Contacts of the helix formed by residues 152 - 161 (chain B) in PDB entry 5W4A
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 GLU 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B GLU* 1.3 88.7 + - + +
153B ASN* 1.3 67.4 + - - +
154B TYR* 3.3 7.4 - - + +
155B GLU* 3.3 13.6 + - + +
156B LYS* 3.0 23.0 + - - +
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Residues in contact with ASN 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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151B GLU 5.6 0.2 - - - +
152B GLU* 1.3 75.9 + - - +
154B TYR* 1.3 58.3 + - - +
156B LYS* 3.6 11.1 - - - +
157B PHE* 2.8 31.2 + - - +
179B LEU 4.3 6.8 + - - +
180B GLY 4.2 12.3 + - - -
181B LEU* 3.7 28.4 - - + +
183B ASP* 5.9 2.5 - - - +
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Residues in contact with TYR 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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152B GLU* 3.3 5.3 - - + +
153B ASN* 1.3 78.5 - - - +
155B GLU* 1.3 60.9 + - - +
157B PHE* 3.4 7.0 + + - +
158B THR* 2.9 45.8 + - - -
183B ASP* 5.5 2.7 - - - +
185B ASP* 4.2 23.9 + - + -
186B THR* 3.7 29.4 - - + -
189B GLU* 4.6 14.1 + - - -
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Residues in contact with GLU 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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146B LYS 5.2 0.5 - - - +
149B ASN 4.4 4.4 - - - +
150B SER* 3.5 22.3 + - - +
151B GLU* 3.1 24.1 + - - +
152B GLU* 3.3 15.2 + - + +
154B TYR* 1.3 79.1 - - - +
156B LYS* 1.3 66.2 + - - +
158B THR* 3.1 8.1 + - - -
159B GLU* 2.9 34.7 + - + +
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Residues in contact with LYS 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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82B LEU 5.0 0.6 + - - -
83B ALA 2.8 29.3 + - - -
84B LEU 3.9 14.5 + - - -
85B GLY* 4.0 7.7 - - - +
86B PRO* 5.4 1.8 - - - +
147B THR* 3.6 33.7 - - + +
148B ILE* 5.9 0.7 - - - +
150B SER* 3.6 17.2 - - - +
151B GLU 6.1 0.2 - - - -
152B GLU 3.0 18.0 + - - +
153B ASN* 3.2 13.0 + - - +
155B GLU* 1.3 75.0 - - - +
157B PHE* 1.3 58.5 + - - +
159B GLU* 3.3 2.5 + - - +
160B LEU* 2.9 40.6 + - + +
179B LEU* 3.9 20.5 - - + +
181B LEU* 4.9 7.2 - - + -
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Residues in contact with PHE 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 ASN 2.8 17.4 + - - +
154B TYR* 3.6 9.2 - + - +
156B LYS* 1.3 73.8 - - - +
158B THR* 1.3 64.9 + - - +
160B LEU* 3.4 3.9 + - + -
161B SER* 2.8 50.5 + - - -
172B ALA* 6.4 0.2 - - + -
176B THR* 3.6 25.8 - - - -
181B LEU* 4.1 28.8 - - + +
186B THR* 3.6 27.1 - - + -
189B GLU* 3.4 32.3 - - + -
190B VAL* 3.7 25.1 - - + -
193B ILE* 3.9 17.3 - - + -
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Residues in contact with THR 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 TYR* 2.9 34.9 + - - -
155B GLU* 3.1 11.6 + - - -
157B PHE* 1.3 81.1 - - - +
159B GLU* 1.3 72.1 + - - +
161B SER* 3.4 16.9 + - - -
162B GLU* 3.8 12.3 + - - +
189B GLU* 5.6 1.4 + - - -
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Residues in contact with GLU 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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131B LYS* 5.7 0.2 + - - -
143B ILE* 3.7 9.2 - - - +
146B LYS* 3.6 49.1 + - + +
147B THR* 4.1 6.3 - - - +
150B SER* 3.6 16.8 - - - +
155B GLU* 2.9 30.0 + - + +
156B LYS 3.9 2.7 - - - +
158B THR* 1.3 82.7 - - - +
160B LEU* 1.3 63.9 + - - +
162B GLU* 3.1 31.2 + - - +
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Residues in contact with LEU 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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18B PHE* 5.7 2.0 - - + -
83B ALA* 5.0 1.3 - - + -
143B ILE* 4.6 2.9 - - + -
147B THR* 3.4 29.2 - - + +
156B LYS* 2.9 32.7 + - + +
157B PHE* 3.9 5.8 - - + +
159B GLU* 1.3 75.5 - - - +
161B SER* 1.3 57.2 + - - +
163B LEU* 2.9 43.0 + - + +
172B ALA* 3.9 10.1 - - + +
175B PHE* 3.7 46.0 - - + -
176B THR* 6.1 0.4 - - - +
179B LEU* 4.5 5.2 - - + -
181B LEU* 3.8 26.0 - - + -
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Residues in contact with SER 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 PHE* 2.8 47.4 + - - -
158B THR* 3.4 10.9 - - - -
159B GLU 3.1 0.6 - - - -
160B LEU* 1.3 76.5 - - - +
162B GLU* 1.3 63.7 + - - +
164B CYS* 3.0 26.3 + - - +
165B GLY 4.3 0.3 + - - -
172B ALA* 4.8 0.7 - - - -
189B GLU* 5.1 1.8 + - - +
193B ILE* 3.8 16.1 - - - +
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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