Contacts of the helix formed by residues 163 - 173 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I MET* 3.8 11.7 - - - -
161I ASP 4.4 0.7 - - - -
162I CYS* 1.3 74.0 - - - +
164I ARG* 1.3 72.3 + - + +
165I LYS* 3.4 23.9 - - + +
166I THR* 2.9 40.5 + - - +
167I ARG* 2.9 10.4 + - - +
207I GLU* 3.1 21.1 + - - +
211I ASN* 4.3 19.3 - - - +
500I PLP 3.7 35.0 - + + +
608I PMC 3.0 67.1 + + - -
110K ARG* 3.4 13.3 + - - -
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Residues in contact with ARG 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I CYS 3.2 5.8 + - - -
163I TYR* 1.3 77.6 - - + +
165I LYS* 1.3 69.8 + - + +
167I ARG* 2.8 25.5 + - - +
168I ILE* 3.0 33.4 + - + +
211I ASN* 5.6 1.2 - - - +
403I SER* 3.0 22.0 + - - -
404I TYR* 3.4 39.9 + - + +
406I ASP* 2.8 42.5 + - - -
407I LEU* 3.7 25.3 - - - +
608I PMC 5.5 4.0 - - - +
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Residues in contact with LYS 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I MET* 4.0 11.9 - - - -
163I TYR* 3.4 21.4 - - + +
164I ARG* 1.3 88.2 - - + +
166I THR* 1.3 61.8 + - - +
168I ILE* 3.3 24.7 + - - +
169I PHE* 3.1 21.7 + - - +
608I PMC 4.3 13.7 + - - +
110K ARG* 4.3 11.9 - - - +
111K TYR* 3.4 31.9 + - - +
289K HIS* 4.5 5.9 + - - +
290K ILE* 4.3 29.6 - - + +
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Residues in contact with THR 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I MET* 3.8 17.1 - - + +
142I SER* 4.7 13.9 + - - -
146I LEU* 4.8 6.3 - - + -
162I CYS* 4.2 5.8 - - - -
163I TYR* 2.9 29.9 + - - +
165I LYS* 1.3 79.1 - - - +
167I ARG* 1.3 63.3 + - - +
169I PHE* 3.3 5.6 + - + +
170I ILE* 3.1 39.9 + - + +
205I PHE* 4.0 30.1 - - + -
207I GLU* 5.5 0.3 + - - -
500I PLP 4.7 3.8 + - - -
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Residues in contact with ARG 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I THR* 6.1 0.7 - - - -
159I THR 5.2 2.0 - - - -
160I THR* 3.5 20.6 + - - +
162I CYS* 4.6 20.8 - - + +
163I TYR 2.9 9.8 + - - +
164I ARG* 2.8 16.4 + - + +
166I THR* 1.3 76.8 - - - +
168I ILE* 1.3 65.2 + - + +
170I ILE* 2.9 12.3 + - - +
171I GLU* 2.8 57.5 + - + +
183I VAL* 4.2 23.3 - - - +
415I TYR* 2.7 52.6 + - - -
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Residues in contact with ILE 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I ARG* 3.0 32.8 + - + +
165I LYS* 3.4 34.8 - - + +
167I ARG* 1.3 76.8 - - + +
169I PHE* 1.3 57.9 + - - +
171I GLU* 3.0 4.6 + - - +
172I THR* 2.8 56.9 + - + +
290K ILE* 4.1 21.3 - - + -
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Residues in contact with PHE 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I MET* 5.1 2.5 - - + -
143I THR* 3.8 23.8 - - + +
146I LEU* 3.7 32.8 - - + -
147I LEU* 3.7 28.7 - - + -
165I LYS 3.1 9.9 + - - +
166I THR* 3.5 11.2 - - + +
168I ILE* 1.3 78.7 - - - +
170I ILE* 1.3 59.7 + - - +
173I ILE* 3.1 55.1 + - + +
174I LEU* 3.3 31.1 + - + -
290K ILE* 4.1 18.8 - - + +
291K LEU* 3.7 23.3 - - + -
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Residues in contact with ILE 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I LEU* 4.3 15.3 - - + -
156I ILE* 4.1 11.2 - - + -
158I THR* 4.3 26.9 - - + +
162I CYS* 4.9 4.5 - - - -
166I THR* 3.1 29.6 - - + +
167I ARG* 2.9 10.8 + - - +
169I PHE* 1.3 77.3 - - - +
171I GLU* 1.3 62.0 + - + +
172I THR 3.5 0.2 - - - -
174I LEU* 3.7 27.4 - - + +
175I PRO* 3.4 16.0 - - - +
179I ILE* 5.0 2.9 - - + +
181I ALA* 4.0 27.2 - - + +
205I PHE* 4.9 2.5 - - + -
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Residues in contact with GLU 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167I ARG* 2.8 59.2 + - + +
168I ILE* 4.1 3.3 - - - +
170I ILE* 1.3 82.5 - - + +
172I THR* 1.3 65.8 + - + +
175I PRO* 3.7 12.1 - - - +
183I VAL* 4.8 6.5 - - + +
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Residues in contact with THR 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I ILE* 2.8 43.2 + - + +
171I GLU* 1.3 87.5 - - + +
173I ILE* 1.3 78.0 + - - +
175I PRO* 3.7 9.2 - - - +
176I LYS* 3.8 19.4 - - - +
290K ILE* 5.6 0.3 - - - +
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Residues in contact with ILE 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I LEU* 5.4 6.1 - - + -
169I PHE* 3.1 44.5 + - + +
172I THR* 1.3 95.8 - - - +
174I LEU* 1.3 69.9 + - + +
175I PRO* 3.1 2.0 - - - -
176I LYS* 2.9 43.8 + - + +
177I MET* 3.9 4.2 + - + +
147K LEU* 5.9 7.0 - - + -
177K MET* 5.5 7.6 - - - -
287K LEU* 4.1 25.6 - - + -
290K ILE* 5.6 6.1 - - + -
291K 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