Contacts of the helix formed by residues 163 - 173 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139F MET* 3.9 10.5 - - - -
161F ASP 4.4 0.7 - - - -
162F CYS* 1.3 75.3 - - - +
164F ARG* 1.3 73.8 + - + +
165F LYS* 3.4 27.9 - - + +
166F THR* 3.1 27.5 + - - +
167F ARG* 2.9 18.7 + - - +
207F GLU* 3.1 17.6 + - - +
211F ASN* 4.4 17.9 - - - +
500F PLP 3.7 35.7 - + + +
605F PMC 3.1 69.7 + + - -
110H ARG* 3.4 14.8 + - - -
111H TYR* 4.6 0.2 + - - -
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Residues in contact with ARG 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F CYS 3.4 4.1 + - - -
163F TYR* 1.3 78.4 - - + +
165F LYS* 1.3 74.2 + - + +
167F ARG* 2.8 22.0 + - + +
168F ILE* 3.0 32.3 + - + +
211F ASN* 5.6 1.0 - - - +
403F SER* 2.9 27.9 + - - +
404F TYR* 3.3 39.6 + - + +
406F ASP* 3.0 35.9 + - - -
407F LEU* 3.7 25.2 - - - +
605F PMC 5.4 3.8 - - - +
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Residues in contact with LYS 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F MET* 4.1 11.4 - - + -
163F TYR* 3.4 20.3 - - + +
164F ARG* 1.3 86.0 - - - +
166F THR* 1.3 64.8 + - - +
168F ILE* 3.1 24.3 + - + +
169F PHE* 3.0 20.6 + - - +
605F PMC 4.2 15.0 + - - +
110H ARG* 4.3 12.8 - - - +
111H TYR* 3.3 33.9 + - - +
289H HIS* 4.4 6.8 + - - +
290H ILE* 4.4 27.7 - - + +
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Residues in contact with THR 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F MET* 3.9 16.8 - - + +
142F SER* 4.7 14.1 + - - -
146F LEU* 4.8 6.7 - - + -
162F CYS* 4.0 11.0 - - - -
163F TYR* 3.1 29.2 + - - +
165F LYS* 1.3 77.2 - - - +
167F ARG* 1.3 63.0 + - - +
169F PHE* 3.2 6.1 + - + +
170F ILE* 3.0 37.7 + - + +
205F PHE* 4.0 30.3 - - + -
500F PLP 4.7 3.3 + - - -
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Residues in contact with ARG 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F THR 5.1 2.7 - - - -
160F THR* 3.7 19.4 + - - +
162F CYS* 4.5 19.2 - - + +
163F TYR 2.9 11.7 + - - +
164F ARG* 2.8 17.8 + - - +
166F THR* 1.3 75.7 - - - +
168F ILE* 1.3 56.9 + - + +
170F ILE* 3.1 11.1 + - - +
171F GLU* 2.8 67.9 + - - +
183F VAL* 4.2 25.3 - - - +
415F TYR* 2.7 52.6 + - - -
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Residues in contact with ILE 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F ARG* 3.0 34.5 + - + +
165F LYS* 3.3 30.5 - - + +
167F ARG* 1.3 78.3 - - + +
169F PHE* 1.3 54.9 + - - +
171F GLU* 4.6 3.8 - - - -
172F THR* 2.7 60.8 + - + +
290H ILE* 4.0 21.8 - - + -
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Residues in contact with PHE 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F MET* 5.2 2.2 - - + -
143F THR* 3.9 21.3 - - + +
146F LEU* 3.6 35.0 - - + -
147F LEU* 3.7 30.5 - - + -
165F LYS 3.0 11.2 + - - +
166F THR* 3.2 11.4 + - + +
168F ILE* 1.3 77.5 - - - +
170F ILE* 1.3 59.1 + - + +
172F THR* 4.2 0.2 - - - -
173F ILE* 3.0 54.8 + - + +
174F LEU* 3.3 31.9 + - + -
290H ILE* 4.0 20.8 - - + +
291H LEU* 3.7 22.2 - - + -
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Residues in contact with ILE 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F LEU* 4.2 15.0 - - + -
156F ILE* 4.2 9.6 - - + -
158F THR* 4.3 26.9 - - + +
162F CYS* 4.6 6.7 - - - -
166F THR* 3.0 30.5 - - + +
167F ARG* 3.1 7.9 + - - +
169F PHE* 1.3 77.2 - - - +
171F GLU* 1.3 62.7 + - + +
172F THR 3.4 0.2 - - - -
174F LEU* 3.6 29.2 - - + +
175F PRO* 3.2 18.2 - - - +
179F ILE* 4.9 3.1 - - + +
181F ALA* 4.0 27.1 - - + +
205F PHE* 5.0 2.7 - - + -
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Residues in contact with GLU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ARG* 2.8 61.5 + - - +
168F ILE* 4.1 3.5 - - - +
170F ILE* 1.3 81.8 - - + +
172F THR* 1.3 66.4 + - + +
175F PRO* 3.6 12.5 - - - +
181F ALA* 6.5 0.9 - - + -
183F VAL* 4.9 6.7 - - + +
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Residues in contact with THR 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ILE* 2.7 44.2 + - + +
171F GLU* 1.3 89.0 - - + +
173F ILE* 1.3 79.7 + - - +
175F PRO* 3.7 8.5 - - - +
176F LYS* 3.9 15.4 - - - +
290H ILE* 5.5 0.5 - - - +
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Residues in contact with ILE 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F LEU* 5.3 7.6 - - + -
169F PHE* 3.0 45.1 + - + +
172F THR* 1.3 95.4 - - - +
174F LEU* 1.3 58.1 + - - +
175F PRO* 3.2 2.2 - - - -
176F LYS* 2.8 56.0 + - + +
177F MET* 4.0 3.4 + - + +
147H LEU* 5.8 8.7 - - + +
177H MET* 5.5 9.0 - - + -
287H LEU* 3.9 28.3 - - + -
290H ILE* 5.6 5.2 - - + -
291H LEU* 5.9 0.7 - - + -
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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