Contacts of the helix formed by residues 158 - 168 (chain D) in PDB entry 1YI2
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 158 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D ASP 4.4 0.8 + - - -
102D GLY* 3.7 4.7 - - - -
136D ARG* 4.9 1.2 + - - -
153D THR 5.2 2.1 - - - +
154D LYS 5.4 0.9 - - - +
156D ARG* 3.5 11.8 - - - +
157D LEU* 1.3 84.0 - - - +
159D PRO* 1.3 78.5 - - + +
160D ALA* 3.3 7.0 - - + +
161D ASP* 3.1 24.0 + - - +
162D ALA* 2.9 24.1 + - - +
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Residues in contact with PRO 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D PHE* 4.2 11.5 - - + -
99D ASP 3.3 26.9 - - - +
100D ASP* 3.8 16.6 - - - +
102D GLY* 4.2 2.0 - - - -
158D ASN* 1.3 90.7 - - + +
160D ALA* 1.3 63.2 + - + +
162D ALA* 3.0 9.1 + - + +
163D VAL* 2.9 29.6 + - + +
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D ASN* 3.3 4.4 - - + -
159D PRO* 1.3 79.7 - - - +
161D ASP* 1.3 68.1 + - - +
162D ALA 2.8 1.9 + - - -
163D VAL* 2.9 20.3 + - - +
164D ALA* 3.0 13.1 + - - +
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Residues in contact with ASP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG* 5.9 1.2 + - - -
16D PRO* 4.1 6.6 - - + +
136D ARG* 4.2 14.4 + - - +
157D LEU* 3.7 22.7 - - + -
158D ASN* 3.1 34.9 + - - +
160D ALA* 1.3 80.1 - - - +
162D ALA* 1.3 60.6 + - - +
164D ALA* 3.7 7.9 - - - +
165D PHE* 3.3 22.3 + - - +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D PHE* 3.8 14.6 - - + -
102D GLY* 3.4 31.6 - - - +
134D LEU* 4.3 6.1 - - + -
157D LEU* 4.4 8.7 - - + +
158D ASN 2.9 13.5 + - - +
159D PRO 3.1 10.5 - - - +
160D ALA 2.8 1.0 + - - -
161D ASP* 1.3 74.7 - - - +
163D VAL* 1.3 66.7 + - - +
164D ALA 3.2 0.2 + - - -
165D PHE* 3.2 4.1 + - - +
166D ILE* 3.1 26.7 + - - +
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Residues in contact with VAL 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D THR* 6.2 4.5 - - + -
98D PHE* 4.0 29.4 - - + -
159D PRO* 2.9 22.9 + - + +
160D ALA* 2.9 10.0 + - - +
162D ALA* 1.3 74.6 - - - +
164D ALA* 1.3 55.9 + - - +
166D ILE* 4.0 1.1 - - - +
167D GLU* 2.6 46.0 + - + +
173D GLU* 3.4 40.4 - - + +
174D VAL* 5.2 0.7 - - + +
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ALA 3.0 14.6 + - - +
161D ASP* 3.7 10.3 - - - +
163D VAL* 1.3 76.2 - - - +
165D PHE* 1.3 59.1 + - - +
167D GLU* 3.7 7.9 - - - +
168D SER* 2.8 35.8 + - - -
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Residues in contact with PHE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 5.4 2.0 - - + -
16D PRO* 3.4 50.9 - - + -
17D ARG* 4.0 11.4 - - - -
18D ILE* 4.3 14.1 - - + -
134D LEU* 4.2 21.5 - - + -
161D ASP 3.3 14.5 + - - +
162D ALA* 3.2 5.6 + - - +
164D ALA* 1.3 79.0 - - - +
166D ILE* 1.3 75.4 + - + +
168D SER* 3.5 10.0 + - - -
169D THR* 3.1 26.2 + - + -
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Residues in contact with ILE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 6.2 1.6 - - + -
88D LEU* 4.5 15.5 - - + -
93D LEU* 4.6 12.1 - - + -
98D PHE* 4.2 9.9 - - + -
104D PHE* 3.1 37.5 - - + -
132D VAL* 5.0 0.9 - - + -
134D LEU* 3.3 27.8 - - + -
162D ALA 3.1 13.9 + - - +
163D VAL* 4.0 2.2 - - - +
165D PHE* 1.3 82.6 - - + +
167D GLU* 1.3 58.7 + - - +
168D SER 2.9 1.8 - - - -
169D THR* 2.6 41.0 + - - +
171D ASP* 3.8 16.6 - - - +
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Residues in contact with GLU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D VAL* 2.6 32.1 + - + +
164D ALA* 3.7 5.7 - - - +
166D ILE* 1.3 73.6 - - - +
168D SER* 1.3 52.0 + - - +
169D THR* 2.7 11.4 + - - -
170D TYR 4.1 0.5 + - - -
171D ASP* 3.4 34.8 + - - +
172D VAL* 3.9 5.9 - - - +
173D GLU* 2.9 60.9 + - - +
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Residues in contact with SER 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ALA 2.8 20.9 + - - -
165D PHE* 3.5 7.4 - - - -
166D ILE 2.9 0.4 - - - -
167D GLU* 1.3 73.4 - - - +
169D THR* 1.3 66.2 + - - +
170D TYR 4.2 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