Contacts of the strand formed by residues 150 - 158 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.3 24.0 + - + +
146B GLU* 2.9 62.0 + - - +
147B LYS 4.5 2.1 + - - +
148B GLY 3.8 8.7 + - - +
149B ALA* 1.3 80.7 - - - +
151B ASP* 1.3 63.9 + - - +
152B VAL* 4.3 1.8 - - + -
194B PHE* 3.9 23.1 - - + -
218B GLY 3.0 9.6 + - - +
219B ALA* 3.1 3.1 - - - +
220B ARG* 2.8 27.6 + - - +
249B VAL* 3.5 20.9 - - + -
250B ASP* 3.9 14.8 - - + +
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ALA 4.9 0.5 - - - +
150B LYS* 1.3 73.0 - - - +
152B VAL* 1.3 60.9 + - - +
153B VAL* 5.9 0.4 - - - -
220B ARG* 2.8 53.3 + - - +
248B ALA 3.7 0.9 - - - +
249B VAL* 3.5 19.9 - - - +
250B ASP 4.0 4.7 + - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LYS* 4.3 0.7 - - + -
151B ASP* 1.3 77.7 - - - +
153B VAL* 1.3 73.0 + - - +
154B LEU* 4.2 0.9 - - + +
190B LEU* 4.3 4.5 - - + -
194B PHE* 3.7 23.3 - - + -
219B ALA* 3.9 14.1 - - + -
220B ARG 2.9 11.2 + - - +
221B VAL* 3.4 20.6 - - + -
222B ARG* 2.9 27.5 + - - +
247B ILE* 3.7 26.0 - - + -
248B ALA 3.2 9.0 - - - +
249B VAL* 3.7 19.7 - - + -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP 5.9 0.2 - - - -
152B VAL* 1.3 78.3 - - - +
154B LEU* 1.3 59.9 + - - +
155B THR* 4.0 6.8 + - - +
222B ARG* 3.4 37.9 - - + +
246B SER* 3.8 2.1 + - - +
247B ILE* 3.6 2.3 - - - -
248B ALA* 2.9 44.4 + - + +
306B HIS* 3.5 31.6 - - + +
307B PRO* 4.0 14.8 - - + -
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B VAL* 4.1 1.3 - - + -
153B VAL* 1.3 72.2 - - - +
155B THR* 1.3 66.3 + - - +
156B TYR* 3.9 18.2 - - + -
186B PHE* 3.6 49.1 - - + -
189B LEU* 4.4 11.0 - - + -
190B LEU* 4.4 8.5 - - + -
221B VAL* 4.1 11.4 - - + -
222B ARG 2.8 10.2 + - - +
223B TRP* 3.2 10.5 - - + -
224B PHE 3.0 25.9 + - - +
246B SER 3.5 11.7 - - - +
247B ILE* 3.8 26.9 - - + -
256B PHE* 4.7 3.4 - - + -
306B HIS* 3.4 3.5 + - - -
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Residues in contact with THR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B VAL* 4.0 7.1 + - - +
154B LEU* 1.3 72.5 - - - +
156B TYR* 1.3 63.4 + - - +
157B VAL* 4.3 7.0 - - + -
224B PHE* 3.5 5.4 - - + -
244B TYR* 3.5 27.7 - - + +
245B ARG* 3.5 2.1 - - - -
246B SER* 2.9 38.9 + - - +
306B HIS* 2.9 23.1 + - + +
308B PHE* 3.5 37.1 - - + -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 4.7 0.7 - - + -
154B LEU* 3.9 3.4 - - + -
155B THR* 1.3 75.5 - - - +
157B VAL* 1.3 60.5 + - - +
158B THR* 4.0 6.3 - - + -
182B ILE* 3.9 17.5 - - + -
185B HIS* 3.6 25.6 - - + +
186B PHE* 3.7 38.4 - + + -
224B PHE 2.8 13.4 + - - +
225B LEU* 3.2 20.2 - - + +
226B SER 2.9 24.1 + - - -
244B TYR 3.5 2.0 - - - -
245B ARG* 3.7 23.1 - - + -
256B PHE* 4.0 21.1 - + - -
260B PHE* 3.3 19.9 - - - -
312B AKG 2.6 29.9 + - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B THR* 4.3 15.9 - - + -
156B TYR* 1.3 78.0 - - - +
158B THR* 1.3 67.6 + - - +
224B PHE* 4.3 9.0 - - + -
226B SER* 3.2 8.1 - - - +
228B ASP 3.5 25.1 - - - +
229B PRO* 4.2 3.8 - - + -
231B PHE* 3.8 27.1 - - + +
232B VAL* 3.8 22.7 - - + +
242B ARG 4.8 0.2 - - - +
243B THR* 3.2 4.4 - - - -
244B TYR* 2.8 50.0 + - + +
245B ARG* 4.3 1.9 - - - +
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B TYR* 4.0 5.6 - - + -
157B VAL* 1.3 76.5 - - - +
159B GLY* 1.3 65.4 + - - +
160B ARG* 2.9 22.0 + - - +
182B ILE* 3.6 24.7 - - + -
226B SER 2.9 13.3 + - - +
227B ILE* 3.2 19.0 - - + +
242B ARG 3.9 2.5 - - - -
243B THR* 3.8 1.9 - - - +
245B ARG* 3.5 7.7 + - - -
312B AKG 2.8 41.6 + - - +
313B EDO 3.4 10.0 - - - -
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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