Contacts of the strand formed by residues 182 - 190 (chain D) in PDB entry 1YY9
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 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D THR* 5.3 6.7 - - + +
149D LYS 3.8 0.2 - - - -
150D ASP* 2.7 27.0 + - - -
151D TYR* 2.8 42.5 + - + +
152D PHE* 3.6 31.3 - + - -
153D PRO* 5.3 0.2 - - + -
154D GLU* 3.9 37.4 - - + +
174D ALA* 4.0 17.3 - - + -
175D VAL 3.4 15.3 - - - -
176D LEU* 4.0 28.1 - - + +
177D GLN* 3.4 0.2 - - - +
181D LEU* 1.3 74.2 - - - +
183D SER* 1.3 62.1 + - - +
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Residues in contact with SER 183 (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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178C THR* 6.0 1.6 - - - +
147D LEU* 4.0 11.4 - - - +
148D VAL 3.3 7.5 + - - -
149D LYS* 3.6 18.6 - - - +
151D TYR* 4.2 2.2 - - - -
174D ALA* 3.3 4.3 - - - +
175D VAL* 3.0 32.1 + - - +
177D GLN* 3.3 30.6 + - - -
182D TYR* 1.3 79.3 - - - +
184D LEU* 1.3 69.9 + - - +
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Residues in contact with LEU 184 (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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147D LEU* 3.0 16.8 - - - +
148D VAL* 2.6 45.2 + - + +
151D TYR* 4.3 10.3 - - + +
154D GLU* 5.3 0.7 - - - +
156D VAL* 4.5 9.9 - - + -
158D VAL* 4.0 15.9 - - + -
171D THR* 3.8 17.9 - - + -
172D PHE* 2.7 26.0 - - - +
173D PRO* 4.6 1.1 - - + -
174D ALA* 3.5 24.2 - - + +
183D SER* 1.3 77.2 + - - +
185D SER* 1.3 88.9 + - - +
186D SER 4.2 0.2 - - - +
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Residues in contact with SER 185 (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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133C VAL* 5.3 7.2 - - - -
176C SER* 3.7 14.3 + - - -
178C THR* 5.8 2.2 - - - -
130D LEU* 4.8 6.7 - - - -
146D CYS 3.2 10.5 - - - -
147D LEU* 4.8 5.8 - - - -
148D VAL 5.4 0.2 - - - -
172D PHE* 3.1 52.4 + - - +
184D LEU* 1.3 88.8 - - - +
186D SER* 1.3 60.2 + - - +
187D VAL* 4.1 8.7 - - - -
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Residues in contact with SER 186 (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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146D CYS* 3.0 24.1 + - - -
148D VAL* 5.4 1.1 - - - -
158D VAL* 3.0 36.6 - - - +
160D TRP* 2.8 46.1 + - - -
169D VAL* 4.4 0.5 - - - +
170D HIS 3.7 4.3 - - - -
171D THR* 3.4 15.5 + - - +
184D LEU* 4.2 0.6 - - - +
185D SER* 1.3 73.9 - - - +
187D VAL* 1.3 59.3 + - - +
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Residues in contact with VAL 187 (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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118C PHE* 6.0 1.3 - - + -
135C LEU* 4.3 30.1 - - + -
137C ASN* 5.0 1.1 - - - +
176C SER* 6.0 1.3 - - - -
130D LEU* 4.3 21.3 - - + -
144D LEU 3.9 9.0 - - - +
160D TRP* 4.9 2.0 - - - -
168D GLY 3.5 0.4 - - - +
169D VAL* 3.3 4.5 - - - +
170D HIS* 2.6 72.4 + - + +
172D PHE* 3.2 28.0 - - + -
185D SER* 4.7 4.0 - - - -
186D SER* 1.3 78.5 + - - +
188D VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 188 (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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135C LEU* 6.4 0.7 - - - -
142D ALA 4.1 0.3 - - - +
143D ALA* 3.9 3.9 - - - +
144D LEU* 3.0 55.2 + - + +
145D GLY* 4.8 0.2 - - - -
160D TRP* 4.8 17.5 - - + -
165D LEU* 4.6 17.3 - - + -
167D SER 4.0 6.5 - - - +
168D GLY 3.5 11.7 - - - -
169D VAL* 3.4 29.2 - - + -
187D VAL* 1.3 75.9 - - - +
189D THR* 1.3 71.0 + - - +
190D VAL* 3.9 11.1 + - + +
200D TYR* 5.3 0.7 - - + -
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Residues in contact with THR 189 (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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114C SER* 5.9 0.7 - - - +
116C PHE* 5.5 2.7 - - + -
137C ASN* 2.8 29.5 + - + +
138C ASN* 4.9 6.0 + - - +
141D THR* 3.8 28.9 - - + -
142D ALA 3.8 6.5 - - - +
143D ALA* 4.8 6.7 - - + +
165D LEU* 5.9 0.7 - - - +
167D SER 4.6 1.9 - - - +
168D GLY* 3.4 24.3 + - - -
170D HIS* 5.0 0.3 - - - -
188D VAL* 1.3 83.5 - - - +
190D VAL* 1.3 66.1 + - - +
191D PRO* 4.8 0.7 - - - +
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Residues in contact with VAL 190 (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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140D GLY 3.1 9.4 - - - +
141D THR* 3.5 0.5 - - - -
142D ALA* 2.7 53.0 + - + +
144D LEU* 4.6 14.4 - - + -
165D LEU* 5.3 4.7 - - + -
188D VAL* 4.5 15.3 - - + +
189D THR* 1.3 80.8 - - - +
191D PRO* 1.4 83.1 - - + +
192D SER 4.4 0.2 - - - +
194D SER* 4.5 5.4 - - - +
200D TYR* 3.4 42.2 - - + +
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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