Contacts of the helix formed by residues 158 - 174 (chain A) in PDB entry 3E0D
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 ARG 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A PHE* 3.1 21.6 + - + +
156A GLN* 3.1 21.5 - - + +
157A ASP* 1.3 79.2 - - - +
159A LEU* 1.3 63.3 + - - +
160A ASP* 3.2 34.2 + - - +
161A LEU* 3.2 52.4 + - + +
162A ALA 3.2 9.0 + - - -
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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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154A ILE* 4.3 24.7 - - + +
157A ASP* 3.3 12.0 + - - +
158A ARG* 1.3 73.6 - - - +
160A ASP* 1.3 56.6 + - - +
162A ALA* 3.6 6.2 - - - +
163A GLU* 3.0 32.9 + - - +
191A LYS* 6.4 0.4 - - - -
195A VAL* 3.9 34.5 - - + -
199A PHE* 4.1 6.9 - - + -
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Residues in contact with ASP 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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158A ARG* 3.3 44.1 + - - -
159A LEU* 1.3 75.9 + - - +
161A LEU* 1.3 68.5 + - - +
163A GLU* 4.2 4.4 - - - +
164A ALA* 3.1 28.8 + - - +
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Residues in contact with LEU 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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153A PHE* 3.5 40.1 - - + -
156A GLN* 5.8 0.4 - - - +
158A ARG* 3.2 53.5 + - + +
160A ASP* 1.3 86.1 + - - +
162A ALA* 1.3 55.7 + - - +
164A ALA* 3.4 7.1 + - + +
165A ARG* 2.7 37.9 + - - +
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Residues in contact with ALA 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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150A ILE* 3.9 19.7 - - + +
153A PHE* 3.5 29.3 - - + +
154A ILE* 4.0 15.5 - - + -
158A ARG 3.2 6.1 + - - +
159A LEU* 3.3 9.4 + - - +
161A LEU* 1.3 75.7 - - - +
163A GLU* 1.3 53.8 + - - +
165A ARG* 3.3 3.0 + - - +
166A LEU* 2.8 33.3 + - - +
199A PHE* 4.1 10.3 - - + -
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Residues in contact with GLU 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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159A LEU 3.0 16.5 + - - +
160A ASP* 4.2 5.2 - - - +
162A ALA* 1.3 72.5 - - - +
164A ALA* 1.3 60.3 + - - +
166A LEU* 3.1 6.0 + - + +
167A ASN* 2.8 36.8 + - - +
199A PHE* 3.7 30.2 - - + -
202A LYS* 2.7 30.3 + - - -
203A TYR* 2.5 36.3 + - + +
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Residues in contact with ALA 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 ASP 3.1 20.4 + - - +
161A LEU* 3.5 8.7 - - + +
163A GLU* 1.3 77.2 - - - +
165A ARG* 1.3 58.5 + - - +
167A ASN* 3.5 11.4 + - - +
168A GLU* 3.0 25.3 + - - +
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Residues in contact with ARG 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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77A ALA* 4.0 6.1 + - - +
78A GLU* 4.8 4.8 + - - -
94A PHE* 5.7 2.8 - - - -
129A ARG* 3.3 37.3 - - - +
149A GLU* 2.7 33.1 + - + +
150A ILE* 4.3 14.1 - - + -
153A PHE* 4.0 30.4 - - + -
161A LEU* 2.7 23.9 + - - +
162A ALA 3.7 4.7 - - - +
164A ALA* 1.3 71.4 - - - +
166A LEU* 1.3 65.4 + - - +
168A GLU* 3.2 25.2 + - - +
169A ASP* 3.0 31.3 + - - +
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Residues in contact with LEU 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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150A ILE* 3.8 15.2 - - + +
162A ALA 2.8 18.6 + - - +
163A GLU* 3.1 9.6 + - + +
165A ARG* 1.3 73.6 - - - +
167A ASN* 1.3 56.0 + - - +
169A ASP* 3.4 2.6 + - - +
170A LEU* 3.0 38.1 + - + +
