Contacts of the helix formed by residues 177 - 187 (chain A) in PDB entry 1E1K
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 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A TRP* 4.0 7.4 + - - +
130A TYR 3.3 14.2 + - - +
131A ASN 4.3 1.3 - - - -
132A GLY* 3.6 27.4 - - - +
175A ASP 3.5 1.3 + - - -
176A ILE* 1.3 78.8 - - - +
178A GLU* 1.3 66.0 + - - +
179A ALA* 3.7 5.7 + - - +
180A ALA* 2.9 27.4 + - - +
181A LEU* 2.9 22.3 + - - +
446A GLU* 3.6 7.2 - - - +
447A LYS* 4.9 9.0 - - + -
449A LEU* 3.8 24.6 - - + +
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Residues in contact with GLU 178 (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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176A ILE 3.5 0.6 + - - -
177A THR* 1.3 72.8 - - - +
179A ALA* 1.3 67.6 + - + +
181A LEU* 3.4 5.9 + - - +
182A GLY* 2.9 22.0 + - - -
185A ARG* 5.6 0.5 + - - -
443A LYS* 3.7 8.1 - - - +
446A GLU* 2.8 41.5 + - - +
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Residues in contact with ALA 179 (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 TRP* 4.6 6.6 - - - +
137A ARG 6.1 1.1 - - - +
177A THR* 3.0 6.9 - - - +
178A GLU* 1.3 86.5 - - + +
180A ALA* 1.3 62.5 + - - +
182A GLY* 3.3 2.1 + - - -
183A ALA* 3.1 20.8 + - - +
449A LEU* 5.0 11.7 - - + -
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Residues in contact with ALA 180 (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 TRP* 3.5 32.6 - - + +
130A TYR* 3.7 26.7 - - + -
176A ILE* 4.2 5.2 - - + -
177A THR* 2.9 22.7 + - - +
179A ALA* 1.3 73.4 - - - +
181A LEU* 1.3 61.0 + - - +
183A ALA* 3.1 3.6 + - - +
184A LEU* 2.8 35.0 + - + +
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Residues in contact with LEU 181 (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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168A PRO* 3.7 33.0 - - + +
171A LEU* 4.1 21.3 - - + +
172A GLU* 4.1 20.9 - - - +
176A ILE* 4.0 12.2 - - + +
177A THR 2.9 15.7 + - - +
178A GLU* 3.8 6.1 - - - +
180A ALA* 1.3 75.0 - - - +
182A GLY* 1.3 64.6 + - - +
184A LEU* 3.0 11.1 + - + +
185A ARG* 2.8 57.9 + - - +
443A LYS* 5.2 8.5 - - + +
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Residues in contact with GLY 182 (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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178A GLU 2.9 17.2 + - - -
179A ALA* 3.7 2.5 - - - -
180A ALA 3.2 0.2 - - - -
181A LEU* 1.3 76.5 - - - +
183A ALA* 1.3 60.3 + - - +
185A ARG* 3.2 25.2 + - - +
186A GLN* 3.4 16.7 + - - +
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Residues in contact with ALA 183 (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 TRP* 3.7 25.8 - - + -
141A PRO 5.6 2.9 - - - +
143A LEU* 3.8 14.9 - - + +
179A ALA 3.1 9.2 + - - +
180A ALA 3.1 8.4 + - - +
182A GLY* 1.3 74.4 - - - +
184A LEU* 1.3 61.1 + - - +
186A GLN* 3.2 9.4 + - - +
187A SER* 3.1 16.6 + - - -
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Residues in contact with LEU 184 (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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126A PHE* 5.2 0.7 - - + -
129A TRP* 4.7 9.2 - - + -
143A LEU* 4.0 17.3 - - + -
163A ILE* 3.7 36.1 - - + +
164A LEU* 4.4 18.2 - - + +
168A PRO* 3.8 17.1 - - + +
171A LEU* 4.2 9.6 - - + -
176A ILE* 3.6 31.2 - - + -
180A ALA* 2.8 21.2 + - + +
181A LEU* 3.0 12.8 + - + +
183A ALA* 1.3 72.1 - - - +
185A ARG* 1.3 63.3 + - - +
187A SER* 3.1 22.8 + - - +
270A ARG* 5.1 3.8 + - - -
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Residues in contact with ARG 185 (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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168A PRO* 4.0 22.8 + - + +
169A ASP* 4.6 8.1 + - - -
172A GLU* 3.3 39.6 + - - +
178A GLU 5.6 0.6 + - - -
181A LEU* 2.8 49.4 + - + +
182A GLY* 3.2 15.2 + - - +
184A LEU* 1.3 78.1 - - - +
186A GLN* 1.3 71.1 + - - +
187A SER 3.4 2.1 + - - +
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Residues in contact with GLN 186 (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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143A LEU 4.5 1.7 - - - +
144A SER* 5.6 0.5 - - - -
182A GLY 3.7 11.6 + - - +
183A ALA* 3.2 9.7 + - - +
184A LEU 3.2 0.4 - - - -
185A ARG* 1.3 89.8 + - - +
187A SER* 1.3 65.8 + - - +
188A ARG* 3.5 10.6 + - - +
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Residues in contact with SER 187 (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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143A LEU* 3.4 31.4 + - - +
164A LEU* 5.0 4.9 + - - +
183A ALA 3.1 4.8 + - - -
184A LEU* 3.1 22.1 + - - +
185A ARG 4.7 2.3 - - - +
186A GLN* 1.3 80.2 - - - +
188A ARG* 1.3 56.9 + - - +
189A VAL* 3.0 32.8 + - - +
190A LYS* 4.8 4.2 + - - -
270A ARG* 4.6 15.8 + - - -
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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