Contacts of the helix formed by residues 163 - 173 (chain B) in PDB entry 1I43
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 TYR 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B MET* 3.9 10.8 - - - -
161B ASP 4.4 0.4 - - - -
162B CYS* 1.3 76.5 - - - +
164B ARG* 1.3 73.1 + - + +
165B LYS* 3.4 23.3 - - + +
166B THR* 3.1 32.5 + - - +
167B ARG* 2.9 16.1 + - - +
207B GLU* 3.1 20.4 + - - +
211B ASN* 4.6 16.8 - - - +
500B PLP 3.7 36.3 - + + +
601B PMC 3.0 70.3 + + - -
110D ARG* 3.3 12.5 + - - -
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Residues in contact with ARG 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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162B CYS 3.3 5.2 + - - -
163B TYR* 1.3 77.1 - - + +
165B LYS* 1.3 66.9 + - + +
167B ARG* 2.6 36.2 + - - +
168B ILE* 3.0 27.9 + - + +
211B ASN* 5.8 1.0 - - - +
403B SER* 2.9 29.8 + - - -
404B TYR* 3.5 38.3 + - + +
406B ASP* 2.9 36.9 + - - -
407B LEU* 3.6 27.0 - - - +
601B PMC 5.7 2.0 - - - +
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Residues in contact with LYS 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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139B MET* 4.1 11.0 - - + -
163B TYR* 3.4 18.8 - - + +
164B ARG* 1.3 86.6 - - + +
166B THR* 1.3 61.2 + - - +
168B ILE* 3.1 25.7 + - + +
169B PHE* 3.1 21.0 + - - +
601B PMC 3.9 14.5 + - - +
110D ARG* 4.3 12.1 - - - +
111D TYR* 3.3 35.1 + - - +
289D HIS* 4.5 11.2 + - - +
290D ILE* 4.5 20.8 - - + +
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Residues in contact with THR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET* 3.7 17.9 - - + +
142B SER* 4.7 14.1 + - - -
146B LEU* 4.9 5.6 - - + -
162B CYS* 4.1 6.5 - - - -
163B TYR* 3.1 29.0 + - - +
165B LYS* 1.3 77.2 - - - +
167B ARG* 1.3 63.2 + - - +
169B PHE* 3.3 5.4 + - + +
170B ILE* 3.1 40.9 + - + +
205B PHE* 3.9 30.9 - - + -
500B PLP 4.7 3.5 + - - -
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B THR* 5.9 1.3 - - - -
159B THR 5.0 2.5 - - - -
160B THR* 3.5 20.2 + - - +
162B CYS* 4.5 21.7 - - + +
163B TYR 2.9 10.9 + - - +
164B ARG* 2.6 22.7 + - + +
166B THR* 1.3 71.5 - - - +
168B ILE* 1.3 56.0 + - + +
170B ILE* 3.3 8.5 + - - +
171B GLU* 2.9 66.5 + - - +
183B VAL* 4.2 25.6 - - - +
415B TYR* 2.8 51.7 + - - -
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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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164B ARG* 3.0 39.4 + - + +
165B LYS* 3.4 25.8 - - + +
167B ARG* 1.3 77.0 - - + +
169B PHE* 1.3 59.9 + - - +
171B GLU* 4.4 3.1 - - - +
172B THR* 2.8 56.6 + - + +
290D ILE* 4.4 20.0 - - + -
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Residues in contact with PHE 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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139B MET* 5.2 1.3 - - + -
143B THR* 4.0 22.9 - - + +
146B LEU* 3.6 33.9 - - + -
147B LEU* 3.9 28.3 - - + -
165B LYS 3.1 11.8 + - - +
166B THR* 3.5 11.9 - - + +
168B ILE* 1.3 75.8 - - - +
170B ILE* 1.3 59.6 + - + +
173B ILE* 2.9 59.1 + - + +
174B LEU* 3.3 35.0 + - + -
290D ILE* 4.0 20.2 - - + +
291D LEU* 3.9 20.4 - - + -
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Residues in contact with ILE 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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146B LEU* 4.0 17.7 - - + -
156B ILE* 4.2 10.5 - - + -
158B THR* 4.3 26.9 - - + +
162B CYS* 4.7 5.4 - - - -
166B THR* 3.1 31.5 + - + +
167B ARG* 3.7 7.2 - - - +
169B PHE* 1.3 75.9 - - - +
171B GLU* 1.3 61.1 + - + +
172B THR 3.5 0.4 - - - -
174B LEU* 3.5 28.8 - - + +
175B PRO* 3.5 15.6 - - - +
179B ILE* 4.9 3.6 - - + +
181B ALA* 4.0 27.3 - - + +
205B PHE* 4.8 2.7 - - + -
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Residues in contact with GLU 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 ARG* 2.9 60.7 + - + +
168B ILE* 3.2 3.6 + - - +
170B ILE* 1.3 83.0 - - + +
172B THR* 1.3 64.6 + - + +
175B PRO* 3.9 10.1 - - - +
181B ALA* 6.5 1.1 - - + -
183B VAL* 4.8 6.7 - - + +
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Residues in contact with THR 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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168B ILE* 2.8 39.8 + - + +
170B ILE 3.5 0.6 - - - -
171B GLU* 1.3 89.3 - - + +
173B ILE* 1.3 79.7 + - - +
175B PRO* 3.6 11.2 - - - +
176B LYS* 4.0 15.6 - - - +
290D ILE* 5.6 0.5 - - - +
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Residues in contact with ILE 173 (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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147B LEU* 5.5 7.0 - - + -
169B PHE* 2.9 48.1 + - + +
172B THR* 1.3 93.5 - - - +
174B LEU* 1.3 61.4 + - - +
175B PRO* 3.1 2.0 - - - -
176B LYS* 2.8 48.6 + - + +
177B MET* 4.0 3.8 + - + +
147D LEU* 5.9 8.3 - - + +
177D MET* 5.6 7.4 - - + -
287D LEU* 4.0 26.2 - - + -
290D ILE* 5.5 6.3 - - + -
291D LEU* 6.0 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