Contacts of the helix formed by residues 161 - 172 (chain B) in PDB entry 3IEU
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 ASN 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B VAL* 4.1 8.4 - - + +
153B PRO* 2.6 36.8 + - - +
154B ILE* 3.5 5.6 - - + +
159B GLY 2.9 2.6 + - - -
160B LEU* 1.3 92.7 - - - +
162B VAL* 1.3 64.4 + - - +
163B ASP* 3.2 14.4 + - - +
164B THR* 3.1 28.4 + - - +
165B ILE* 3.3 9.0 + - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.6 23.8 - - + -
27B LYS* 3.9 28.5 - - + +
28B LEU* 3.9 20.1 - - + +
154B ILE* 4.5 10.1 - - + -
155B SER 4.4 10.1 - - - +
156B ALA* 4.5 5.4 - - - -
159B GLY* 2.9 25.1 + - - +
160B LEU 4.4 2.9 - - - +
161B ASN* 1.3 78.4 - - - +
163B ASP* 1.3 58.6 + - - +
165B ILE* 2.9 9.4 + - - +
166B ALA* 2.9 25.2 + - + +
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Residues in contact with ASP 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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159B GLY 4.4 2.9 + - - +
161B ASN* 3.4 18.0 + - - -
162B VAL* 1.3 75.4 + - - +
164B THR* 1.3 65.0 + - - -
166B ALA* 3.5 10.1 - - - +
167B ALA* 3.0 29.8 + - - +
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Residues in contact with THR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASP* 5.8 1.3 - - - +
152B VAL* 4.4 17.9 - - + -
161B ASN* 3.1 30.7 + - - +
163B ASP* 1.3 86.4 + - - +
165B ILE* 1.3 61.7 + - - +
167B ALA* 3.6 4.8 + - - +
168B ILE* 3.2 37.1 + - + +
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Residues in contact with ILE 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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24B LEU* 4.9 9.2 - - + -
28B LEU* 4.4 13.2 - - + -
93B ILE* 3.6 31.4 - - + -
120B ILE* 4.2 11.7 - - + -
122B ALA* 4.1 22.0 - - + -
152B VAL* 3.9 30.3 - - + -
154B ILE* 4.2 11.2 - - + -
161B ASN 3.7 11.9 - - - +
162B VAL* 2.9 11.1 + - - +
164B THR* 1.3 76.5 - - - +
166B ALA* 1.3 64.0 + - - +
168B ILE* 3.3 7.8 + - + +
169B VAL* 3.0 23.8 + - + +
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Residues in contact with ALA 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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28B LEU* 4.0 17.7 - - + +
60B TYR* 5.4 0.4 - - - -
162B VAL* 2.9 12.2 + - + +
163B ASP* 3.5 14.6 - - - +
164B THR 3.2 0.2 - - - -
165B ILE* 1.3 78.2 - - - +
167B ALA* 1.3 57.4 + - - +
169B VAL* 3.2 7.9 + - - +
170B ARG* 2.8 39.5 + - - +
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Residues in contact with ALA 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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163B ASP 3.0 16.4 + - - +
164B THR* 4.0 6.7 - - - +
166B ALA* 1.3 77.0 - - - +
168B ILE* 1.3 63.4 + - + +
170B ARG* 3.5 9.2 + - - +
171B LYS* 3.2 29.6 + - - +
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Residues in contact with ILE 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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91B LEU* 4.1 11.0 - - + -
120B ILE* 3.6 33.9 - - + -
149B LEU* 4.7 3.4 - - + -
150B ASP* 3.7 20.2 - - + +
152B VAL* 4.8 5.4 - - + -
164B THR* 3.2 25.1 - - + +
165B ILE* 3.3 9.4 + - + +
166B ALA 3.2 0.2 - - - -
167B ALA* 1.3 76.5 - - + +
169B VAL* 1.3 67.2 + - - +
171B LYS* 3.1 29.6 + - - +
172B HIS* 3.0 41.9 + - + +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.8 23.6 - - + +
58B ALA* 4.2 12.3 - - + -
60B TYR* 3.6 24.9 - - - +
91B LEU* 3.8 23.6 - - + -
93B ILE* 3.9 21.5 - - + -
165B ILE* 3.0 16.8 + - + +
166B ALA* 3.3 9.6 - - - +
168B ILE* 1.3 77.1 - - + +
170B ARG* 1.3 65.2 + - - +
172B HIS* 2.9 15.2 + - - +
173B LEU* 3.6 10.8 + - + +
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Residues in contact with ARG 170 (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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7B TYR* 5.4 0.5 - - - +
51B HIS* 4.4 12.5 + - - -
53B GLU* 2.5 54.2 + - - +
56B TYR* 3.3 57.2 - - + +
166B ALA* 2.8 26.8 + - - +
167B ALA* 3.7 10.0 - - - +
168B ILE 3.3 0.2 - - - -
169B VAL* 1.3 72.7 - - - +
171B LYS* 1.3 61.5 + - - +
173B LEU* 3.2 27.7 + - - +
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Residues in contact with LYS 171 (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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167B ALA* 3.2 18.8 + - - +
168B ILE* 3.1 30.6 + - - +
170B ARG* 1.3 78.9 - - - +
172B HIS* 1.3 66.1 + - + +
173B LEU 3.4 3.0 + - - +
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Residues in contact with HIS 172 (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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11B ILE* 5.0 2.0 - - + +
90B GLU* 3.5 33.5 - - + +
91B LEU* 4.2 22.8 - - + +
118B PRO* 4.0 12.9 - - + +
149B LEU* 3.2 34.4 - - + +
168B ILE* 3.0 34.5 + - + +
169B VAL 2.9 11.4 + - - +
171B LYS* 1.3 86.2 - - + +
173B LEU* 1.3 60.8 + - - +
174B PRO* 3.0 14.4 - - - +
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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