Contacts of the helix formed by residues 150 - 158 (chain A) in PDB entry 1Y88
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A MET* 4.0 18.6 - - + -
13A ARG* 3.3 42.6 - - + -
14A LEU* 4.0 13.9 - - + -
17A GLU* 4.1 2.2 - - - -
122A LEU* 3.6 21.3 - - + -
127A LEU* 3.7 38.1 - - + -
128A TYR 3.3 14.1 - - - +
129A PRO* 3.9 8.1 - - + -
130A ILE* 3.4 12.2 - - - +
149A VAL* 1.3 97.2 - - + +
151A CYS* 1.3 66.6 + - - +
152A ARG* 3.9 7.4 - - + -
153A ASP* 2.9 24.1 + - - +
154A VAL 3.5 1.7 + - - -
201A CL 3.8 11.9 - - + -
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Residues in contact with CYS 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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128A TYR* 2.8 32.0 + - + +
129A PRO 4.3 1.6 - - - -
130A ILE* 3.7 5.6 - - - +
132A ILE* 3.9 20.2 - - - -
133A LEU* 3.9 22.7 - - - -
150A PHE* 1.3 70.9 - - - +
152A ARG* 1.3 62.4 + - - +
154A VAL* 3.1 15.8 + - - +
155A VAL* 3.3 9.7 + - - +
179A ALA* 3.7 14.8 - - + +
182A VAL* 4.1 9.2 - - - -
183A ILE* 3.7 22.2 - - + -
201A CL 3.6 4.9 - - + +
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Residues in contact with ARG 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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13A ARG* 4.6 7.2 - - - +
17A GLU* 5.5 1.8 + - - -
125A LYS* 3.0 26.7 + - - +
126A GLY* 3.5 15.0 + - - -
127A LEU* 3.4 23.6 - - - +
150A PHE* 3.9 7.2 - - + -
151A CYS* 1.3 76.6 - - - +
153A ASP* 1.3 70.5 + - - +
155A VAL* 3.3 5.4 + - - +
156A SER* 2.9 31.3 + - - -
183A ILE* 3.6 13.2 - - + +
201A CL 3.1 15.7 - - + +
308A SO4 3.2 30.3 + - - -
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Residues in contact with ASP 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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13A ARG* 2.7 47.8 + - - -
147A GLY 4.3 2.7 - - - -
148A LEU* 3.8 26.8 - - + +
149A VAL 3.0 5.5 + - - -
150A PHE* 2.9 31.0 + - - +
152A ARG* 1.3 80.2 - - - +
154A VAL* 1.3 59.5 + - - +
156A SER* 3.6 7.5 + - - -
157A ALA* 2.9 32.4 + - - +
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Residues in contact with VAL 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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130A ILE* 3.8 28.0 - - + -
133A LEU* 4.5 4.7 - - + -
143A LEU* 4.4 13.9 - - + -
148A LEU* 4.7 10.8 - - + -
150A PHE 4.0 1.1 - - - +
151A CYS* 3.1 8.4 + - - +
153A ASP* 1.3 76.9 - - - +
155A VAL* 1.3 61.1 + - - +
157A ALA* 3.4 6.4 + - - +
158A GLY 3.3 17.2 + - - -
162A LEU* 4.1 8.3 - - + +
175A VAL* 3.6 40.2 - - + +
176A ILE* 4.0 24.3 - - + +
179A ALA* 4.0 4.7 - - + -
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Residues in contact with VAL 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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151A CYS 3.3 12.6 + - - +
152A ARG* 3.7 9.0 - - - +
153A ASP 3.3 0.2 - - - -
154A VAL* 1.3 78.6 - - - +
156A SER* 1.3 63.8 + - - +
157A ALA 3.4 0.2 + - - -
158A GLY* 3.5 10.6 + - - -
176A ILE* 4.5 10.9 - - + +
179A ALA* 4.0 15.9 - - + -
180A LYS* 4.0 33.9 - - + -
183A ILE* 4.2 12.8 - - + -
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Residues in contact with SER 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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152A ARG 2.9 17.4 + - - -
153A ASP* 3.6 10.0 + - - -
155A VAL* 1.3 75.9 - - - +
157A ALA* 1.3 65.9 + - - +
158A GLY* 4.5 0.6 - - - -
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Residues in contact with ALA 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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148A LEU* 3.8 28.0 - - + -
153A ASP 2.9 19.8 + - - +
154A VAL 3.6 4.9 - - - +
155A VAL 3.3 0.2 - - - -
156A SER* 1.3 79.8 + - - +
158A GLY* 1.3 60.0 + - - +
160A GLU* 5.7 0.2 - - - +
161A LYS* 3.2 33.7 + - + +
162A LEU* 4.2 5.2 - - + -
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Residues in contact with GLY 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 VAL 3.3 7.9 + - - -
155A VAL 3.5 10.5 + - - -
156A SER 3.4 1.6 - - - -
157A ALA* 1.3 78.5 - - - +
159A GLU* 1.3 68.5 + - - -
160A GLU* 3.1 4.3 - - - -
161A LYS 3.0 12.5 + - - -
162A LEU* 3.1 12.9 + - - +
176A ILE* 3.8 7.4 - - - -
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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