Contacts of the helix formed by residues 146 - 161 (chain A) in PDB entry 3IE7
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 THR 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A HIS* 3.8 15.7 - - - +
145A TYR* 1.3 77.1 - - - +
147A LEU* 1.3 59.8 + - - +
148A SER* 3.3 11.3 + - - -
149A ASP* 3.0 32.3 + - - +
150A PHE* 3.0 27.2 + - - +
172A TYR* 4.2 4.6 - - - -
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Residues in contact with LEU 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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146A THR* 1.3 75.7 - - - +
148A SER* 1.3 58.1 + - - +
150A PHE* 3.3 1.3 + - - +
151A LYS* 2.9 28.8 + - - +
171A GLU* 3.6 44.9 - - + +
172A TYR* 3.5 35.6 + - + +
175A LEU* 3.5 14.9 - - + +
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Residues in contact with SER 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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146A THR* 3.1 10.6 + - - -
147A LEU* 1.3 77.7 - - - +
149A ASP* 1.3 66.1 + - - +
151A LYS* 3.2 11.1 + - - +
152A GLU* 3.1 32.2 + - - +
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Residues in contact with ASP 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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115A GLN* 4.8 6.4 + - - +
118A LYS* 2.7 43.1 + - + +
122A LEU* 5.5 0.5 - - - +
144A HIS 3.7 0.5 - - - +
145A TYR* 3.6 24.2 + - + -
146A THR* 3.0 36.6 + - - +
148A SER* 1.3 78.9 + - - +
150A PHE* 1.3 61.9 + - - +
152A GLU* 3.2 20.6 + - - +
153A LEU* 3.1 20.6 + - - +
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Residues in contact with PHE 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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7A LEU* 4.1 17.3 - - + -
137A ILE* 3.9 22.4 - - + -
139A GLY 5.3 0.4 - - - -
141A PRO* 4.0 19.3 - - + -
145A TYR* 3.6 5.8 - + + -
146A THR 3.0 11.7 + - - +
147A LEU* 3.6 8.1 - - - +
148A SER 3.2 0.2 - - - -
149A ASP* 1.3 73.3 - - - +
151A LYS* 1.3 66.5 + - - +
153A LEU* 3.1 10.2 + - + +
154A LEU* 2.9 55.9 + - + +
168A ASN* 3.7 32.1 - - - -
172A TYR* 3.6 43.5 - + + -
175A LEU* 4.1 8.5 - - + -
176A ALA* 4.9 1.6 - - + -
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Residues in contact with LYS 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 LEU 2.9 14.9 + - - +
148A SER* 3.4 13.7 - - - +
149A ASP 3.2 0.2 - - - -
150A PHE* 1.3 75.7 - - - +
152A GLU* 1.3 57.8 + - + +
154A LEU* 3.3 5.9 + - - +
155A ARG* 2.9 62.1 + - - +
175A LEU* 3.8 31.7 - - + +
179A MSE 3.5 26.0 - - - +
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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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115A GLN* 5.1 5.2 + - - -
118A LYS* 6.0 1.6 - - - +
119A ASP* 5.0 5.2 - - - +
122A LEU* 3.9 23.8 - - + +
148A SER* 3.1 22.0 + - - +
149A ASP* 3.2 20.1 + - - +
151A LYS* 1.3 76.0 - - + +
153A LEU* 1.3 55.5 + - - +
155A ARG* 3.4 12.9 + - - +
156A THR* 2.8 38.0 + - - -
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Residues in contact with LEU 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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5A ILE* 4.3 9.2 - - + -
7A LEU* 3.9 25.8 - - + -
121A LEU* 4.1 11.4 - - + -
122A LEU* 3.7 17.0 - - + +
125A ILE* 3.4 32.8 - - + -
137A ILE* 3.9 24.2 - - + -
145A TYR* 3.7 23.6 - - - +
149A ASP 3.1 6.4 + - - +
150A PHE* 3.1 17.0 + - + +
152A GLU* 1.3 75.9 - - - +
154A LEU* 1.3 63.4 + - - +
