Contacts of the helix formed by residues 161 - 167 (chain D) in PDB entry 1EJI
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 SER 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C PRO 4.0 13.9 + - - -
299C GLY 4.0 2.4 + - - -
149D LEU* 3.3 40.2 + - - +
150D THR* 4.5 1.4 - - - +
153D PHE 3.2 18.8 + - - -
160D ILE* 1.3 80.3 - - - +
162D ALA* 1.3 73.7 + - - +
163D THR* 2.9 16.2 + - - -
164D SER* 3.3 3.0 + - - -
165D ILE* 2.8 27.1 + - - +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C THR* 5.7 0.4 - - + -
299C GLY 2.7 25.5 + - - +
300C LEU* 3.6 29.2 - - + -
125D PHE* 4.0 14.6 - - + -
161D SER* 1.3 78.5 + - - +
163D THR* 1.3 61.9 + - - +
165D ILE* 3.0 23.9 + - + +
166D PHE* 3.0 23.3 + - + +
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Residues in contact with THR 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D PHE* 4.9 5.4 - - - -
128D TYR* 3.6 24.3 - - + -
138D ILE* 4.3 14.8 - - + -
150D THR* 2.9 27.0 + - - +
151D HIS 4.1 2.2 - - - -
152D GLY* 3.6 25.4 - - - +
161D SER* 2.9 9.6 + - - -
162D ALA* 1.3 78.3 - - - +
164D SER* 1.3 57.5 + - - +
167D PHE* 3.0 42.8 + - + +
169D SER* 5.2 4.2 - - - -
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ARG* 5.9 0.2 + - - -
152D GLY* 4.1 0.4 - - - -
153D PHE 3.1 28.9 + - - -
154D MSE 3.8 22.5 - - - +
159D LYS* 3.1 20.8 - - - +
160D ILE 3.8 3.8 + - - -
161D SER 3.3 11.9 + - - -
162D ALA 3.4 0.2 - - - -
163D THR* 1.3 79.2 - - - +
165D ILE* 1.3 58.0 + - - +
167D PHE 2.9 18.0 - - - +
169D SER* 3.3 26.6 + - - +
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C THR* 4.9 14.6 - - + -
134C PRO* 4.0 31.1 - - + +
299C GLY* 5.5 2.9 - - - -
135D HIS* 4.9 7.1 - - - -
159D LYS* 3.5 34.0 + - + +
160D ILE 3.6 13.0 - - - +
161D SER 2.8 26.2 - - - +
162D ALA* 3.0 14.4 + - + +
164D SER* 1.3 81.2 - - - +
166D PHE* 1.3 72.3 + - + +
167D PHE 3.8 1.0 + - - +
168D GLU* 5.4 0.2 - - - +
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Residues in contact with PHE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PHE* 3.9 12.1 - + - -
129C THR* 3.4 41.3 - - + -
134C PRO* 3.5 32.1 - - + -
166C PHE* 3.7 44.9 - + + -
167C PHE* 4.0 14.8 - + - -
125D PHE* 3.7 15.9 - + - -
134D PRO* 3.6 7.3 - - - +
135D HIS* 2.9 28.0 + - - -
162D ALA* 3.0 28.5 + - + +
165D ILE* 1.3 86.3 - - + +
167D PHE* 1.3 71.5 + - + +
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Residues in contact with PHE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C PHE* 4.0 17.7 - + - -
125D PHE* 3.9 24.2 - + - -
128D TYR* 3.5 44.4 - + + -
129D THR* 3.8 4.9 - - - -
132D VAL* 3.7 11.7 - - + -
133D GLU* 3.4 36.1 - - - -
134D PRO* 4.0 2.9 - - + -
135D HIS 4.0 3.1 - - - +
136D GLY 3.5 7.4 - - - +
138D ILE* 3.8 16.6 - - + -
163D THR* 3.0 26.6 + - + +
164D SER* 2.9 24.9 - - - +
165D ILE 4.2 0.7 - - - +
166D PHE* 1.3 85.3 - - + +
168D GLU* 1.3 73.2 + - - +
169D SER* 5.9 0.4 - - - -
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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