Contacts of the strand formed by residues 150 - 158 (chain D) in PDB entry 3O9Z
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 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D LEU* 3.9 18.4 + - - +
146D GLU* 2.7 46.1 + - - -
147D LYS 4.4 3.6 + - - -
148D GLY 3.1 19.1 + - - +
149D ALA* 1.3 77.5 - - - +
151D ASP* 1.3 60.9 + - - +
152D VAL* 4.3 1.6 - - + -
194D PHE* 3.8 21.3 - - + -
218D GLY 3.1 8.6 + - - +
219D ALA* 3.1 13.6 - - + -
220D ARG* 3.0 27.2 + - - +
249D VAL* 3.9 21.1 - - + -
250D ASP* 3.2 20.9 - - - +
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Residues in contact with ASP 151 (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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150D LYS* 1.3 72.9 - - - +
152D VAL* 1.3 64.3 + - - +
153D VAL* 4.9 1.0 - - - +
220D ARG* 2.8 40.3 + - + +
222D ARG* 3.2 26.3 + - - -
248D ALA 3.7 1.0 - - - +
249D VAL 3.7 0.3 - - - -
250D ASP* 2.8 47.2 + - - +
251D GLY 4.8 0.2 + - - -
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Residues in contact with VAL 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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150D LYS* 4.3 4.7 - - + -
151D ASP* 1.3 79.9 + - - +
153D VAL* 1.3 74.4 + - - +
154D LEU* 4.8 0.4 - - + -
190D LEU* 4.3 8.1 - - + -
194D PHE* 3.9 28.9 - - + -
219D ALA* 4.0 10.1 - - + -
220D ARG 2.9 17.0 + - - +
221D VAL* 3.3 17.6 - - + -
222D ARG* 3.0 26.2 + - - +
247D ILE* 3.7 25.4 - - + -
248D ALA 3.3 8.7 - - - +
249D VAL* 4.2 9.4 - - + -
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Residues in contact with VAL 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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151D ASP* 4.9 0.9 - - - +
152D VAL* 1.3 77.1 - - - +
154D LEU* 1.3 61.3 + - - +
155D THR* 4.0 6.0 + - - +
222D ARG* 3.4 40.8 - - + +
246D SER* 3.7 2.6 + - - +
247D ILE* 3.5 2.4 - - - -
248D ALA* 3.0 42.6 + - + +
306D HIS* 3.6 28.0 - - + +
307D PRO* 4.3 11.9 - - + -
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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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152D VAL* 4.2 2.4 - - + -
153D VAL* 1.3 72.9 - - - +
155D THR* 1.3 74.3 + - - +
156D TYR* 4.2 3.6 - - + +
186D PHE* 4.1 28.9 - - + -
187D PHE* 6.2 1.8 - - + -
189D LEU* 5.5 0.2 - - + -
190D LEU* 4.5 15.3 - - + -
221D VAL* 4.2 10.1 - - + -
222D ARG 2.9 6.8 + - - +
223D TRP* 3.2 21.8 - - + -
224D PHE 3.0 22.5 + - - -
225D LEU* 4.3 17.3 - - + -
246D SER 3.4 2.0 - - - +
247D ILE* 3.2 46.0 - - + -
306D HIS* 3.3 4.7 + - - -
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Residues in contact with THR 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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153D VAL* 4.0 7.3 + - - +
154D LEU* 1.3 75.4 - - - +
156D TYR* 1.3 63.9 + - - +
157D VAL* 4.3 6.7 - - + -
186D PHE* 5.9 0.2 - - - -
224D PHE* 3.5 6.5 - - + +
244D TYR* 3.6 26.7 - - + +
245D ARG* 3.6 0.9 - - - -
246D SER* 2.8 39.0 + - - +
306D HIS* 2.8 25.4 + - + +
308D PHE* 3.5 36.3 - - + -
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Residues in contact with TYR 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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154D LEU* 4.2 1.5 - - + +
155D THR* 1.3 75.5 - - - +
157D VAL* 1.3 73.3 + - - +
158D THR* 3.1 26.8 + - + -
182D ILE* 3.6 22.0 - - + -
185D HIS* 6.0 0.2 - + - -
186D PHE* 3.4 26.2 - + + -
224D PHE 2.9 10.7 + - - +
225D LEU* 3.3 18.6 - - + +
226D SER 2.9 25.1 + - - +
243D THR* 4.1 1.3 - - + -
244D TYR 3.2 9.4 - - - -
245D ARG* 1.8 71.3 + - + -
312D AKG 1.9 31.7 + - + -
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Residues in contact with VAL 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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155D THR* 4.3 16.2 - - + -
156D TYR* 1.3 79.1 - - - +
158D THR* 1.3 65.4 + - - +
159D GLY 4.2 0.2 - - - -
224D PHE* 4.3 10.3 - - + -
226D SER* 3.3 7.6 - - - +
228D ASP 3.3 29.4 - - - +
229D PRO* 4.1 2.2 - - + -
231D PHE* 3.9 26.5 - - + +
232D VAL* 3.8 27.8 - - + +
242D ARG 4.8 0.2 - - - +
243D THR* 3.2 3.9 - - - +
244D TYR* 2.7 44.9 + - + +
308D PHE* 4.5 0.4 - - + -
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Residues in contact with THR 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 TYR* 3.1 46.5 + - + +
157D VAL* 1.3 72.7 - - - +
159D GLY* 1.3 64.7 + - - +
160D ARG* 2.7 31.7 + - - +
182D ILE* 3.9 17.5 - - + -
226D SER 2.9 12.6 + - - +
227D ILE* 3.1 19.4 - - + +
242D ARG 3.9 2.2 - - - -
243D THR* 3.9 10.9 + - - +
245D ARG* 5.1 0.9 + - - -
312D AKG 3.5 5.8 + - - +
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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