Contacts of the helix formed by residues 156 - 168 (chain A) in PDB entry 1Y24
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 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 5.9 3.8 - - + -
131A GLU* 4.7 15.9 - - - +
135A SER* 5.0 8.7 - - - +
154A ASP 4.7 3.6 - - - +
155A LEU* 1.3 77.3 - - - +
157A SER* 1.3 62.9 + - - +
158A SER 3.4 2.2 - - - -
159A LEU* 3.1 20.5 + - + +
160A ALA* 3.1 25.9 + - + -
177A PHE* 6.0 6.1 - - + -
204A ALA* 4.5 22.0 - - + +
207A GLU* 2.8 33.2 + - + +
208A GLY* 5.1 6.7 - - - +
218A LEU* 6.5 0.2 - - + -
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Residues in contact with SER 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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155A LEU* 3.5 24.6 - - - +
156A VAL* 1.3 73.7 - - - +
158A SER* 1.3 58.4 + - - +
160A ALA* 3.2 8.9 + - - +
161A ARG* 2.8 47.6 + - - +
207A GLU* 3.8 28.2 + - - +
210A ARG* 5.6 2.5 - - - +
211A ALA* 5.0 4.3 - - - -
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Residues in contact with SER 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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110A ASN* 5.1 5.5 + - - -
111A PHE* 3.8 12.6 - - - -
155A LEU* 3.6 22.5 + - - +
156A VAL 4.6 0.9 + - - -
157A SER* 1.3 73.7 - - - +
159A LEU* 1.3 62.0 + - - +
161A ARG* 3.4 28.2 + - - +
162A ARG* 2.9 30.5 + - - +
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Residues in contact with LEU 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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93A LEU* 4.3 0.9 - - + -
94A LEU* 5.1 4.5 - - + -
100A ARG* 3.4 48.0 - - - +
110A ASN* 5.5 1.3 - - - +
111A PHE* 3.8 16.3 - - + -
114A LEU* 3.7 9.0 - - + -
131A GLU* 4.0 17.7 - - - +
155A LEU 5.4 2.2 - - - +
156A VAL* 3.1 22.0 - - + +
158A SER* 1.3 80.1 + - - +
160A ALA* 1.3 62.1 - - - +
162A ARG* 3.3 5.5 + - - +
163A TYR* 3.1 62.3 + - + +
177A PHE* 6.2 1.1 - - + -
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Residues in contact with ALA 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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156A VAL* 3.1 18.8 + - + +
157A SER* 3.4 9.9 - - - +
159A LEU* 1.3 73.3 - - - +
161A ARG* 1.3 64.3 + - - +
163A TYR* 3.1 18.9 + - + +
164A ILE* 3.0 30.6 + - + +
172A VAL* 5.9 0.9 - - + -
177A PHE* 6.0 5.4 - - + -
208A GLY* 5.6 5.6 - - - -
211A ALA* 4.2 18.6 - - + -
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 4.3 8.5 - - - +
157A SER* 2.8 31.1 + - - +
158A SER* 3.4 32.4 - - - +
160A ALA* 1.3 71.0 - - - +
162A ARG* 1.3 55.6 + - - +
164A ILE* 3.2 12.8 + - + +
165A GLY* 2.8 26.5 + - - -
211A ALA* 4.8 14.1 - - + -
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Residues in contact with ARG 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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109A TYR* 3.0 36.8 + - - -
111A PHE* 3.4 55.8 - - + +
115A ASP* 4.2 5.2 - - - +
158A SER 2.9 7.3 + - - +
159A LEU 3.3 3.3 + - - +
161A ARG* 1.3 73.2 - - - +
163A TYR* 1.3 60.0 + - + +
165A GLY* 3.1 5.6 + - - -
166A ARG* 2.9 90.3 + - + +
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Residues in contact with TYR 163 (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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93A LEU* 3.4 29.3 - - - +
111A PHE* 5.9 1.6 - + - -
114A LEU* 3.4 15.7 - - + +
118A LEU* 3.4 32.7 - - + +
159A LEU* 3.1 45.2 + - + +
160A ALA* 3.1 16.1 + - - +
162A ARG* 1.3 75.6 - - + +
164A ILE* 1.3 56.6 + - - +
167A TYR* 2.8 48.6 + + - +
172A VAL* 3.4 25.2 - - + +
175A TRP* 3.8 17.0 - + + -
177A PHE* 4.5 17.8 - + - -
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Residues in contact with ILE 164 (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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160A ALA* 3.0 22.1 + - + +
161A ARG* 3.3 11.0 - - + +
163A TYR* 1.3 73.1 - - - +
165A GLY* 1.3 59.2 + - - +
168A GLY* 2.9 29.7 + - - -
169A LEU* 3.8 43.3 - - + +
172A VAL* 3.8 30.5 - - + -
211A ALA* 5.8 7.0 - - + +
212A ALA* 5.5 5.4 - - + -
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Residues in contact with GLY 165 (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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161A ARG 2.8 16.8 + - - -
162A ARG* 3.1 9.2 + - - -
164A ILE* 1.3 75.8 - - - +
166A ARG* 1.3 59.2 + - - +
168A GLY* 4.6 0.9 + - - -
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Residues in contact with ARG 166 (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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109A TYR* 5.2 0.2 + - - -
115A ASP* 3.5 29.8 + - - +
119A ASP* 3.1 28.3 + - - -
122A ARG* 5.5 0.4 - - - +
162A ARG* 2.9 56.4 + - - +
163A TYR 4.1 0.9 - - - +
165A GLY* 1.3 73.4 - - - +
167A TYR* 1.3 97.8 + - + +
168A GLY 3.6 0.2 - - - -
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Residues in contact with TYR 167 (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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114A LEU 4.0 0.2 + - - -
115A ASP* 3.3 11.5 + - - -
118A LEU* 3.3 39.6 - - + +
119A ASP* 2.8 23.9 + - - -
122A ARG* 3.1 40.8 - - - +
163A TYR* 2.8 35.6 + + - +
166A ARG* 1.3 100.7 - - + +
168A GLY* 1.3 61.0 + - - +
171A HIS* 3.2 25.2 - - + +
172A VAL* 3.8 10.5 - - + -
175A TRP* 3.5 19.3 - + - -
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Residues in contact with GLY 168 (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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164A ILE* 2.9 17.8 + - - -
165A GLY 4.6 0.6 + - - -
166A ARG 3.6 1.2 - - - -
167A TYR* 1.3 78.0 - - - +
169A LEU* 1.3 67.7 + - - +
170A ALA* 3.3 3.4 - - - -
171A HIS 3.0 14.3 + - - -
172A VAL* 3.1 12.3 + - - +
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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