Contacts of the helix formed by residues 143 - 159 (chain A) in PDB entry 1HE9
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 GLY 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.4 27.1 - - - +
138A LEU* 3.9 3.8 - - - -
139A ALA 3.9 2.2 - - - -
140A SER 2.5 23.9 + - - -
141A GLY 3.4 0.6 - - - -
142A ASP* 1.3 70.6 - - - +
144A ALA* 1.3 65.2 + - - -
145A LEU 3.3 2.0 - - - -
146A ARG* 3.5 2.9 + - - +
147A SER* 2.8 28.9 + - - -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS 3.7 21.5 + - - +
120A ALA* 3.9 8.1 - - - +
122A GLU* 4.8 11.0 - - + +
123A LEU* 3.5 33.5 - - + +
137A ARG* 4.7 3.4 - - - +
138A LEU* 3.8 13.1 - - + +
142A ASP 3.8 0.2 + - - -
143A GLY* 1.3 71.5 - - - -
145A LEU* 1.3 66.2 + - - +
147A SER* 3.2 2.6 + - - -
148A LEU* 3.0 24.3 + - - +
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.2 39.3 - - + -
131A LEU* 5.1 2.2 - - + -
138A LEU* 2.9 40.6 + - + +
139A ALA* 3.9 2.5 - - + -
143A GLY 3.3 0.6 - - - -
144A ALA* 1.3 80.5 - - - +
146A ARG* 1.3 61.9 + - - +
148A LEU* 3.4 2.8 + - + +
149A SER* 3.3 22.0 + - - -
181A LEU* 4.8 8.5 - - + +
184A TRP* 3.3 53.6 - - + +
185A GLY* 4.0 3.6 + - - -
210A LEU* 4.0 22.0 - - + -
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Residues in contact with ARG 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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139A ALA 4.0 7.6 - - - +
140A SER* 4.1 20.9 - - - +
141A GLY* 4.2 20.6 + - - +
143A GLY 3.5 5.1 + - - +
144A ALA 3.3 0.6 - - - -
145A LEU* 1.3 77.5 - - - +
147A SER* 1.3 58.7 + - - +
149A SER* 3.1 4.7 + - - +
150A THR* 3.0 45.2 + - - +
185A GLY* 3.5 31.5 + - - +
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Residues in contact with SER 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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116A GLY* 3.7 25.7 - - - +
119A LYS* 3.9 21.6 - - - +
141A GLY 5.1 0.9 + - - -
142A ASP* 3.2 16.6 + - - -
143A GLY 2.8 19.3 + - - -
144A ALA 3.8 3.1 - - - -
146A ARG* 1.3 77.4 - - - +
148A LEU* 1.3 57.7 + - - +
150A THR* 3.9 6.4 - - - +
151A ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 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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116A GLY 4.7 0.4 - - - -
117A LEU* 4.0 11.9 - - + -
120A ALA* 3.9 13.6 - - + +
123A LEU* 3.8 20.9 - - + -
144A ALA 3.0 17.1 + - - +
145A LEU* 3.7 4.7 - - + +
147A SER* 1.3 76.7 - - - +
149A SER* 1.3 58.6 + - - +
151A ALA* 3.2 5.3 + - - +
152A LEU* 2.8 52.6 + - + +
181A LEU* 3.9 25.4 - - + -
210A LEU* 5.2 1.8 - - + -
213A VAL* 3.9 11.4 - - + -
214A MSE 3.9 17.9 - - + -
217A VAL* 3.9 20.4 - - + -
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Residues in contact with SER 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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145A LEU 3.3 11.4 + - - -
146A ARG* 3.1 13.7 + - - +
148A LEU* 1.3 76.2 - - - +
150A THR* 1.3 62.9 + - - +
152A LEU* 4.5 2.5 - - - -
153A ALA* 2.8 31.0 + - - +
172A LEU* 3.6 26.2 - - - +
181A LEU* 4.6 7.6 - - - -
182A GLN* 4.2 19.2 + - - -
185A GLY* 4.4 6.8 - - - -
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLY* 5.9 2.5 - - - -
146A ARG* 3.0 36.7 + - - +
147A SER* 3.9 8.1 - - - +
149A SER* 1.3 80.6 + - - +
151A ALA* 1.3 65.6 + - - +
153A ALA* 3.3 6.6 + - - +
154A GLY* 3.0 18.9 + - - -
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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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113A THR* 3.2 39.2 + - - +
116A GLY* 3.9 3.6 - - - -
117A LEU* 3.5 24.5 - - + +
147A SER 2.9 19.7 + - - +
148A LEU 3.5 0.7 - - - +
150A THR* 1.3 80.8 - - - +
152A LEU* 1.3 55.8 + - - +
