Contacts of the strand formed by residues 153 - 161 (chain D) in PDB entry 3Q2K
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 ILE 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C LEU* 4.8 1.0 - - - +
145D ILE* 4.3 30.7 - - + -
150D PHE* 3.9 23.6 - - + -
151D GLY 3.2 3.3 + - - +
152D ARG* 1.3 81.1 + - - +
154D TYR* 1.3 63.8 + - - +
156D VAL* 4.2 5.6 - - + -
200D VAL* 4.1 26.0 - - + +
231D HIS* 4.4 14.7 + - + +
233D ALA* 3.4 30.0 + - + +
254D ILE* 4.1 28.7 - - + -
255D LEU 4.2 2.2 - - - +
256D GLY* 3.9 3.6 - - - -
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Residues in contact with TYR 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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213C LEU* 3.6 39.1 - - + +
214C ALA* 3.9 16.7 - - + +
222C THR* 3.8 8.0 - - + +
240C THR* 4.8 2.7 - - - +
242C LEU* 3.6 48.2 - - + -
152D ARG* 3.7 24.5 - - + +
153D ILE* 1.3 77.4 - - - +
155D MET* 1.3 66.4 + - + +
233D ALA* 3.3 7.0 - - - -
234D MET 2.9 21.7 + - - +
255D LEU* 2.9 12.5 + - + +
256D GLY* 3.5 8.3 - - - -
257D GLU* 3.0 55.9 + - + +
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Residues in contact with MET 155 (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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161C PHE* 3.9 20.9 - - + -
222C THR* 4.0 11.9 - - + -
223C GLY 3.3 17.3 - - - +
224C VAL* 5.1 0.9 - - + -
238C ASN* 4.1 19.5 - - - +
239C VAL 3.2 35.2 - - - +
240C THR* 4.3 9.0 - - + -
153D ILE* 4.5 0.4 - - - +
154D TYR* 1.3 80.5 - - + +
156D VAL* 1.3 80.2 + - - +
157D THR* 4.5 0.4 - - - +
233D ALA* 4.3 0.6 - - - +
234D MET* 3.2 15.7 - - + +
235D GLY* 4.3 5.2 - - - -
253D THR* 6.3 0.7 - - + -
254D ILE* 3.7 0.2 - - - -
255D LEU* 2.8 48.2 + - + +
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Residues in contact with VAL 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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153D ILE* 4.2 11.4 - - + -
155D MET* 1.3 81.2 - - - +
157D THR* 1.3 69.3 + - - +
158D VAL* 4.6 5.4 - - + -
196D LEU* 5.0 1.1 - - + -
200D VAL* 4.2 26.9 - - + -
227D LEU* 5.2 0.4 - - + +
229D TRP* 3.6 36.7 - - + -
233D ALA* 4.7 0.7 - - + -
234D MET 2.9 8.2 + - - +
235D GLY* 2.7 29.6 - - - -
236D SER 3.0 4.0 + - - +
252D ILE* 4.4 13.7 - - + -
253D THR 3.5 12.1 - - - +
254D ILE* 4.3 12.6 - - + -
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Residues in contact with THR 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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157C THR* 5.0 1.1 - - + -
159C ASN* 4.3 8.5 + - - +
161C PHE* 3.4 27.2 - - - -
238C ASN* 4.0 15.2 - - - +
155D MET* 4.5 1.7 - - - +
156D VAL* 1.3 77.2 + - - +
158D VAL* 1.3 66.5 + - - +
159D ASN* 3.9 13.1 + - - +
236D SER* 3.4 21.3 - - - +
238D ASN* 3.8 12.8 - - - +
251D SER* 3.9 1.7 + - - +
252D ILE* 3.4 1.4 - - - -
253D THR* 3.0 40.9 + - - -
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Residues in contact with VAL 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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156D VAL* 4.6 3.4 - - + -
157D THR* 1.3 76.1 - - - +
159D ASN* 1.3 67.5 + - - +
160D VAL* 4.3 5.4 - - + -
192D TYR* 4.0 26.2 - - + +
195D LEU* 5.5 0.7 - - + -
196D LEU* 3.9 25.4 - - + -
236D SER 2.9 11.2 + - - +
237D ILE* 3.2 28.6 - - + +
238D ASN* 2.9 26.2 + - - -
251D SER 3.2 11.0 - - - +
252D ILE* 3.7 28.0 - - + -
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Residues in contact with ASN 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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157C THR* 4.4 7.2 + - - +
159C ASN* 5.4 4.9 - - - +
262C ARG* 4.5 7.1 - - - +
157D THR* 3.9 10.2 - - - +
158D VAL* 1.3 73.4 - - - +
160D VAL* 1.3 63.4 + - - +
161D PHE* 3.6 30.4 - - + -
238D ASN* 2.9 33.5 + - - +
249D GLU* 3.6 20.0 + - - +
250D GLY* 3.0 6.1 - - - -
251D SER* 2.8 46.1 + - - +
262D ARG* 4.5 3.8 - - - +
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Residues in contact with VAL 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 VAL* 4.3 5.6 - - + -
159D ASN* 1.3 76.5 - - - +
161D PHE* 1.3 61.3 + - - +
162D TRP* 3.8 39.0 - - + -
189D ALA* 3.9 25.4 - - + -
192D TYR* 3.7 37.5 - - + -
237D ILE* 4.9 0.4 - - + -
238D ASN 2.9 10.8 + - - +
239D VAL* 3.5 9.9 - - + +
240D THR 3.1 27.2 + - - +
241D MET* 4.2 6.1 - - + -
249D GLU 3.6 2.0 - - - -
250D GLY* 4.4 0.7 - - - -
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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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155C MET* 3.8 15.5 - - + -
157C THR* 3.6 23.1 - - - -
253C THR* 4.1 18.8 - - + -
255C LEU* 3.5 28.5 - - + -
159D ASN* 3.6 31.0 - - + -
160D VAL* 1.3 81.3 - - - +
162D TRP* 1.3 52.1 + - - +
238D ASN* 3.2 27.6 - - + -
240D THR* 4.0 6.7 - - + -
243D THR* 3.3 10.3 + - - +
248D LEU* 2.8 43.1 + - + +
249D GLU* 2.7 37.6 + - + +
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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