Contacts of the helix formed by residues 152 - 162 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLU* 1.3 97.3 - - + +
153A ASN* 1.3 70.0 + - - +
154A TYR* 3.2 8.3 - - + +
155A GLU* 3.2 13.4 + - + +
156A LYS* 2.9 23.5 + - - +
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Residues in contact with ASN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLU 5.3 0.5 - - - +
152A GLU* 1.3 73.7 + - - +
154A TYR* 1.3 58.5 + - - +
156A LYS* 3.2 24.8 + - - +
157A PHE* 2.8 31.6 + - - +
179A LEU 4.0 8.5 + - - +
180A GLY 3.8 20.0 + - - -
181A LEU* 3.7 22.1 - - + +
183A ASP* 5.8 4.3 - - - +
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Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLU* 3.2 6.0 - - + +
153A ASN* 1.3 78.6 - - - +
155A GLU* 1.3 60.2 + - - +
157A PHE* 3.3 5.5 + - - +
158A THR* 2.9 35.1 + - - -
183A ASP* 5.9 1.1 - - - -
185A ASP* 4.2 24.7 + - + -
186A THR* 3.8 30.5 - - + -
189A GLU* 4.6 1.8 + - - -
124C ASN* 4.8 4.3 + - - -
125C LEU* 4.9 6.2 - - - +
128C ARG* 3.0 48.7 + - - -
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS 5.0 0.5 - - - +
149A ASN 4.3 5.2 - - - +
150A SER* 3.4 32.3 + - - +
151A GLU* 3.4 8.1 + - - +
152A GLU* 3.2 16.4 + - + +
154A TYR* 1.3 79.7 - - - +
156A LYS* 1.3 65.7 + - - +
158A THR* 3.1 7.5 + - - -
159A GLU* 2.9 35.2 + - + +
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA 5.0 3.1 - - - +
84A LEU 4.9 5.4 + - - -
85A GLY* 5.6 3.6 - - - -
86A PRO* 5.9 2.2 - - - +
147A THR* 4.1 19.0 + - + +
150A SER* 3.6 29.3 - - - +
151A GLU 4.6 7.6 + - - -
152A GLU 2.9 11.5 + - - +
153A ASN* 3.5 33.7 + - - +
155A GLU* 1.3 74.8 - - - +
157A PHE* 1.3 58.3 + - - +
159A GLU* 3.3 2.7 + - - +
160A LEU* 2.8 38.5 + - + +
179A LEU* 4.5 30.6 + - + +
181A LEU* 4.7 10.8 - - + -
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Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASN 2.8 20.7 + - - +
154A TYR* 3.6 5.8 - - - +
156A LYS* 1.3 72.8 - - - +
158A THR* 1.3 59.6 + - - +
160A LEU* 3.8 3.3 - - + -
161A SER* 2.8 48.7 + - - -
172A ALA* 6.4 0.2 - - + -
176A THR* 3.5 26.7 - - - -
181A LEU* 4.0 25.7 - - + +
186A THR* 3.6 27.4 - - + -
189A GLU* 3.4 32.3 - - + -
190A VAL* 3.7 25.1 - - + -
193A ILE* 3.8 20.2 - - + -
128C ARG* 4.0 9.0 - - - -
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A TYR* 2.9 22.6 + - - -
155A GLU* 3.1 9.1 + - - -
157A PHE* 1.3 79.2 - - - +
159A GLU* 1.3 70.3 + - - +
161A SER* 3.4 15.7 - - - -
162A GLU* 3.8 11.9 + - - +
128C ARG* 2.9 43.3 + - - +
146C LYS* 5.9 3.4 - - - +
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LYS* 5.5 0.9 + - - -
143A ILE* 3.7 8.9 - - - +
146A LYS* 3.5 43.4 - - + +
147A THR* 4.0 14.8 - - - +
150A SER* 3.6 14.8 - - - +
155A GLU* 2.9 31.4 + - + +
156A LYS 4.0 2.5 - - - +
158A THR* 1.3 81.7 - - - +
160A LEU* 1.3 66.2 + - - +
162A GLU* 3.1 30.2 + - - +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 5.8 1.6 - - + -
83A ALA* 4.9 2.9 - - + -
143A ILE* 4.5 4.7 - - + -
147A THR* 3.4 33.7 - - + +
156A LYS* 2.8 28.3 + - + +
157A PHE* 4.0 5.2 - - + +
159A GLU* 1.3 72.5 - - - +
161A SER* 1.3 61.2 + - - +
163A LEU* 2.9 38.4 + - + +
172A ALA* 3.9 10.4 - - - +
175A PHE* 3.8 50.7 - - + -
176A THR* 6.2 0.2 - - - +
179A LEU* 4.4 8.1 - - + -
181A LEU* 3.9 18.8 - - + -
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Residues in contact with SER 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A PHE* 2.8 47.9 + - - -
158A THR* 3.4 10.5 - - - -
159A GLU 3.2 0.2 - - - -
160A LEU* 1.3 76.6 - - - +
162A GLU* 1.3 58.6 + - - +
164A CYS* 2.9 35.2 + - - +
165A GLY 4.3 0.2 + - - -
172A ALA* 4.8 0.4 - - - -
189A GLU* 5.0 1.2 + - - -
193A ILE* 3.8 8.6 - - - +
128C ARG* 5.4 0.4 + - - -
132C LEU* 4.1 18.9 - - - +
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LYS* 3.5 26.0 + - - +
143A ILE* 3.8 24.4 - - + +
146A LYS* 6.1 0.7 - - + -
158A THR* 4.1 10.3 - - - +
159A GLU* 3.3 25.1 - - - +
160A LEU 3.0 0.8 - - - -
161A SER* 1.3 75.5 - - - +
163A LEU* 1.3 64.7 + - - +
164A CYS 3.1 0.2 - - - -
165A GLY* 2.9 17.5 + - - +
166A LEU* 4.0 2.1 + - - +
131C LYS* 2.7 45.7 + - - +
162C GLU* 3.8 2.5 - - - +
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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