156A THR* 3.2 3.5 + - - -
157A VAL* 3.0 27.1 + - + +
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Residues in contact with LEU 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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137A ILE* 3.7 26.2 - - + -
150A PHE* 2.9 41.6 + - + +
151A LYS 3.7 3.4 - - - +
153A LEU* 1.3 75.0 - - - +
155A ARG* 1.3 57.9 + - - +
157A VAL* 3.3 6.0 + - - +
158A LYS* 2.9 36.0 + - + +
164A LEU* 4.1 12.3 - - + +
166A CYS* 3.7 20.4 - - - -
175A LEU* 4.2 5.8 - - + -
176A ALA* 3.6 29.4 - - - +
179A MSE 3.9 25.1 - - + -
181A VAL* 4.6 1.3 - - + -
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Residues in contact with ARG 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 LYS* 2.9 58.0 + - - +
152A GLU* 3.7 12.5 - - - +
154A LEU* 1.3 79.0 - - - +
156A THR* 1.3 63.2 + - - +
158A LYS* 3.2 7.5 + - + +
159A ALA* 3.0 24.7 + - + +
179A MSE 4.3 20.2 - - + +
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Residues in contact with THR 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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122A LEU* 3.5 50.7 - - + +
125A ILE* 4.0 15.0 - - + -
126A ALA* 4.4 9.2 - - + +
152A GLU* 2.8 21.6 + - - +
153A LEU 3.6 4.7 - - - -
155A ARG* 1.3 76.2 - - - +
157A VAL* 1.3 64.0 + - - +
159A ALA* 3.4 13.2 + - - +
160A THR* 3.4 16.3 + - - +
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Residues in contact with VAL 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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5A ILE* 4.4 5.6 - - + -
125A ILE* 4.2 25.8 - - + -
135A VAL* 3.9 32.8 - - + -
137A ILE* 4.6 7.2 - - + -
153A LEU* 3.0 17.2 + - + +
154A LEU 3.6 6.3 - - - +
156A THR* 1.3 76.2 - - - +
158A LYS* 1.3 61.6 + - - +
160A THR* 2.7 32.6 + - - +
161A GLY 3.8 1.4 + - - -
162A ALA* 4.3 6.5 + - + +
164A LEU* 3.7 33.4 - - + -
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Residues in contact with LYS 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 LEU* 2.9 19.8 + - + +
155A ARG* 3.2 6.5 + - + +
157A VAL* 1.3 77.7 - - - +
159A ALA* 1.3 61.6 + - - +
161A GLY* 3.1 15.2 + - - -
162A ALA 5.5 3.6 - - - -
164A LEU* 4.1 16.8 - - + -
179A MSE 2.5 59.6 + - + +
180A GLY 3.7 16.2 - - - +
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Residues in contact with ALA 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 ARG* 3.0 17.5 + - + +
156A THR* 3.7 8.5 - - - +
157A VAL 3.2 0.2 - - - -
158A LYS* 1.3 76.4 - - - +
160A THR* 1.3 62.6 + - + +
161A GLY* 3.4 0.7 + - - -
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Residues in contact with THR 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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125A ILE* 4.2 16.2 - - + +
126A ALA* 4.7 7.9 - - - +
129A VAL* 3.6 39.0 - - + +
130A LYS* 4.7 0.3 - - - -
131A LYS* 3.3 25.6 + - - +
156A THR 3.4 17.0 - - - +
157A VAL* 2.7 15.8 + - - +
159A ALA* 1.3 77.3 - - + +
161A GLY* 1.3 57.0 + - - +
162A ALA* 3.1 19.6 + - - +
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Residues in contact with GLY 161 (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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131A LYS* 3.5 17.6 - - - +
158A LYS 3.1 14.7 + - - -
159A ALA 3.2 1.9 - - - -
160A THR* 1.3 77.7 + - - +
162A ALA* 1.3 66.6 + - - +
163A PHE 3.8 0.5 + - - -
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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