154A GLY 2.9 15.8 + - - -
155A ILE* 2.9 15.4 + - - +
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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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117A LEU* 4.5 6.5 - - + -
148A LEU* 2.8 41.9 + - + +
149A SER 4.0 0.4 - - - +
151A ALA* 1.3 69.4 - - - +
153A ALA* 1.3 61.4 + - - +
155A ILE* 3.2 4.0 + - + +
156A ARG* 2.8 30.1 + - - +
168A ALA* 3.5 13.2 - - + +
171A LEU* 3.9 25.8 - - + -
172A LEU* 3.7 21.3 - - + -
181A LEU* 3.4 32.5 - - + -
217A VAL* 4.4 6.1 - - + -
220A LEU* 4.0 26.9 - - + -
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Residues in contact with ALA 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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149A SER 2.8 19.1 + - - +
150A THR* 3.7 6.7 - - - +
152A LEU* 1.3 76.6 - - - +
154A GLY* 1.3 56.7 + - - +
156A ARG* 3.3 6.6 + - - +
157A ALA* 3.0 30.1 + - - +
172A LEU* 3.5 17.8 - - + +
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Residues in contact with GLY 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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106A LEU* 4.9 2.9 - - - +
110A LEU* 4.2 4.3 - - - +
113A THR* 3.7 12.6 - - - -
150A THR 3.0 10.3 + - - -
151A ALA 2.9 8.2 + - - -
153A ALA* 1.3 72.8 - - - +
155A ILE* 1.3 62.1 + - - +
157A ALA* 4.6 2.7 - - - -
158A GLY* 2.7 29.9 + - - -
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Residues in contact with ILE 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 LEU* 4.0 6.7 - - + -
113A THR* 3.2 32.8 - - + -
117A LEU* 3.8 23.6 - - + -
151A ALA 2.9 17.9 + - - +
152A LEU* 3.7 7.2 - - - +
154A GLY* 1.3 78.3 - - - +
156A ARG* 1.3 63.7 + - - +
159A SER* 3.0 34.0 + - - -
164A SER* 3.8 23.1 - - - +
165A ARG* 4.1 1.6 - - - +
168A ALA* 3.9 4.7 - - + -
220A LEU* 4.0 15.7 - - + -
224A VAL* 3.8 28.0 - - + -
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Residues in contact with ARG 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 LEU 2.8 17.0 + - - +
153A ALA* 3.6 6.3 - - - +
155A ILE* 1.3 79.0 - - - +
157A ALA* 1.3 59.7 + - - +
165A ARG* 3.5 37.9 + - + +
168A ALA* 3.8 13.9 - - + +
169A GLY* 3.7 23.8 - - - +
172A LEU* 3.9 24.5 - - - +
173A GLU* 4.0 27.9 + - - +
182A GLN* 4.3 8.7 + - - -
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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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103A GLN* 4.2 13.3 - - - +
106A LEU* 3.6 34.9 - - + +
107A GLN* 4.9 2.8 - - - +
153A ALA 3.0 15.3 + - - +
154A GLY* 4.3 3.4 - - - +
156A ARG* 1.3 79.2 - - + +
158A GLY* 1.3 60.8 + - - +
159A SER 3.7 3.6 + - - +
165A ARG* 4.9 2.6 - - - -
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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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106A LEU* 3.6 25.1 - - - +
107A GLN* 3.2 29.2 - - - +
110A LEU* 3.9 11.8 - - - +
154A GLY 2.7 21.5 + - - -
157A ALA* 1.3 75.9 - - - +
159A SER* 1.3 58.8 + - - +
160A GLN* 3.8 0.9 + - - +
227A GLU* 4.5 1.2 - - - +
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Residues in contact with SER 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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107A GLN* 5.1 2.3 - - - +
110A LEU* 4.3 7.0 - - - -
154A GLY 4.2 0.2 + - - -
155A ILE* 3.0 32.3 + - - -
157A ALA 3.7 2.0 - - - +
158A GLY* 1.3 79.3 - - - +
160A GLN* 1.3 60.7 + - - +
161A VAL 3.0 16.9 + - - -
164A SER* 3.5 8.0 - - - -
165A ARG* 3.1 29.7 + - - +
224A VAL* 5.7 0.4 - - - -
227A GLU* 2.7 27.0 + - - -
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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