177A PHE* 3.7 29.2 - - + -
179A ILE* 4.0 6.5 - - + -
199A PHE* 3.8 28.9 - - + -
203A TYR* 3.6 38.8 - - + -
205A LEU* 3.7 17.9 - - + -
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Residues in contact with ASN 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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163A GLU* 2.8 24.7 + - - +
164A ALA* 3.6 10.7 - - - +
166A LEU* 1.3 72.8 - - - +
168A GLU* 1.3 65.2 - - - +
170A LEU* 3.1 9.8 + - - +
171A SER* 2.9 24.5 + - - -
203A TYR* 3.2 42.0 + - - -
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Residues in contact with GLU 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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129A ARG* 3.1 47.0 + - - +
133A ARG* 4.0 9.6 + - - +
164A ALA 3.0 14.8 + - - +
165A ARG* 3.2 31.0 + - - +
167A ASN* 1.3 74.5 - - - +
169A ASP* 1.3 62.6 + - - +
171A SER* 3.2 20.8 + - - -
172A ILE* 3.3 17.6 + - + +
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Residues in contact with ASP 169 (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 LEU* 5.1 6.6 - - - +
129A ARG* 4.8 6.7 - - - +
132A LEU* 4.7 6.4 - - - +
149A GLU* 4.5 9.8 - - - +
150A ILE* 4.6 4.2 - - - +
165A ARG* 3.0 32.1 + - - +
166A LEU* 3.8 4.0 - - - +
168A GLU* 1.3 72.8 - - - +
170A LEU* 1.3 60.4 + - - +
172A ILE* 3.0 13.8 + - - +
173A PHE* 2.9 49.3 + - - +
177A PHE* 3.7 36.1 - - + -
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Residues in contact with LEU 170 (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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166A LEU* 3.0 37.0 + - + +
167A ASN* 3.1 13.9 + - - +
169A ASP* 1.3 75.8 - - - +
171A SER* 1.3 57.9 + - - +
174A GLY* 3.0 47.0 + - - +
177A PHE* 4.3 10.1 - - + -
203A TYR* 3.9 31.0 - - + -
205A LEU* 3.7 32.8 - - + -
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Residues in contact with SER 171 (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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133A ARG* 2.9 30.2 + - - -
167A ASN 2.9 12.9 + - - -
168A GLU* 3.2 13.5 - - - -
169A ASP 3.2 0.2 - - - -
170A LEU* 1.3 77.1 - - - +
172A ILE* 1.3 56.8 + - - +
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Residues in contact with ILE 172 (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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129A ARG* 3.8 35.2 - - + +
132A LEU* 4.5 3.1 - - + -
133A ARG* 3.4 45.5 - - + +
136A ALA* 3.8 27.5 - - + +
168A GLU* 3.3 15.7 + - - +
169A ASP* 3.0 21.3 + - - +
171A SER* 1.3 80.4 - - - +
173A PHE* 1.3 81.8 + - + +
174A GLY 3.7 0.4 - - - -
176A ARG* 4.8 1.9 + - - -
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Residues in contact with PHE 173 (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 LEU* 4.8 1.6 - - + -
98A LEU* 4.0 4.5 - - + -
132A LEU* 3.7 37.7 - - + -
136A ALA* 4.1 12.6 - - + -
139A LEU* 3.6 39.3 - - + -
141A ALA* 3.7 31.9 - - + -
169A ASP* 2.9 28.1 + - - +
172A ILE* 1.3 91.5 - - + +
174A GLY* 1.3 64.0 + - - +
175A ASP* 3.4 1.0 + - - +
176A ARG* 3.1 40.9 + - - +
177A PHE* 4.1 21.5 - + + -
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Residues in contact with GLY 174 (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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170A LEU* 3.0 31.3 + - - +
171A SER 4.9 0.2 - - - -
172A ILE 3.7 1.6 - - - -
173A PHE* 1.3 77.4 - - - +
175A ASP* 1.3 58.0 + - - -
176A ARG 3.1 3.5 + - - -
177A PHE* 3.6 14.9 + - - +
205A LEU* 5.9 0.2 - - - +
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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