Contacts of the helix formed by residues 153 - 165 (chain B) in PDB entry 5U07
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 ASN 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B VAL* 4.1 3.3 - - - +
152B LEU* 1.3 75.7 - - - +
154B ALA* 1.3 75.8 + - - +
155B ASP* 3.3 7.6 + - - +
156B SER* 3.5 18.8 - - - -
157B THR* 3.0 27.7 + - - +
21E ASP* 5.5 2.2 - - + +
220F HIS* 2.2 52.3 - - - +
33K G 4.1 15.1 + - - +
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Residues in contact with ALA 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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147B VAL* 3.5 27.6 - - + -
152B LEU 3.3 2.8 + - - +
153B ASN* 1.3 77.6 + - - +
155B ASP* 1.3 70.7 + - - +
156B SER 3.2 1.3 - - - -
157B THR* 3.4 1.7 + - - -
158B GLU* 2.9 23.3 + - - +
217B TYR* 3.8 10.8 + - - +
221B LEU* 5.6 5.8 - - + -
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Residues in contact with ASP 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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153B ASN* 3.3 3.1 + - - +
154B ALA* 1.3 79.2 - - - +
156B SER* 1.3 53.9 + - - +
158B GLU* 2.7 27.7 - - - +
159B GLN* 3.2 7.3 + - - +
220F HIS* 3.2 30.8 + - + +
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Residues in contact with SER 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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153B ASN* 3.5 27.5 + - - -
154B ALA 3.2 0.6 - - - -
155B ASP* 1.3 73.9 - - - +
157B THR* 1.3 64.5 + - - +
158B GLU 2.9 5.0 + - - -
159B GLN* 3.1 10.0 + - - +
160B ARG* 3.1 10.0 + - - +
21E ASP* 2.5 32.1 + - - +
203F PHE* 3.2 30.3 - - - -
220F HIS* 3.3 9.3 + - - -
221F MET 5.0 2.4 + - - -
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Residues in contact with THR 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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143B LEU* 3.8 24.7 - - + -
147B VAL* 4.7 11.2 - - + +
152B LEU* 4.8 10.0 - - + +
153B ASN* 3.0 23.7 + - - +
154B ALA 3.4 3.7 + - - -
156B SER* 1.3 78.4 - - - +
158B GLU* 1.3 56.2 + - - +
160B ARG* 3.4 18.3 + - + +
161B LEU* 2.9 44.8 + - + +
179B LEU* 5.5 2.9 - - + -
217B TYR* 5.0 4.7 - - + -
21E ASP* 5.1 1.0 + - - -
22E LEU* 5.7 2.8 - - - +
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Residues in contact with GLU 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 ALA 2.9 13.1 + - - +
155B ASP* 2.7 23.6 - - - +
156B SER 2.9 0.4 - - - -
157B THR* 1.3 74.4 - - - +
159B GLN* 1.3 62.7 + - - +
161B LEU* 3.2 7.9 + - - +
162B HIS* 2.8 55.4 + - + +
214B VAL* 5.6 0.2 - - - +
217B TYR* 2.9 28.6 + - - +
218B HIS* 2.4 32.0 + - - -
49J ARG* 4.7 12.7 - - - +
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Residues in contact with GLN 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 ASP 3.2 6.3 + - - +
156B SER* 3.1 8.1 + - - +
158B GLU* 1.3 79.3 - - - +
160B ARG* 1.3 58.3 + - - +
162B HIS* 3.1 11.5 + - + +
163B LEU* 2.9 30.6 + - - +
201F VAL* 4.9 5.1 - - + +
203F PHE* 4.3 13.2 - - + -
223F ALA* 4.3 16.8 - - + +
225F GLN* 6.0 3.8 - - - +
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Residues in contact with ARG 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 SER 3.1 7.0 + - - +
157B THR* 3.8 22.3 + - - +
159B GLN* 1.3 78.0 - - - +
161B LEU* 1.3 63.9 + - - +
163B LEU* 3.0 20.0 - - + +
164B ILE* 3.0 25.2 + - + +
175B HIS 4.9 0.2 - - - -
178B ARG* 3.4 34.7 - - - +
179B LEU* 3.4 37.9 - - + +
20E ASP* 4.7 1.8 - - - +
21E ASP* 2.2 47.8 + - - -
22E LEU* 3.4 22.3 - - - +
203F PHE* 3.2 22.4 - - + -
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Residues in contact with LEU 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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139B LEU* 4.7 9.9 - - + -
140B GLY* 5.6 1.1 - - - -
143B LEU* 3.4 34.1 - - + -
157B THR* 2.9 36.9 + - + +
158B GLU* 3.2 11.4 + - - +
160B ARG* 1.3 75.9 - - - +
162B HIS* 1.3 63.0 + - + +
164B ILE* 3.2 7.5 + - + +
165B ALA* 3.0 25.3 + - - +
179B LEU* 3.8 13.5 - - + -
213B TRP* 5.0 16.4 - - + -
214B VAL* 4.6 20.8 - - + +
217B TYR* 5.0 18.6 - - + -
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Residues in contact with HIS 162 (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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158B GLU* 2.8 62.1 + - + +
159B GLN* 3.1 11.4 + - + +
161B LEU* 1.3 77.4 - - + +
163B LEU* 1.3 55.9 + - - +
165B ALA* 3.9 1.6 + - - -
166B ARG* 2.4 30.5 + - - +
214B VAL* 4.8 10.9 - - + +
218B HIS* 4.4 9.8 - + - -
45J LEU* 3.0 64.7 + - + +
46J ALA* 4.6 4.7 - - - -
49J ARG* 5.0 8.7 - - + +
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Residues in contact with LEU 163 (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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159B GLN 2.9 8.9 + - - +
160B ARG* 3.0 33.4 - - + +
161B LEU 3.1 0.4 - - - -
162B HIS* 1.3 76.4 - - - +
164B ILE* 1.3 79.5 + - + +
165B ALA 3.2 0.2 - - - -
166B ARG* 3.2 31.0 + - - +
167B GLN* 3.4 20.1 + - - +
175B HIS* 3.6 31.0 - - + +
178B ARG* 3.2 24.5 - - - +
199F VAL 5.5 1.6 - - - +
201F VAL* 3.4 35.2 - - + +
203F PHE* 4.6 1.8 - - + -
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Residues in contact with ILE 164 (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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160B ARG* 3.0 12.1 + - + +
161B LEU* 3.2 7.2 + - + +
163B LEU* 1.3 84.0 - - + +
165B ALA* 1.3 64.6 + - - +
166B ARG 2.9 6.5 + - - -
167B GLN* 3.1 16.8 + - - +
172B VAL* 4.5 24.2 - - + -
175B HIS* 4.0 18.8 - - + +
176B LEU* 4.1 13.5 - - + -
179B LEU* 3.3 39.3 - - + -
202B TRP* 3.7 10.1 - - + -
213B TRP* 4.2 26.2 - - + -
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Residues in contact with ALA 165 (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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161B LEU 3.0 16.5 + - - +
162B HIS 3.9 0.2 + - - -
163B LEU 3.2 0.8 - - - -
164B ILE* 1.3 77.9 - - - +
166B ARG* 1.3 58.3 + - - +
202B TRP* 4.6 3.7 - - - -
207B ARG* 5.4 1.9 - - - -
210B ALA* 3.2 34.2 - - + +
213B TRP* 6.4 1.3 - - - -
214B VAL* 3.8 22.2 - - + -
42J PRO* 4.3 8.8 - - - +
45J LEU* 3.7 22.2 - - + +
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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