - + -
190B LEU* 4.2 23.1 - - + -
191B PHE* 4.7 8.3 - - + -
198B LEU* 4.8 3.8 - - + -
208B ILE* 4.4 15.5 - - + -
226B TRP* 4.0 20.9 - - + -
230B TYR* 3.4 30.1 - - + +
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Residues in contact with ALA 149 (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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253A PHE* 3.8 16.5 - - + -
145B ALA 2.8 14.6 + - - +
146B TYR* 3.3 11.4 - - - +
148B LEU* 1.3 78.2 - - - +
150B GLN* 1.3 51.1 + - - +
152B CYS* 2.9 5.7 + - - +
153B ALA* 2.8 34.0 + - - +
230B TYR* 3.4 14.3 - - + -
231B LEU* 3.9 16.1 - - + +
234B PHE* 4.1 16.8 - - + -
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Residues in contact with GLN 150 (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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253A PHE* 4.1 13.9 - - + -
87B PHE* 3.5 35.2 - - + -
146B TYR* 2.8 69.9 + - + +
147B LYS* 3.7 7.2 - - - +
149B ALA* 1.3 73.0 - - - +
151B THR* 1.3 59.3 + - - +
153B ALA* 3.5 3.0 + - - +
154B LYS* 2.9 41.1 + - - +
6E T 4.3 2.6 + - - -
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Residues in contact with THR 151 (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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84B THR* 3.8 11.2 - - + +
87B PHE* 3.6 8.2 - - + -
88B LEU* 3.5 32.3 - - + +
147B LYS* 2.5 24.0 + - - +
148B LEU* 3.5 12.0 - - + -
150B GLN* 1.3 74.3 - - - +
152B CYS* 1.3 65.5 + - - +
154B LYS* 3.1 6.6 + - - +
155B MET* 3.0 29.6 + - + +
164B PHE* 3.6 31.4 - - + -
166B ILE* 5.1 2.5 - - + -
191B PHE* 5.9 0.4 - - + -
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Residues in contact with CYS 152 (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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148B LEU* 2.8 14.9 + - - +
149B ALA 3.3 5.8 - - - +
151B THR* 1.3 79.8 - - - +
153B ALA* 1.3 57.1 + - - +
154B LYS 3.4 0.2 + - - -
155B MET* 3.4 26.3 + - + +
156B ILE* 2.9 30.1 + - - +
226B TRP* 3.7 18.2 - - - -
227B ALA* 3.7 10.7 - - + +
230B TYR* 3.5 26.5 - - + -
231B LEU* 3.1 24.9 - - + -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PHE* 3.9 14.4 - - + -
256A TYR* 3.6 37.5 - - + +
149B ALA 2.8 14.1 + - - +
150B GLN* 3.8 6.3 - - - +
151B THR 3.2 0.2 - - - -
152B CYS* 1.3 78.7 - - - +
154B LYS* 1.3 62.2 + - + +
156B ILE* 3.3 4.2 - - - +
157B ASP* 3.2 29.3 + - - +
231B LEU* 4.1 1.5 - - - +
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Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO* 4.0 14.1 - - + +
84B THR* 3.6 18.2 - - + +
87B PHE* 3.4 51.6 - - + -
150B GLN* 2.9 28.8 + - - +
151B THR* 3.1 4.4 + - - +
153B ALA* 1.3 74.9 - - + +
155B MET* 1.3 66.4 + - - +
156B ILE 3.0 2.0 - - - -
157B ASP* 4.5 2.7 - - - -
158B ASN* 2.8 40.2 + - - +
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Residues in contact with MET 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 3.9 9.8 + - + -
148B LEU* 5.8 0.7 - - + -
151B THR* 3.0 17.8 + - + +
152B CYS* 3.4 42.4 - - - +
153B ALA 3.4 0.2 - - - -
154B LYS* 1.3 74.9 - - - +
156B ILE* 1.3 52.8 + - - +
159B LYS* 2.8 30.0 + - - -
160B GLU 2.8 30.6 + - - +
161B PHE* 3.4 12.7 - - + -
164B PHE* 3.7 32.1 - - + -
191B PHE* 4.4 19.3 - - + -
223B ARG* 4.5 17.3 - - + -
227B ALA* 3.7 14.4 - - + +
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Residues in contact with ILE 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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256A TYR* 4.1 19.3 - - + -
152B CYS 2.9 21.5 - - - +
153B ALA* 3.3 8.5 - - - +
154B LYS 3.0 0.4 - - - -
155B MET* 1.3 73.0 - - - +
157B ASP* 1.3 67.5 + - - +
158B ASN 3.0 2.2 - - - -
159B LYS* 2.6 38.0 + - - +
161B PHE* 3.5 28.9 - - + -
224B GLU* 5.1 2.9 - - + +
227B ALA* 3.6 17.0 - - + -
228B LYS* 4.3 22.7 - - + +
231B LEU* 5.1 2.5 - - + -
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Residues in contact with ASP 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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255A LYS* 5.4 1.3 + - - -
256A TYR* 3.2 35.1 + - - -
153B ALA 3.2 12.7 + - - +
154B LYS* 4.5 1.1 - - - -
156B ILE* 1.3 75.3 - - - +
158B ASN* 1.3 71.9 + - - +
159B LYS* 3.9 2.1 + - - +
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Residues in contact with ASN 158 (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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83B PRO* 3.2 37.3 - - + +
84B THR* 4.4 0.8 + - - -
154B LYS* 2.8 35.3 + - - +
156B ILE 2.7 1.4 + - - -
157B ASP* 1.3 85.9 - - - +
159B LYS* 1.3 70.1 + - - +
160B GLU* 3.2 23.6 + - - +
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Residues in contact with LYS 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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155B MET 2.8 9.1 + - - -
156B ILE* 2.6 23.9 + - - +
157B ASP 5.1 1.8 - - - +
158B ASN* 1.3 75.1 - - - +
160B GLU* 1.3 57.5 + - - +
161B PHE* 3.1 29.8 + - + +
224B GLU* 3.3 31.1 + - - -
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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