Contacts of the helix formed by residues 150 - 159 (chain B) in PDB entry 2W5X
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 LEU 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B ALA* 4.5 2.9 - - + -
146B LEU* 4.3 14.1 - - + +
147B ASN* 2.9 39.2 + - + +
148B ARG 3.1 1.0 - - - -
149B GLY* 1.3 75.4 - - - +
151B GLU* 1.3 59.2 + - - +
152B GLU 3.4 2.0 - - - -
153B GLU* 3.1 36.7 + - + +
154B ILE* 2.9 29.7 + - - +
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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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132B SER* 4.2 2.6 + - - -
134B THR* 2.6 46.0 + - - +
135B GLU* 3.6 14.4 + - - +
148B ARG 3.7 14.8 - - - +
149B GLY* 2.9 13.6 + - - +
150B LEU* 1.3 70.4 - - - +
152B GLU* 1.3 61.8 + - - +
154B ILE* 3.5 5.8 - - - +
155B ALA* 2.9 28.6 + - - +
173B TYR* 3.5 39.1 + - + -
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Residues in contact with GLU 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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150B LEU 3.4 0.6 - - - -
151B GLU* 1.3 74.6 - - - +
153B GLU* 1.3 65.4 + - - +
155B ALA* 3.4 2.0 + - - -
156B MET* 3.1 10.4 + - - +
173B TYR* 4.4 15.7 - - + +
176B LYS 4.6 0.7 - - - +
177B ARG* 2.8 59.7 + - + +
178B LYS* 2.8 55.8 + - - +
179B ASP* 3.7 13.6 + - - +
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Residues in contact with GLU 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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144B HIS 3.9 5.9 - - - +
145B ALA* 3.5 24.1 - - + +
146B LEU 4.8 0.5 + - - -
150B LEU* 3.1 38.4 + - + +
152B GLU* 1.3 78.1 - - - +
154B ILE* 1.3 58.4 + - - +
156B MET* 3.3 7.2 + - + +
157B ASP* 2.9 39.0 + - - +
177B ARG* 5.2 0.9 - - - +
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Residues in contact with ILE 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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102B ILE* 4.3 16.2 - - + -
134B THR* 3.8 21.8 - - - +
139B ALA* 3.6 24.0 - - + -
142B TYR* 3.4 28.2 - - + +
143B ALA* 4.1 8.7 - - + -
145B ALA* 4.2 17.3 - - + -
148B ARG* 3.9 20.2 - - - +
150B LEU 2.9 19.0 + - - +
151B GLU* 3.2 8.3 + - - +
153B GLU* 1.3 78.0 - - - +
155B ALA* 1.3 62.4 + - - +
157B ASP* 3.1 17.9 + - - +
158B MET 3.1 10.0 + - - -
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Residues in contact with ALA 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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134B THR* 3.9 11.2 - - + +
142B TYR* 5.0 0.4 - - - -
151B GLU 2.9 16.5 + - - +
152B GLU 3.6 3.8 - - - +
154B ILE* 1.3 76.6 - - - +
156B MET* 1.3 62.2 + - - +
158B MET* 3.0 21.6 + - - +
159B THR 3.8 1.6 + - - -
173B TYR* 3.4 26.0 - - + +
174B PHE* 3.6 33.7 - - + -
177B ARG* 3.7 1.3 - - - +
183B VAL* 4.0 3.4 - - - +
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Residues in contact with MET 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 GLU 3.1 13.6 + - - +
153B GLU* 3.5 11.2 - - - +
155B ALA* 1.3 76.4 - - - +
157B ASP* 1.3 62.0 + - - +
159B THR* 2.7 33.2 + - - -
160B GLU* 3.8 15.7 - - - +
177B ARG* 4.0 9.7 - - - +
181B LYS* 4.0 29.8 - - + +
183B VAL* 3.9 28.7 - - + -
186B ILE* 3.9 26.5 - - + -
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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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142B TYR* 4.4 3.4 - - - +
143B ALA* 3.4 31.2 - - + +
144B HIS 3.6 20.7 + - - +
145B ALA* 4.7 1.2 - - - +
153B GLU* 2.9 31.8 + - - +
154B ILE* 3.1 14.8 + - - +
156B MET* 1.3 73.3 - - - +
158B MET* 1.3 66.3 + - - +
160B GLU* 2.9 28.8 + - - +
161B SER* 3.1 12.5 + - - -
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Residues in contact with MET 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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133B ILE* 4.0 12.1 - - + -
142B TYR* 3.4 50.9 - - + +
154B ILE 3.1 5.1 + - - -
155B ALA 3.0 18.2 + - - +
157B ASP* 1.3 75.9 - - - +
159B THR* 1.3 59.7 + - - +
161B SER* 2.9 25.2 + - - +
163B LEU* 3.7 28.5 - - + -
166B PHE* 3.8 33.0 - - + -
174B PHE* 4.2 10.8 - - + -
187B LEU* 3.7 21.0 - - + +
192B PHE* 4.5 6.8 - - - -
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Residues in contact with THR 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 4.1 1.6 - - - +
156B MET* 2.7 24.1 + - - +
157B ASP 3.0 1.2 - - - -
158B MET* 1.3 77.9 - - - +
160B GLU* 1.3 64.6 + - - +
161B SER 3.4 2.7 - - - +
183B VAL* 3.5 32.3 - - + -
186B ILE* 3.7 28.8 - - + +
187B LEU* 3.8 26.5 - - + +
190B ASN* 3.2 32.5 + - - +
192B PHE* 5.6 2.2 - - - -
210B LYS* 5.9 0.2 + - - -
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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