Contacts of the helix formed by residues 161 - 172 (chain A) in PDB entry 1EH6
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ASN* 5.8 0.4 - - - -
158A TYR* 2.8 34.7 + - - -
159A SER 3.2 2.8 + - - -
160A GLY* 1.3 78.5 - - - +
162A LEU* 1.3 65.8 + - - +
163A ALA* 3.4 2.9 - - - -
164A VAL* 3.3 8.3 + - - -
165A LYS 3.4 0.3 + - - -
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Residues in contact with LEU 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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155A VAL* 3.7 20.2 - - + -
156A GLY 3.6 24.9 - - - +
157A ASN* 5.4 5.3 - - - +
158A TYR* 4.5 5.1 + - - +
161A GLY* 1.3 71.4 - - - -
163A ALA* 1.3 64.3 + - - +
165A LYS* 3.1 6.2 + - + +
166A GLU* 3.0 42.4 + - + +
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Residues in contact with ALA 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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161A GLY 3.4 1.4 - - - -
162A LEU* 1.3 78.5 - - - +
164A VAL* 1.3 57.7 + - + +
166A GLU* 3.4 8.4 + - - +
167A TRP* 2.9 25.3 + - - +
179A PRO* 3.1 27.6 - - + +
180A GLY 5.4 0.4 - - - +
181A LEU* 3.6 23.8 - - + -
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Residues in contact with VAL 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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16A LEU* 3.9 33.9 - - + +
33A LEU* 4.1 13.2 - - + -
158A TYR* 3.5 20.0 - - + -
160A GLY 3.2 21.8 - - - +
161A GLY 3.3 7.1 + - - +
162A LEU 3.2 0.6 - - - -
163A ALA* 1.3 73.8 - - + +
165A LYS* 1.3 66.9 + - - +
167A TRP* 3.1 1.9 + - - +
168A LEU* 2.9 27.4 + - + +
181A LEU* 4.0 23.3 - - + -
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Residues in contact with LYS 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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114A TYR* 3.4 7.9 + - - -
145A CYS 4.4 2.3 + - - -
146A HIS* 3.5 29.8 - - + +
148A VAL 2.8 28.3 + - - -
149A VAL* 4.3 2.2 - - - -
155A VAL* 2.8 41.7 + - + -
156A GLY 3.6 3.6 - - - +
157A ASN 2.8 29.1 + - - +
158A TYR* 3.6 28.2 - - + -
161A GLY 3.4 2.8 + - - -
162A LEU* 3.1 9.0 + - - +
164A VAL* 1.3 78.2 - - - +
166A GLU* 1.3 58.6 + - - +
168A LEU* 3.3 7.1 + - - +
169A LEU* 2.9 34.9 + - + +
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Residues in contact with GLU 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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155A VAL* 4.2 20.1 - - + +
162A LEU* 3.0 44.3 + - + +
163A ALA* 3.7 12.6 - - - +
165A LYS* 1.3 73.7 - - - +
167A TRP* 1.3 60.2 + - - +
169A LEU* 3.7 6.8 - - - +
170A ALA* 2.8 32.9 + - - +
176A LEU* 4.4 18.6 - - + +
177A GLY 4.9 4.0 - - - +
179A PRO* 4.2 16.2 - - + +
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Residues in contact with TRP 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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15A PRO* 3.5 33.7 + - + +
16A LEU* 3.5 14.1 - - + -
70A PHE* 3.9 26.7 - + + -
163A ALA 2.9 15.1 + - - +
164A VAL* 3.4 7.9 - - - +
166A GLU* 1.3 76.5 - - - +
168A LEU* 1.3 66.1 + - + +
170A ALA* 3.3 4.3 + - - +
171A HIS* 2.8 50.9 + + + +
178A LYS* 3.5 50.7 - - + +
179A PRO* 3.8 23.9 + - + +
181A LEU* 3.6 21.7 - - + +
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Residues in contact with LEU 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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16A LEU* 3.9 24.0 - - + -
69A TYR* 3.5 31.4 - - + +
70A PHE* 4.4 0.4 - - + -
141A ILE* 4.6 9.0 - - + -
146A HIS* 3.6 35.0 - - + +
158A TYR* 3.6 24.2 - - + +
164A VAL* 2.9 27.8 + - + +
165A LYS 3.6 3.1 - - - +
167A TRP* 1.3 88.2 - - + +
169A LEU* 1.3 62.8 + - - +
171A HIS* 3.1 5.8 + - - +
172A GLU* 3.0 26.4 + - - +
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Residues in contact with LEU 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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111A VAL* 4.0 17.7 - - + -
146A HIS* 3.5 34.1 - - + +
147A ARG* 4.5 4.3 - - + -
149A VAL* 4.2 10.5 - - + -
155A VAL* 4.0 35.0 - - + -
165A LYS* 2.9 22.9 + - + +
166A GLU 3.3 0.2 + - - -
168A LEU* 1.3 74.7 - - - +
170A ALA* 1.3 63.1 + - - +
172A GLU* 3.1 12.7 + - - +
174A HIS* 3.1 45.1 + - + +
176A LEU* 3.8 16.6 - - + -
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Residues in contact with ALA 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 GLU 2.8 21.7 + - - +
167A TRP 3.6 4.3 - - - +
169A LEU* 1.3 73.7 - - - +
171A HIS* 1.3 63.2 + - - +
173A GLY* 3.1 13.9 + - - -
174A HIS 3.7 13.5 + - - +
176A LEU* 3.3 28.8 - - + +
177A GLY 4.1 0.2 - - - -
178A LYS* 3.6 25.5 - - + +
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Residues in contact with HIS 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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69A TYR* 2.8 55.8 + + - -
70A PHE* 3.5 23.4 - - - -
73A PRO* 4.2 16.3 - - + +
108A PHE* 3.9 11.7 - + - -
167A TRP* 2.8 34.2 + + + +
168A LEU 3.1 10.7 + - - +
170A ALA* 1.3 78.3 - - - +
172A GLU* 1.3 54.4 + - - +
173A GLY 3.3 3.2 + - - -
178A LYS* 3.3 26.6 + - - +
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Residues in contact with GLU 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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69A TYR* 2.7 16.3 + - - +
108A PHE* 3.7 26.5 - - + -
109A GLY* 2.9 37.8 + - - +
110A GLU 4.6 0.2 - - - +
146A HIS* 2.7 29.3 + - - -
147A ARG* 2.8 41.3 + - - +
168A LEU 3.0 13.7 + - - +
169A LEU* 3.1 7.0 + - - +
171A HIS* 1.3 77.4 - - - +
173A GLY* 1.3 57.6 + - - +
174A HIS* 3.6 11.2 + - + -
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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