Contacts of the helix formed by residues 163 - 173 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ARG* 3.3 20.1 + - - -
139C MET* 4.0 10.1 - - - -
161C ASP 4.3 0.4 - - - -
162C CYS* 1.3 73.2 - - - +
164C ARG* 1.3 70.0 + - + +
165C LYS* 3.4 23.1 - - + +
166C THR* 2.8 43.1 + - - +
167C ARG 2.9 9.9 + - - -
207C GLU* 3.3 20.1 + - - +
211C ASN* 4.6 17.7 - - - +
500C PLP 3.6 39.7 - + + +
602C PMC 3.3 59.7 + + - -
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Residues in contact with ARG 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C CYS 3.1 7.5 + - - -
163C TYR* 1.3 75.9 - - + +
165C LYS* 1.3 73.9 + - + +
167C ARG* 2.9 19.0 + - - +
168C ILE* 3.0 33.3 + - + +
211C ASN* 5.9 0.8 - - - +
403C SER* 3.0 23.3 + - - -
404C TYR* 3.4 40.1 + - + +
406C ASP* 3.0 39.5 + - - -
407C LEU* 3.7 26.8 - - - +
602C PMC 5.6 4.3 - - - +
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Residues in contact with LYS 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 4.2 11.7 - - - +
111A TYR* 3.3 34.3 + - - +
289A HIS* 4.6 11.1 + - - +
290A ILE* 4.6 20.2 - - + +
139C MET* 4.1 12.5 - - + +
163C TYR* 3.4 20.9 - - + +
164C ARG* 1.3 88.1 - - + +
166C THR* 1.3 62.6 + - - +
168C ILE* 3.3 24.5 + - + +
169C PHE* 3.2 21.1 + - - +
602C PMC 4.3 14.6 + - - +
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Residues in contact with THR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C MET* 3.8 16.8 - - + +
142C SER* 4.7 13.9 + - - -
146C LEU* 4.9 5.8 - - + -
162C CYS* 4.1 4.5 - - - -
163C TYR* 2.8 32.5 + - - +
165C LYS* 1.3 78.9 - - - +
167C ARG* 1.3 62.6 + - - +
169C PHE* 3.4 4.8 + - + +
170C ILE* 3.0 41.3 + - + +
205C PHE* 3.9 30.4 - - + -
500C PLP 4.7 3.6 - - - -
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Residues in contact with ARG 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C THR* 6.1 0.7 - - - -
159C THR 5.1 1.8 - - - -
160C THR* 3.6 19.6 + - - +
162C CYS* 4.4 20.6 - - + +
163C TYR 2.9 10.9 + - - +
164C ARG* 3.1 14.6 - - - +
166C THR* 1.3 75.1 - - - +
168C ILE* 1.3 61.1 + - + +
170C ILE* 3.2 11.9 + - - +
171C GLU* 2.9 62.3 + - + +
183C VAL* 4.2 25.9 - - - +
415C TYR* 2.8 52.7 + - - -
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Residues in contact with ILE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ILE* 4.2 20.9 - - + -
164C ARG* 3.0 36.9 + - + +
165C LYS* 3.3 32.1 + - + +
167C ARG* 1.3 77.9 - - + +
169C PHE* 1.3 60.6 + - - +
171C GLU* 4.5 3.1 - - - +
172C THR* 2.8 52.0 + - + +
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Residues in contact with PHE 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ILE* 4.0 22.6 - - + +
291A LEU* 3.8 22.2 - - + -
139C MET* 5.1 2.5 - - + -
143C THR* 4.0 17.0 - - + +
146C LEU* 3.7 32.3 - - + -
147C LEU* 3.7 24.9 - - + -
165C LYS 3.2 10.3 + - - +
166C THR* 3.6 11.0 - - + +
168C ILE* 1.3 79.4 - - - +
170C ILE* 1.3 59.4 + - + +
173C ILE* 3.0 63.4 + - + +
174C LEU* 3.3 34.8 + - + -
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Residues in contact with ILE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LEU* 4.2 14.6 - - + -
156C ILE* 4.3 8.5 - - + -
158C THR* 4.4 25.6 - - + +
162C CYS* 4.4 7.6 - - - -
166C THR* 3.0 31.9 - - + +
167C ARG* 3.2 7.3 + - - +
169C PHE* 1.3 78.2 - - - +
171C GLU* 1.3 61.3 + - + +
174C LEU* 3.7 29.9 - - + +
175C PRO* 3.3 17.2 - - - +
179C ILE* 5.0 3.2 - - + +
181C ALA* 4.0 27.2 - - + +
205C PHE* 5.0 2.7 - - + -
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Residues in contact with GLU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ARG* 2.9 59.5 + - + +
168C ILE* 4.2 3.2 - - - +
170C ILE* 1.3 81.8 - - + +
172C THR* 1.3 65.6 + - + +
175C PRO* 3.6 10.7 - - - +
181C ALA* 6.5 0.7 - - + -
183C VAL* 4.9 4.5 - - - +
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Residues in contact with THR 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ILE* 5.5 0.9 - - - +
168C ILE* 2.8 38.8 + - + +
171C GLU* 1.3 89.5 - - + +
173C ILE* 1.3 76.2 + - - +
175C PRO* 3.6 9.7 - - - +
176C LYS* 3.7 19.2 - - - +
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Residues in contact with ILE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 5.9 6.5 - - + +
177A MET* 5.7 7.0 - - + -
287A LEU* 3.7 28.9 - - + -
290A ILE* 5.4 5.4 - - + -
291A LEU* 5.9 0.7 - - + -
147C LEU* 5.3 6.3 - - + -
169C PHE* 3.0 47.3 + - + +
172C THR* 1.3 93.2 - - - +
174C LEU* 1.3 70.0 + - + +
175C PRO* 3.1 2.0 - - - -
176C LYS* 2.8 44.8 + - + +
177C MET* 4.0 3.8 + - + +
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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