Contacts of the helix formed by residues 156 - 170 (chain B) in PDB entry 4O9U
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 VAL 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B PHE* 3.8 33.9 - - + -
152B GLY 3.4 17.9 - - - +
153B GLN 3.3 6.6 + - - +
155B ALA* 1.3 78.7 - - - +
157B ASN* 1.3 60.8 + - - +
158B ALA 3.3 0.2 - - - -
159B LEU* 3.9 1.0 - - - +
160B VAL* 3.0 41.0 + - + +
193B LEU* 3.9 17.7 - - + -
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Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLN* 3.0 31.5 + - - +
154B LYS* 5.1 3.5 - - - +
156B VAL* 1.3 76.0 - - - +
158B ALA* 1.3 57.3 + - - +
160B VAL* 3.8 0.2 - - - +
161B LEU* 3.0 24.1 + - - +
190B PHE* 3.3 24.9 - - + -
193B LEU* 3.4 49.9 + - - +
194B MET* 4.0 16.8 - - - +
197B PRO* 4.6 5.1 - - - +
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Residues in contact with ALA 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 LYS 3.4 21.9 + - - +
155B ALA* 4.7 2.5 - - - -
156B VAL 3.3 0.8 - - - +
157B ASN* 1.3 79.2 - - + +
159B LEU* 1.3 60.7 + - + +
161B LEU* 4.4 8.3 - - - +
162B ALA* 3.1 25.5 + - - +
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Residues in contact with LEU 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 ALA* 3.4 29.2 + - + +
156B VAL* 3.5 2.9 + - - +
157B ASN 3.3 0.4 - - - -
158B ALA* 1.3 77.7 - - + +
160B VAL* 1.3 64.4 + - - +
161B LEU 3.3 0.9 - - - -
162B ALA* 3.8 15.1 - - + +
163B LEU* 3.3 21.5 + - - +
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Residues in contact with VAL 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 VAL* 3.0 29.2 + - + +
157B ASN 3.8 2.9 - - - +
159B LEU* 1.3 76.4 - - - +
161B LEU* 1.3 53.8 + - - +
163B LEU* 3.6 0.3 + - - +
164B THR* 2.4 34.0 + - - -
186B LEU* 3.3 20.7 - - + +
189B LEU* 3.5 29.2 - - + -
190B PHE* 3.9 21.3 - - + -
193B LEU* 3.8 18.2 - - + -
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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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123B LEU* 4.5 20.9 - - + -
157B ASN 3.0 17.8 + - - +
158B ALA* 4.4 6.7 - - - +
160B VAL* 1.3 74.8 - - - +
162B ALA* 1.3 58.2 + - - +
163B LEU 3.1 2.0 - - - -
164B THR* 3.0 10.8 + - - -
165B VAL* 2.9 45.2 + - + +
190B PHE* 3.7 43.3 - - + -
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Residues in contact with ALA 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 ALA 3.1 21.8 + - - +
159B LEU* 4.0 18.2 - - + +
160B VAL 3.5 0.4 - - - -
161B LEU* 1.3 78.4 - - - +
163B LEU* 1.3 56.3 + - - +
165B VAL* 3.8 6.6 + - - +
166B VAL* 3.3 31.4 + - - +
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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 LEU 3.3 15.7 + - - +
160B VAL 3.9 3.1 - - - +
161B LEU 3.1 0.6 - - - -
162B ALA* 1.3 75.5 - - - +
164B THR* 1.3 58.8 + - - +
165B VAL 3.0 2.0 - - - -
166B VAL* 3.1 10.9 + - + +
167B ILE* 2.7 57.5 + - + +
182B LEU* 6.1 3.1 - - + -
186B LEU* 3.9 20.9 - - + -
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Residues in contact with THR 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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123B LEU* 3.7 16.5 - - + +
160B VAL 2.4 28.3 + - - -
161B LEU* 3.0 15.3 + - + -
163B LEU* 1.3 75.5 - - - +
165B VAL* 1.3 57.2 + - - +
167B ILE* 3.6 6.7 - - - -
168B GLY 3.3 4.2 + - - -
183B PHE* 3.1 44.0 - - + +
186B LEU* 3.2 20.4 + - + +
187B ALA* 3.6 33.9 - - + +
190B PHE* 4.7 1.0 - - + +
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Residues in contact with VAL 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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123B LEU* 4.2 17.9 - - + -
161B LEU* 2.9 30.6 + - + +
162B ALA* 3.9 7.6 - - - +
164B THR* 1.3 76.0 - - - +
166B VAL* 1.3 63.3 + - + +
167B ILE 3.2 1.6 - - - -
168B GLY* 3.0 2.6 + - - -
169B LEU* 2.9 51.5 + - + +
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Residues in contact with VAL 166 (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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162B ALA 3.3 17.1 + - - +
163B LEU* 3.1 13.7 + - + +
165B VAL* 1.3 81.0 - - + +
167B ILE* 1.3 59.2 + - - +
169B LEU* 3.7 7.9 + - + +
170B SER* 3.3 20.4 + - - -
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Residues in contact with ILE 167 (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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163B LEU* 2.7 40.4 + - + +
164B THR* 3.4 16.6 - - - +
166B VAL* 1.3 71.1 - - - +
168B GLY* 1.3 65.0 + - - +
170B SER* 2.6 28.1 + - - +
171B LEU* 3.2 13.2 - - - +
179B SER* 3.5 29.4 - - - +
182B LEU* 3.7 38.1 - - + -
183B PHE* 3.6 19.3 - - + +
186B LEU* 3.8 7.4 - - + -
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Residues in contact with GLY 168 (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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119B ILE* 3.3 38.1 - - - +
123B LEU* 5.7 0.4 - - - -
164B THR 3.3 1.6 + - - -
165B VAL* 3.0 7.6 + - - -
167B ILE* 1.3 84.0 - - - +
169B LEU* 1.3 61.6 + - - +
170B SER 3.4 0.5 + - - -
171B LEU* 3.4 10.6 + - - +
183B PHE* 3.5 23.8 - - - -
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Residues in contact with LEU 169 (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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116B ALA* 5.7 5.8 - - + -
119B ILE* 6.3 0.2 - - + -
120B LEU* 5.9 8.1 - - + -
165B VAL* 2.9 40.2 + - + +
166B VAL* 3.9 9.2 - - - +
168B GLY* 1.3 76.2 - - - +
170B SER* 1.3 63.0 + - - +
171B LEU 3.2 1.1 + - - -
172B LEU* 3.4 45.9 + - + +
173B TRP* 3.9 8.3 + - - +
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Residues in contact with SER 170 (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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166B VAL 3.3 14.0 + - - -
167B ILE* 2.6 30.5 + - - +
168B GLY 3.2 0.4 - - - -
169B LEU* 1.3 71.8 - - - +
171B LEU* 1.3 57.3 + - - +
172B LEU 3.0 7.1 + - - -
173B TRP* 3.5 30.0 + - - +
174B ASN* 2.8 39.7 + - - +
179B SER* 4.4 7.3 + - - -
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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