Contacts of the strand formed by residues 151 - 161 (chain D) in PDB entry 4YO0
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 LYS 151 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C TYR* 6.0 1.6 - - - +
166C LYS* 3.7 28.0 - - - +
146D GLU* 3.2 31.0 + - + +
147D LEU* 3.5 8.7 + - - +
149D GLY* 3.1 18.8 + - - +
150D ASN* 1.3 81.5 - - - +
152D ALA* 1.3 62.2 + - - +
201D LEU 3.7 7.0 - - - +
202D THR* 4.4 0.4 - - - +
203D ALA 4.2 1.8 - - - -
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Residues in contact with ALA 152 (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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166C LYS* 5.4 0.2 - - - -
142D PRO* 3.7 24.9 - - + -
146D GLU* 3.7 4.0 - - - -
147D LEU* 3.8 9.4 - - + -
151D LYS* 1.3 77.7 - - - +
153D THR* 1.3 62.1 + - - +
154D LEU* 4.1 2.5 - - + -
199D LEU 3.7 1.2 - - - +
200D ARG* 3.6 2.8 - - - +
201D LEU* 2.8 47.4 + - + +
202D THR 3.9 4.5 - - - +
206D TRP* 3.9 17.9 - - + -
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Residues in contact with THR 153 (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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147C LEU* 6.1 0.2 - - - +
164C LEU* 3.9 18.9 - - + +
166C LYS* 3.6 16.9 + - + +
199C THR* 5.5 2.9 - - + -
141D PRO 4.1 2.6 - - - +
142D PRO* 3.7 18.9 - - - +
146D GLU* 2.5 33.3 + - - +
152D ALA* 1.3 73.1 - - - +
154D LEU* 1.3 73.2 + - - +
155D VAL* 4.0 6.0 + - + +
198D PHE* 4.0 24.9 - - + -
199D LEU 3.5 7.6 - - - +
200D ARG* 4.7 7.9 - - + +
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Residues in contact with LEU 154 (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 PHE 3.7 2.9 - - - -
142D PRO* 3.5 29.6 - - + -
152D ALA* 5.2 2.0 - - + -
153D THR* 1.3 74.0 - - - +
155D VAL* 1.3 60.6 + - - +
170D TRP* 3.6 24.8 - - + -
198D PHE* 3.2 10.6 - - - +
199D LEU* 2.8 45.1 + - + +
201D LEU* 4.6 7.2 - - + -
206D TRP* 3.6 13.7 - - + -
212D PHE* 3.5 42.2 - - + -
227D LEU* 3.7 14.8 - - + -
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C LEU* 4.4 17.0 - - + -
164C LEU* 4.5 11.0 - - + -
201C THR* 3.8 17.5 - - + +
139D VAL* 3.2 7.8 - - - +
140D PHE* 2.9 47.4 + - + +
153D THR 4.2 10.8 - - - +
154D LEU* 1.3 77.9 - - - +
156D CYS* 1.3 63.3 + - - +
157D LEU* 3.6 30.7 - - + -
170D TRP* 4.3 2.2 - - - -
197D SER 3.9 2.7 - - - -
198D PHE* 4.0 20.2 - - + -
227D LEU* 4.9 0.2 - - - +
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Residues in contact with CYS 156 (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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137D LEU* 4.4 11.4 - - - -
138D THR 3.5 3.4 - - - -
139D VAL* 4.1 8.7 - - + -
155D VAL* 1.3 75.7 - - - +
157D LEU* 1.3 61.7 + - - +
158D ILE* 4.2 14.6 - - - +
170D TRP* 3.6 12.3 - - + -
196D SER* 3.3 6.1 - - - -
197D SER* 2.8 40.3 + - - +
214D CYS* 2.1 53.8 - - + -
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Residues in contact with LEU 157 (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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160C THR* 5.1 0.9 - - + -
189C PHE* 3.9 22.4 - - + -
201C THR* 4.0 24.7 - - + -
203C SER* 3.9 26.7 - - - +
136D THR 3.4 1.9 - - - +
137D LEU* 3.3 7.1 - - - +
138D THR* 2.8 49.0 + - + +
140D PHE* 3.8 25.1 - - + -
155D VAL* 3.6 23.1 - - + -
156D CYS* 1.3 76.8 - - - +
158D ILE* 1.3 61.8 + - - +
159D SER* 4.9 1.5 + - - +
195D ALA 4.1 1.6 - - - -
196D SER* 4.2 12.3 - - - -
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Residues in contact with ILE 158 (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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189C PHE* 3.7 1.3 - - - -
135D PRO* 3.6 28.9 - - + -
136D THR 3.5 3.4 - - - -
137D LEU* 3.9 14.8 - - + -
156D CYS* 4.2 13.9 - - - +
157D LEU* 1.3 75.8 - - - +
159D SER* 1.3 61.1 + - - +
161D PHE* 3.7 15.5 - - + -
166D VAL* 4.9 2.2 - - + -
168D VAL* 3.6 24.5 - - + -
194D ILE* 3.3 5.5 - - - +
195D ALA* 2.9 55.1 + - + +
196D SER* 4.6 5.8 - - - +
197D SER 4.9 0.2 - - - +
216D VAL* 3.5 28.3 - - + -
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Residues in contact with SER 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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187C HIS* 4.9 9.9 - - - -
189C PHE* 4.7 9.1 - - - -
135D PRO* 3.4 3.6 - - - +
136D THR* 2.9 41.5 + - - +
138D THR* 5.3 3.8 + - - -
157D LEU* 4.9 2.4 + - - +
158D ILE* 1.3 76.8 - - - +
160D ASP* 1.3 70.3 + - - +
161D PHE* 3.3 5.5 + - - -
193D TYR 4.0 5.6 - - - -
194D ILE* 3.9 15.0 - - - -
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Residues in contact with ASP 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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187C HIS* 5.9 0.8 + - - -
133D SER* 3.1 17.3 + - - -
134D THR 3.5 12.1 - - - +
136D THR* 4.0 17.6 + - - +
159D SER* 1.3 82.7 - - - +
161D PHE* 1.3 57.9 + - - +
192D LYS* 2.9 40.3 + - - +
193D TYR 3.5 6.8 + - - -
194D ILE* 4.8 0.8 - - - +
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Residues in contact with PHE 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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133D SER* 3.4 14.4 - - - +
135D PRO* 3.8 17.0 - - + -
158D ILE* 3.5 34.3 - - + -
159D SER 3.7 11.2 - - - -
160D ASP* 1.3 79.6 - - - +
162D TYR* 1.4 59.8 + - - +
163D PRO 3.4 18.6 - - - -
164D SER 3.3 23.3 - - - -
166D VAL* 3.6 20.0 - - + -
186D PRO* 3.8 9.6 - - + -
192D LYS* 3.5 6.0 - - - +
193D TYR* 3.1 57.6 + - + +
194D ILE* 3.5 17.9 - - - -
195D ALA* 4.0 6.5 - - + -
218D HIS* 4.0 3.6 - + - +
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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