Contacts of the helix formed by residues 147 - 161 (chain B) in PDB entry 1UK0
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 SER 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B VAL* 4.7 0.2 - - - -
144B ASP* 2.7 46.5 + - - -
146B ASP* 1.3 76.7 - - - +
148B GLU* 1.4 63.6 + - - +
149B GLU* 3.2 23.3 + - - +
150B ALA* 3.2 24.1 + - - +
151B GLU* 3.4 4.5 + - - +
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Residues in contact with GLU 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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146B ASP 4.9 4.7 - - - +
147B SER* 1.4 77.0 + - - +
149B GLU* 1.4 69.0 + - - +
151B GLU* 3.1 25.0 + - + +
152B ILE* 2.9 19.9 + - - +
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Residues in contact with GLU 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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143B VAL* 3.4 24.2 - - + +
147B SER* 3.2 8.0 + - - +
148B GLU* 1.4 73.0 - - - +
150B ALA* 1.3 57.4 - - - +
152B ILE* 2.5 37.8 + - + -
153B ILE* 2.9 26.6 + - + -
177B LYS* 5.4 6.2 - - - +
340B TYR* 2.6 30.3 + - - +
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Residues in contact with ALA 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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143B VAL* 3.5 7.9 - - + +
144B ASP 3.5 9.0 - - - +
145B ARG* 3.2 10.5 - - - +
147B SER 3.2 13.3 + - - +
149B GLU* 1.3 77.5 - - - +
151B GLU* 1.3 65.0 + - - +
153B ILE* 3.1 1.5 + - - +
154B ARG* 2.8 57.7 + - - +
175B ILE* 3.7 18.4 - - + -
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Residues in contact with GLU 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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146B ASP* 4.5 18.2 - - - +
147B SER 3.4 2.7 + - - +
148B GLU* 3.1 35.7 + - + +
149B GLU 2.8 2.8 + - - -
150B ALA* 1.3 78.0 - - - +
152B ILE* 1.3 59.0 + - - +
154B ARG* 3.9 13.1 + - - +
155B LYS* 3.1 33.3 + - - +
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Residues in contact with ILE 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 GLU 2.9 9.8 + - - +
149B GLU* 2.5 22.0 + - + +
151B GLU* 1.3 69.8 - - - +
153B ILE* 1.4 82.6 + - + +
155B LYS* 2.8 26.5 + - + +
156B TYR* 2.8 18.3 + - + +
301B ILE* 3.5 34.3 - - + -
303B LEU* 4.3 20.6 - - + -
308B VAL* 5.9 6.3 - - + -
310B LEU* 4.2 4.6 - - + +
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Residues in contact with ILE 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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143B VAL* 4.6 1.8 - - + -
149B GLU* 2.9 32.1 + - + +
150B ALA 3.9 4.5 - - - +
152B ILE* 1.4 79.2 - - + +
154B ARG* 1.3 56.7 + - - +
156B TYR* 2.5 32.6 + - + +
157B VAL* 2.8 10.2 + - - -
175B ILE* 4.0 21.8 - - + -
198B LEU* 6.4 1.1 - - + -
200B TRP* 4.6 4.5 - - + -
260B LEU* 4.4 15.0 - - + -
340B TYR* 3.7 36.8 - - + -
342B LEU* 3.7 36.8 - - + -
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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
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145B ARG* 2.9 32.7 + - - +
146B ASP* 5.0 1.6 + - - -
150B ALA* 2.8 37.8 + - - +
151B GLU* 3.6 14.3 + - - +
153B ILE* 1.3 71.2 - - + +
155B LYS* 1.3 63.2 + - - +
157B VAL* 3.4 6.5 + - + +
158B LYS* 2.8 27.4 + - - +
172B VAL* 3.4 39.5 - - + +
175B ILE* 3.2 33.3 - - + +
342B LEU* 6.0 0.2 - - + -
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Residues in contact with LYS 155 (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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151B GLU* 3.1 20.6 + - - +
