Contacts of the helix formed by residues 146 - 158 (chain A) in PDB entry 1OMW
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 PHE 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A PHE* 4.3 12.3 - + - -
89A ILE* 3.4 31.1 - - + +
92A TYR* 3.8 28.0 - + + -
105A SER* 3.8 25.6 - - - -
108A ILE* 3.4 38.1 - - + -
109A PHE 4.7 0.7 - - - -
113A ILE* 4.4 8.1 - - + -
132A VAL* 4.3 28.5 - - + -
143A PRO 4.7 1.6 + - - +
144A ASP* 3.1 1.4 - - - +
145A LEU* 1.3 97.8 - - + +
147A GLN* 1.3 64.1 + - - +
148A PRO* 3.3 3.4 - - - -
149A TYR* 2.8 23.6 + + - +
150A ILE* 3.2 9.6 + - - +
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Residues in contact with GLN 147 (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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90A LYS* 5.2 1.2 - - - +
93A GLU* 4.4 6.3 + - - -
144A ASP* 3.2 24.8 + - + +
146A PHE* 1.3 75.4 - - - +
148A PRO* 1.3 72.4 - - + +
150A ILE* 2.9 54.7 + - - +
151A GLU* 3.4 27.3 + - - +
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Residues in contact with PRO 148 (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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128A ALA* 5.3 9.9 - - + -
131A HIS* 3.6 45.3 - - + +
132A VAL* 6.5 0.2 - - + -
144A ASP 4.4 0.9 - - - +
145A LEU 4.1 0.2 - - - +
146A PHE 3.4 3.4 - - - -
147A GLN* 1.3 96.2 - - + +
149A TYR* 1.3 65.5 + - + +
151A GLU* 3.9 14.1 + - - +
152A GLU* 3.4 27.1 + - - +
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Residues in contact with TYR 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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85A PHE* 3.5 33.7 - + + -
89A ILE* 4.2 5.6 - - + -
113A ILE* 3.7 15.7 - - + +
122A HIS* 3.1 13.8 + - - -
124A PHE* 3.4 36.8 - + + -
128A ALA* 3.3 32.5 - - + +
129A ILE* 3.0 32.6 - - - +
132A VAL* 3.4 27.1 - - + -
146A PHE* 2.8 17.5 + + + +
148A PRO* 1.3 81.4 - - + +
150A ILE* 1.3 67.4 + - - +
152A GLU* 3.9 2.5 - - - -
153A ILE* 3.0 28.9 + - - +
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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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86A TYR* 4.2 26.2 - - + +
89A ILE* 4.3 20.2 - - + -
90A LYS* 3.8 13.7 - - - +
93A GLU* 3.6 19.3 - - - +
146A PHE 3.2 6.3 + - - +
147A GLN* 2.9 46.4 + - - +
149A TYR* 1.3 77.1 - - - +
151A GLU* 1.3 72.5 + - + +
153A ILE* 2.8 25.6 + - - +
154A CYS* 3.1 13.0 + - - -
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Residues in contact with GLU 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 GLN* 3.4 37.0 + - - +
148A PRO* 4.1 12.4 - - - +
150A ILE* 1.3 85.6 - - + +
152A GLU* 1.3 57.3 + - + +
154A CYS* 3.2 9.9 + - - +
155A GLN* 3.1 24.8 + - - +
158A ARG* 4.5 3.5 + - - -
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Residues in contact with GLU 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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123A PRO 4.6 1.0 - - - +
124A PHE* 3.3 26.9 - - + -
125A SER* 2.4 51.4 + - - -
127A SER* 5.0 0.7 + - - -
128A ALA* 3.7 11.0 - - - +
148A PRO 3.4 16.6 + - - +
149A TYR 4.1 0.4 - - - +
150A ILE 3.0 1.0 + - - -
151A GLU* 1.3 77.1 - - + +
153A ILE* 1.3 60.3 + - - +
155A GLN* 3.3 9.4 + - - +
156A ASN* 2.9 31.2 + - - +
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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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82A LEU* 4.0 27.1 - - + +
85A PHE* 4.3 12.8 - - + -
86A TYR* 4.2 18.8 - - + +
89A ILE* 4.0 20.4 - - + -
124A PHE* 3.5 22.9 - - + -
149A TYR 3.0 23.1 + - - +
150A ILE* 2.8 10.7 + - - +
152A GLU* 1.3 73.2 - - - +
154A CYS* 1.3 63.8 + - - +
156A ASN* 2.9 6.7 + - - +
157A LEU* 2.8 50.7 + - + +
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Residues in contact with CYS 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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55A PHE* 3.9 24.6 - - + -
59A PHE* 4.7 12.8 - - - -
86A TYR* 4.9 4.9 - - - -
150A ILE* 3.1 21.8 + - - -
151A GLU* 3.2 8.7 + - - +
153A ILE* 1.3 87.3 - - - +
155A GLN* 1.3 57.3 + - - +
157A LEU* 3.1 6.9 + - - +
158A ARG* 2.7 49.8 + - - +
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Residues in contact with GLN 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 GLU 3.1 11.8 + - - +
152A GLU* 3.5 11.9 - - - +
153A ILE 3.2 0.2 - - - -
154A CYS* 1.3 77.9 - - - +
156A ASN* 1.3 65.5 + - - +
158A ARG* 2.6 48.0 + - - +
159A GLY* 4.5 3.3 + - - -
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Residues in contact with ASN 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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82A LEU* 3.7 27.7 - - + +
123A PRO* 3.0 46.4 + - - +
124A PHE* 4.0 5.7 - - - -
152A GLU* 2.9 16.5 + - - +
153A ILE 2.9 10.3 + - - +
155A GLN* 1.3 83.1 - - - +
157A LEU* 1.3 54.9 + - - -
158A ARG 3.6 0.2 - - - -
159A GLY 4.8 1.7 + - - -
160A ASP 5.8 0.2 + - - -
161A VAL* 3.3 18.5 - - - +
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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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55A PHE* 3.6 30.2 - - + -
59A PHE* 4.4 11.2 - - + -
68A PHE* 4.1 13.8 - - + -
79A ALA* 4.5 2.5 - - + +
82A LEU* 3.7 30.7 - - + +
83A VAL* 4.4 20.0 - - + -
86A TYR* 5.5 1.8 - - + -
153A ILE* 2.8 41.3 + - + +
154A CYS* 3.9 3.4 - - - +
156A ASN* 1.3 70.1 - - - +
158A ARG* 1.3 56.1 + - - +
159A GLY 3.3 5.4 - - - -
161A VAL* 3.6 20.4 - - + +
162A PHE* 3.2 26.3 + - - +
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Residues in contact with ARG 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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55A PHE* 3.8 33.0 - - + +
56A GLU* 5.3 13.6 + - - +
151A GLU 4.5 3.6 + - - -
154A CYS* 2.7 33.2 + - - +
155A GLN* 2.6 66.8 + - - +
157A LEU* 1.3 73.1 - - - +
159A GLY* 1.3 56.3 + - - +
162A PHE* 3.7 17.3 - - - +
163A GLN* 5.7 0.3 + - - -
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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