Contacts of the helix formed by residues 137 - 148 (chain D) in PDB entry 5I94
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 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D PRO* 1.3 72.7 - - - +
138D LEU* 1.3 65.8 + - - +
139D GLU* 3.6 13.2 + - - +
140D ASP* 2.5 54.0 + - - +
141D LEU* 3.0 16.4 + - - +
200D LYS* 6.1 0.5 - - - +
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Residues in contact with LEU 138 (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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136D PRO 5.0 3.8 - - - +
137D SER* 1.3 74.8 - - - +
139D GLU* 1.3 63.0 + - + +
141D LEU* 3.9 13.1 - - + +
142D LEU* 3.1 27.7 + - - +
207D ILE* 4.1 22.5 - - + +
208D VAL* 5.5 7.0 - - + -
211D THR* 4.0 28.1 + - + +
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Residues in contact with GLU 139 (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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137D SER* 3.8 11.7 - - - +
138D LEU* 1.3 80.1 - - + +
140D ASP* 1.3 60.7 + - - +
142D LEU* 4.1 0.2 - - - +
143D PHE* 3.4 15.8 + - - +
196D LYS 5.7 0.4 - - - +
199D PHE* 3.6 16.6 - - - -
200D LYS* 3.4 38.7 - - + +
203D VAL* 4.7 4.0 - - + -
204D GLN* 3.2 40.8 - - - +
207D ILE* 3.8 31.2 - - + +
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Residues in contact with ASP 140 (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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136D PRO* 5.1 1.7 - - + +
137D SER* 2.5 38.8 + - - +
139D GLU* 1.3 77.0 - - - +
141D LEU* 1.3 69.7 + - + +
143D PHE* 2.9 22.9 + - - +
144D TYR* 3.4 13.8 + - + -
196D LYS* 2.8 47.1 + - + +
200D LYS* 5.5 3.8 - - - +
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Residues in contact with LEU 141 (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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136D PRO* 4.5 20.6 - - + +
137D SER 3.0 12.5 + - - +
138D LEU* 3.4 17.0 + - + +
140D ASP* 1.3 79.1 - - + +
142D LEU* 1.3 58.0 + - - +
144D TYR* 3.4 4.2 + - - +
145D THR* 2.8 31.4 + - - +
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Residues in contact with LEU 142 (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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138D LEU 3.1 13.5 + - - +
139D GLU 4.1 1.3 - - - +
141D LEU* 1.3 76.0 - - - +
143D PHE* 1.3 69.1 + - - +
145D THR* 3.2 14.0 - - + -
146D ILE* 3.1 42.8 - - + +
158D PHE* 5.6 0.2 - - + -
199D PHE* 3.8 22.9 - - + -
203D VAL* 4.4 2.7 - - + -
207D ILE* 3.6 27.6 - - + -
210D LEU* 4.3 20.2 - - + +
211D THR* 4.9 10.3 - - + +
214D PHE* 3.6 29.2 - - + -
215D ARG* 5.8 4.0 - - - +
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Residues in contact with PHE 143 (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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139D GLU 3.4 12.4 + - - +
140D ASP* 2.9 13.2 + - - +
142D LEU* 1.3 78.2 - - - +
144D TYR* 1.3 94.3 + + - +
146D ILE 3.1 4.2 + - - -
147D ALA* 3.0 23.3 + - + +
151D GLU 3.4 22.2 - - - -
152D LYS* 4.5 0.2 - - - -
153D ILE* 3.5 38.7 - - + +
194D LEU 3.7 13.0 - - - -
195D ASP 3.9 1.8 - - - -
196D LYS* 3.3 48.2 - - + +
199D PHE* 3.7 26.9 - + + -
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Residues in contact with TYR 144 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D ASP* 3.4 10.0 + - + -
141D LEU* 3.4 6.6 + - - +
143D PHE* 1.3 106.0 - + - +
145D THR* 1.3 65.7 + - - +
147D ALA* 3.2 20.5 + - + +
148D GLU 4.2 2.8 + - - -
149D GLY* 4.4 13.6 + - - -
150D GLN 3.4 24.9 - - - -
151D GLU 5.0 1.1 + - - -
196D LYS* 4.7 17.7 - - + +
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Residues in contact with THR 145 (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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141D LEU* 2.8 22.1 + - - +
142D LEU* 3.2 21.2 - - + +
144D TYR* 1.3 80.3 - - - +
146D ILE* 1.3 64.8 + - + +
147D ALA 3.6 0.2 + - - -
148D GLU 5.2 1.0 + - - -
214D PHE* 5.0 6.7 - - + +
215D ARG* 3.3 39.4 + - - +
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Residues in contact with ILE 146 (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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142D LEU* 3.1 40.4 - - + +
143D PHE 3.1 1.8 + - - -
145D THR* 1.3 78.4 - - + +
147D ALA* 1.3 68.8 + - - +
148D GLU* 3.9 1.1 - - - +
153D ILE* 3.8 23.0 - - + +
157D LYS* 3.9 17.9 - - + +
158D PHE* 3.9 22.0 - - + -
161D ALA* 4.3 22.7 - - + -
199D PHE* 4.1 6.3 - - + -
214D PHE* 3.8 28.3 - - + -
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Residues in contact with ALA 147 (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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143D PHE* 3.0 9.2 + - + +
144D TYR* 3.2 35.2 - - + +
145D THR 3.3 1.6 - - - -
146D ILE* 1.3 83.5 - - - +
148D GLU* 1.3 77.4 + - - +
149D GLY 3.6 7.6 - - - +
150D GLN* 3.7 17.3 - - + +
151D GLU 6.1 0.2 - - - -
152D LYS 6.1 0.9 - - - -
153D ILE* 4.2 14.6 - - + +
154D PRO* 5.7 0.3 - - - +
157D LYS* 4.0 9.2 + - - +
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Residues in contact with GLU 148 (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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144D TYR 4.2 1.8 + - - -
145D THR 5.2 1.0 + - - -
146D ILE 3.9 1.1 - - - +
147D ALA* 1.3 82.0 - - - +
149D GLY* 1.3 59.4 + - - +
150D GLN* 3.0 37.2 + - + +
157D LYS* 3.0 25.4 + - - +
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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