Contacts of the helix formed by residues 148 - 159 (chain A) in PDB entry 2WWA
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A LEU* 4.4 17.7 - - + -
146A SER* 3.0 20.4 + - - +
147A VAL* 1.4 79.3 - - - +
149A GLN* 1.4 65.8 + - + +
150A ILE* 3.3 4.8 - - - +
151A GLY* 3.6 7.3 + - - -
152A LEU* 3.3 21.7 + - - +
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Residues in contact with GLN 149 (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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51A VAL* 4.4 13.5 - - + +
52A GLY* 4.1 25.3 - - - +
53A LEU* 4.5 13.1 - - - +
54A PRO* 3.5 27.9 - - - +
145A LEU* 4.9 8.1 - - + +
148A VAL* 1.4 79.3 - - + +
150A ILE* 1.4 59.2 + - - +
151A GLY 3.2 1.3 - - - -
152A LEU* 3.7 18.4 - - + +
153A ILE* 3.1 26.0 + - + +
156A GLN* 5.8 1.8 - - - +
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Residues in contact with ILE 150 (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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136A ILE* 4.0 44.3 - - + +
141A PHE* 6.4 0.2 - - + -
143A ASP* 4.9 3.8 - - - +
144A ASP* 4.4 8.7 - - + -
145A LEU* 3.6 43.2 - - + +
146A SER 3.2 31.2 - - - +
147A VAL* 3.9 6.7 - - + -
149A GLN* 1.4 78.6 - - - +
151A GLY* 1.4 59.4 + - - +
153A ILE* 3.5 15.5 - - + +
154A ASN* 2.9 14.9 - - - +
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Residues in contact with GLY 151 (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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147A VAL* 4.7 13.2 - - - -
148A VAL 3.6 8.3 + - - +
149A GLN 3.2 0.4 - - - -
150A ILE* 1.4 83.1 - - - +
152A LEU* 1.4 63.6 + - - +
154A ASN* 3.2 24.7 + - - +
155A PHE* 3.6 9.9 + - - +
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Residues in contact with LEU 152 (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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148A VAL 3.3 23.8 - - - +
149A GLN* 3.5 18.3 + - + +
150A ILE 3.5 0.2 - - - -
151A GLY* 1.4 76.4 - - - +
153A ILE* 1.4 64.3 + - - +
155A PHE* 3.3 19.9 + - + +
156A GLN* 3.2 34.6 + - + +
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Residues in contact with ILE 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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50A LEU* 3.9 22.2 - - + -
51A VAL 3.9 17.3 - - - +
52A GLY* 5.2 0.9 - - - -
55A LYS* 3.7 36.6 - - + -
136A ILE* 4.5 14.8 - - + -
141A PHE* 4.2 16.4 - - + -
149A GLN* 3.1 17.2 + - + +
150A ILE* 3.5 22.7 - - + +
152A LEU* 1.4 76.1 - - - +
154A ASN* 1.4 64.4 + - - +
156A GLN* 3.4 21.3 + - - +
157A LEU* 3.6 16.7 + - + +
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Residues in contact with ASN 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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129A VAL* 5.7 4.4 - - - +
132A THR* 3.3 46.5 + - + +
133A ASN* 3.9 19.4 + - - +
136A ILE* 4.1 6.1 - - + +
150A ILE 2.9 22.4 - - - +
151A GLY* 3.2 16.4 + - - +
153A ILE* 1.4 80.2 - - + +
155A PHE* 1.4 68.7 + - - +
157A LEU 3.8 0.2 + - - -
158A VAL* 3.4 22.0 + - - +
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Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLY 3.6 10.0 + - - +
152A LEU* 3.3 24.4 + - + +
154A ASN* 1.4 85.0 - - - +
156A GLN* 1.4 64.3 + - + +
158A VAL* 3.5 7.3 + - + +
159A GLY* 3.0 31.8 + - - -
71C PHE* 5.7 8.3 - + - -
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Residues in contact with GLN 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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50A LEU* 4.3 8.3 - - - +
51A VAL* 3.4 56.9 + - + +
79A LEU* 5.9 3.2 - - + +
149A GLN* 5.8 1.4 - - - +
152A LEU* 3.2 28.7 + - + +
153A ILE* 3.6 14.0 + - - +
154A ASN 3.4 0.4 - - - -
155A PHE* 1.4 83.3 - - + +
157A LEU* 1.4 65.0 + - + +
159A GLY 3.3 0.9 + - - -
160A ALA* 3.2 21.0 + - - +
71C PHE* 3.4 32.8 - - + -
75C VAL* 5.1 4.3 - - + +
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Residues in contact with LEU 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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50A LEU* 4.0 20.2 - - + -
78A THR 3.6 12.1 - - - +
79A LEU* 3.5 27.3 - - + +
80A LEU* 4.5 0.2 - - - -
81A GLU* 3.5 45.3 - - + +
82A PHE* 3.8 26.0 - - + -
128A TYR* 4.1 6.2 - - - -
132A THR* 4.1 9.6 - - - +
141A PHE* 5.8 1.1 - - + -
153A ILE* 3.6 17.6 + - + +
154A ASN 4.2 0.2 - - - +
155A PHE 3.4 0.4 - - - -
156A GLN* 1.4 83.7 - - + +
158A VAL* 1.4 59.3 + - - +
160A ALA 3.5 2.4 + - - -
161A GLY* 3.0 24.8 + - - -
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Residues in contact with VAL 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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125A ILE* 5.4 1.8 - - + +
128A TYR* 3.7 34.8 - - + +
129A VAL* 4.3 10.5 - - + +
132A THR* 3.4 24.5 - - + -
154A ASN* 3.4 18.3 + - - +
155A PHE* 3.5 8.6 + - + +
156A GLN 3.4 0.2 - - - -
157A LEU* 1.4 75.2 - - - +
159A GLY* 1.4 56.7 + - - +
160A ALA 3.2 0.4 - - - -
162A ILE* 3.0 50.7 + - + +
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Residues in contact with GLY 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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155A PHE* 3.0 23.2 + - - -
156A GLN* 3.3 6.0 + - - -
158A VAL* 1.4 75.3 - - - +
160A ALA* 1.4 57.3 + - - +
161A GLY 3.5 0.2 - - - -
162A ILE* 4.5 7.4 - - - +
163A PHE* 4.5 3.7 + - - +
67C LEU* 4.1 20.4 - - - +
71C PHE* 4.8 13.7 - - - -
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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