Contacts of the helix formed by residues 145 - 155 (chain A) in PDB entry 1SHZ
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 TYR 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ILE* 4.2 9.6 - - + -
121A LYS* 3.1 46.2 + - + +
122A LEU* 3.6 25.1 - - + -
124A ALA* 4.5 2.4 - - - +
125A PHE* 3.5 39.1 + + + -
141A VAL* 3.3 32.1 - - + -
142A PHE* 2.8 8.1 + - + +
144A GLN* 1.3 86.1 - - + +
146A LEU* 1.3 64.7 + - - +
147A PRO* 3.2 4.3 - - - -
148A ALA* 3.0 8.4 + - + +
149A ILE* 3.0 36.9 + - + +
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Residues in contact with LEU 146 (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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142A PHE* 3.1 38.2 + - + +
143A LEU* 4.1 17.0 - - + +
145A TYR* 1.3 76.8 - - - +
147A PRO* 1.3 65.1 - - + +
149A ILE* 3.2 7.3 + - + +
150A ARG* 2.9 59.2 + - - +
181A LEU* 3.8 28.7 - - + +
185A GLY* 3.6 29.2 - - - +
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Residues in contact with PRO 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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118A HIS* 4.2 8.1 - - + -
121A LYS* 5.9 3.1 - - - +
143A LEU 3.7 13.5 - - - +
144A GLN 4.3 4.3 - - - +
145A TYR* 3.4 4.9 - - - +
146A LEU* 1.3 95.2 - - + +
148A ALA* 1.3 61.2 + - - +
150A ARG* 3.6 9.0 + - + +
151A ALA* 3.3 23.0 + - - +
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Residues in contact with ALA 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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118A HIS* 3.4 44.4 + - - +
121A LYS* 4.3 21.9 - - + +
122A LEU* 4.9 5.2 - - + -
145A TYR* 3.0 8.0 + - - +
147A PRO* 1.3 80.2 - - - +
149A ILE* 1.3 59.0 + - - +
151A ALA* 3.8 0.5 - - - +
152A LEU* 2.9 39.4 + - + +
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Residues in contact with ILE 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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92A VAL* 4.4 9.6 - - + -
93A ILE* 4.7 8.5 - - + -
96A MET* 4.2 9.7 - - + +
122A LEU* 4.1 27.1 - - + -
142A PHE* 4.4 20.0 - - + -
145A TYR* 3.0 36.0 + - + +
146A LEU* 3.2 11.0 + - + +
148A ALA* 1.3 75.4 - - - +
150A ARG* 1.3 64.9 + - - +
152A LEU* 3.9 4.5 - - - +
153A TRP* 3.0 23.4 + - - +
178A LEU* 3.8 19.7 - - + -
181A LEU* 3.6 22.7 - - + -
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Residues in contact with ARG 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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146A LEU* 2.9 48.1 + - + +
147A PRO* 4.0 7.0 - - + +
149A ILE* 1.3 75.2 - - - +
151A ALA* 1.3 63.3 + - - +
153A TRP* 3.2 4.5 + - - +
154A GLU* 3.2 25.3 + - - +
181A LEU* 3.8 40.3 + - + +
182A ASP* 3.4 26.9 + - - +
185A GLY* 4.6 4.6 - - - -
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Residues in contact with ALA 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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114A LYS* 5.0 2.5 - - - +
115A ASN* 3.7 12.6 + - - +
118A HIS* 3.6 31.6 - - + +
147A PRO 3.3 15.2 + - - +
148A ALA 3.8 0.7 - - - +
150A ARG* 1.3 75.9 - - - +
152A LEU* 1.3 65.9 + - - +
153A TRP 3.0 2.6 + - - -
154A GLU* 3.1 14.0 + - - +
155A ASP* 3.2 12.3 + - - +
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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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96A MET* 4.4 12.1 - - + -
100A VAL* 4.4 5.8 - - + -
110A TRP* 3.4 26.7 - - + -
115A ASN* 3.3 29.8 - - + +
118A HIS* 3.5 23.3 - - + +
119A GLY* 3.9 5.8 - - - +
122A LEU* 3.3 31.0 - - + -
148A ALA 2.9 29.5 + - - +
149A ILE 4.2 2.7 - - - +
151A ALA* 1.3 73.3 - - - +
153A TRP* 1.3 59.1 + - - +
155A ASP* 3.4 9.0 - - - +
158A ILE* 3.0 34.7 - - + +
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Residues in contact with TRP 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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96A MET* 3.7 11.4 - - + -
99A LEU* 4.0 16.8 - - + -
149A ILE 3.0 20.7 + - - +
150A ARG* 3.4 7.4 - - - +
151A ALA 3.0 0.4 - - - -
152A LEU* 1.3 79.5 - - - +
154A GLU* 1.3 79.0 + - - +
155A ASP 3.6 1.2 + - - +
158A ILE* 4.1 8.4 - - + +
159A GLN* 3.5 39.3 + - - +
162A TYR* 4.6 21.3 - + + -
175A LYS* 4.5 18.6 - - + -
178A LEU* 3.0 66.8 + - + -
179A ASP* 3.4 21.5 + - - -
181A LEU* 4.7 4.9 - - + -
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Residues in contact with GLU 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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150A ARG 3.2 14.8 + - - +
151A ALA* 3.1 6.9 + - - +
153A TRP* 1.3 94.8 + - - +
155A ASP* 1.3 68.4 + - - +
156A SER* 3.5 1.7 + - - -
159A GLN* 4.2 11.2 + - - +
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Residues in contact with ASP 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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110A TRP* 3.5 20.0 - - + -
111A GLY 3.2 10.9 + - - -
112A ASP* 3.2 21.9 + - - +
115A ASN* 2.6 31.5 + - + +
151A ALA 3.2 5.5 + - - +
152A LEU* 3.4 17.9 - - - +
153A TRP 3.2 3.0 - - - +
154A GLU* 1.3 81.4 - - - +
156A SER* 1.3 64.3 + - - +
157A GLY* 3.1 19.8 + - - -
158A ILE* 3.5 9.2 + - + +
159A GLN* 3.5 20.3 + - - +
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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