152B ILE* 2.8 43.7 + - + +
153B ILE 2.7 3.2 + - - -
154B ARG* 1.3 76.4 - - - +
156B TYR* 1.4 50.5 - - - +
158B LYS* 3.3 7.2 - - + +
159B ASN* 2.8 52.9 + - - +
301B ILE* 5.0 5.8 - - + +
310B LEU* 4.2 18.6 - - + -
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Residues in contact with TYR 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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152B ILE* 2.8 9.0 + - + +
153B ILE* 2.5 20.3 + - - +
155B LYS* 1.4 70.6 - - - +
157B VAL* 1.4 60.9 + - - +
159B ASN 3.7 0.2 + - - -
160B THR* 2.7 54.7 + - + -
198B LEU* 2.7 24.8 + - + -
199B LEU* 3.9 5.2 - - - -
200B TRP* 3.3 26.7 - + + -
238B ASP* 4.1 11.7 - - - +
260B LEU* 3.5 31.0 - - + -
308B VAL* 3.8 18.4 - - + -
309B PRO* 2.8 34.3 - - + +
310B LEU* 3.9 22.2 - - + +
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Residues in contact with VAL 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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153B ILE 2.8 12.0 + - - +
154B ARG* 3.7 8.5 - - - +
156B TYR* 1.4 75.0 - - - +
158B LYS* 1.3 68.9 + - - +
159B ASN 3.0 1.6 + - - -
160B THR 3.2 6.4 + - - -
161B HIS* 3.6 3.9 + - + +
170B LEU* 4.3 29.2 - - + +
172B VAL* 4.5 12.6 - - + -
200B TRP* 3.1 21.0 - - + -
240B VAL* 3.3 34.0 - - + +
342B LEU* 3.3 26.7 - - + -
344B LEU* 4.8 2.5 - - + -
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Residues in contact with LYS 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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154B ARG 2.8 16.9 + - - +
155B LYS* 3.3 10.3 - - + +
157B VAL* 1.3 75.1 - - - +
159B ASN* 1.3 83.6 + - - +
161B HIS* 4.5 6.0 + - - +
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Residues in contact with ASN 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 LYS* 2.8 27.6 + - - +
156B TYR 4.8 0.2 - - - +
157B VAL 3.0 0.6 + - - -
158B LYS* 1.3 100.0 - - - +
160B THR* 1.3 62.1 + - + +
161B HIS* 3.7 1.8 - - - +
299B ALA* 5.9 1.8 - - - +
310B LEU* 2.7 31.0 + - - +
311B GLY* 4.4 1.8 - - - -
312B THR* 3.1 44.3 + - - +
313B GLY 3.5 5.0 + - - -
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Residues in contact with THR 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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156B TYR* 2.7 36.7 + - + +
157B VAL 3.2 2.2 + - - -
159B ASN* 1.3 87.0 - - - +
161B HIS* 1.4 67.7 + - - +
200B TRP* 4.0 1.2 + - - -
238B ASP 3.9 5.8 - - - -
239B MET* 2.9 24.3 - - + +
240B VAL* 2.6 32.7 + - - -
295B PRO* 4.1 9.9 - - + -
309B PRO 3.6 23.8 - - - +
310B LEU 3.8 10.3 - - - +
311B GLY 4.3 0.7 - - - +
312B THR 4.3 1.3 - - - +
313B GLY 5.4 0.2 - - - +
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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
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157B VAL* 3.6 4.2 + - + +
158B LYS* 5.1 4.7 - - - +
159B ASN 3.7 4.1 - - - +
160B THR* 1.4 89.4 - - - +
162B ALA* 1.4 62.7 + - - +
165B HIS 4.4 1.5 + - - -
166B ASN* 3.1 20.8 + - - +
168B TYR* 2.7 55.8 - + - -
169B ASP* 3.8 11.1 + - - +
170B LEU* 2.8 34.2 - - + +
239B MET* 3.5 7.8 - - - +
240B VAL* 3.5 17.0 - - + +
241B SER* 3.3 24.3 - - - -
313B GLY* 5.0 6.9 + - - -
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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
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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