Contacts of the helix formed by residues 159 - 169 (chain B) in PDB entry 1IES
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 ALA 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B VAL* 3.4 36.0 + - + +
157B SER 4.0 0.4 + - - -
158B GLN* 1.3 71.6 - - - +
160B GLY* 1.3 56.3 + - - +
163B GLU* 3.0 31.9 + - - +
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Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLN 3.4 0.6 - - - -
159B ALA* 1.3 74.3 - - - +
161B LEU* 1.3 65.0 + - - +
163B GLU* 3.9 3.3 - - - +
164B TYR* 3.1 19.6 + - - +
153F ARG* 3.5 38.1 - - - -
157F SER* 3.7 10.9 + - - -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLN* 3.3 24.2 + - + +
160B GLY* 1.3 74.5 - - - +
162B GLY* 1.3 56.0 + - - +
164B TYR* 3.3 2.1 + - - +
165B LEU* 2.9 54.5 + - + +
153F ARG 4.2 0.4 + - - -
154F LEU* 3.7 37.7 - - + +
157F SER* 3.3 15.4 + - - +
158F GLN* 4.9 3.6 - - + -
161F LEU* 4.0 25.6 - - + -
162F GLY* 4.7 4.7 - - - +
165F LEU* 3.9 15.9 - - + -
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Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 6.1 0.2 - - - -
154B LEU* 3.6 39.6 - - - +
155B VAL* 4.5 2.2 - - - -
158B GLN 2.6 21.4 + - - -
159B ALA 3.8 1.3 - - - -
161B LEU* 1.3 70.1 - - - +
163B GLU* 1.3 63.7 + - - +
165B LEU* 3.9 0.8 - - - -
166B PHE* 3.0 25.7 + - - +
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 4.9 0.2 - - - -
44B LEU* 3.5 21.1 - - + +
91B THR* 3.8 19.4 - - - +
92B THR* 2.8 46.9 + - - +
93B LEU 5.7 0.2 - - - +
151B ILE* 5.5 1.6 - - + -
155B VAL* 4.0 15.0 - - + +
159B ALA 3.0 20.5 + - - +
160B GLY* 3.9 5.5 - - - +
162B GLY* 1.3 74.5 - - - +
164B TYR* 1.3 61.2 + - - +
166B PHE* 3.4 5.8 + - - +
167B GLU* 3.1 24.6 + - - +
153F ARG* 4.0 18.9 + - - -
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Residues in contact with TYR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.8 3.4 - - - -
160B GLY 3.1 16.4 + - - +
161B LEU 3.3 2.9 + - - +
163B GLU* 1.3 77.0 - - - +
165B LEU* 1.3 65.5 + - + +
167B GLU* 3.3 7.9 + - - +
168B ARG* 2.8 54.0 + - + +
150F ASN* 3.8 23.8 - - - -
153F ARG* 4.2 9.5 - - - +
154F LEU* 3.5 44.4 - - + -
165F LEU* 3.4 16.8 + - + -
166F PHE* 3.5 5.2 - + - -
169F LEU* 3.5 15.8 - - + +
170F THR* 2.5 45.0 + - - -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 4.7 18.6 - - + -
161B LEU* 2.9 47.0 + - + +
162B GLY* 4.0 2.5 - - - +
164B TYR* 1.3 77.9 - - + +
166B PHE* 1.3 53.1 + - - +
168B ARG* 4.0 2.5 - - - -
169B LEU* 2.6 54.0 + - + +
165F LEU* 4.2 19.7 - - + -
169F LEU* 3.7 28.0 - - + -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 4.1 12.3 - - + -
96B MET* 4.6 2.9 - - + -
147B HIS* 3.8 22.2 - + - -
150B ASN* 4.0 19.5 - - + -
151B ILE* 3.7 39.5 - - + -
154B LEU* 3.7 21.4 - - + +
162B GLY 3.0 17.4 + - - +
163B GLU* 3.7 6.7 - - - +
165B LEU* 1.3 75.2 - - - +
167B GLU* 1.3 61.3 + - + +
170B THR* 2.8 65.8 + - + +
171B LEU* 3.1 35.2 + - + -
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA 5.5 0.4 - - - -
44B LEU* 4.1 27.3 - - + +
45B GLU* 3.4 9.6 + - - +
46B GLY* 2.6 38.4 + - - +
47B VAL* 4.0 11.9 - - + +
163B GLU 3.1 13.9 + - - +
164B TYR* 3.6 5.3 - - - +
166B PHE* 1.3 79.8 - - - +
168B ARG* 1.3 98.6 + - - +
171B LEU* 3.3 12.7 - - - -
172B LYS* 2.6 34.7 + - - +
150F ASN* 5.6 0.2 + - - -
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Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLU* 3.8 9.9 + - - +
164B TYR* 2.8 35.6 + - + +
165B LEU* 3.6 7.4 - - - +
167B GLU* 1.3 124.8 + - - +
169B LEU* 1.3 53.7 + - - +
172B LYS* 2.9 52.1 - - - +
173B HIS* 2.6 36.7 + - + +
169F LEU* 3.3 47.8 + - + +
170F THR* 3.8 12.4 + - - +
173F HIS 4.3 0.6 + - - -
174F ASP* 3.5 18.4 - - - +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 2.6 42.7 + - + +
168B ARG* 1.3 80.2 - - + +
170B THR* 1.3 63.1 + - - +
173B HIS* 3.2 32.6 - - + +
174B ASP* 4.7 0.7 - - - +
169F LEU* 4.3 23.6 - - + -
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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