Contacts of the strand formed by residues 228 - 240 (chain B) in PDB entry 5WJ9
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 LEU 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 4.8 0.7 - - + -
167B GLN* 4.6 6.3 - - + -
168B ARG 3.6 9.0 - - - +
169B TYR* 4.2 2.7 - - + -
223B LEU* 4.0 37.0 - - + +
224B LYS 3.1 8.4 + - - +
225B PHE* 3.3 29.9 + - + +
226B HIS 3.4 0.4 - - - -
227B LYS* 1.3 75.0 - - - +
229B VAL* 1.3 56.2 + - - +
230B ASN* 3.2 35.9 - - - +
231B VAL* 3.9 13.0 - - + +
262B PHE* 5.8 1.1 - - + +
264B ASN* 2.8 29.0 + - - +
267B HIS* 3.3 10.1 - - - -
271B ILE* 4.3 20.9 - - + -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 2.8 27.7 + - + +
169B TYR* 4.0 11.9 - - - -
170B TYR* 3.9 36.6 - - + +
188B VAL* 4.2 15.9 - - + -
227B LYS 3.5 0.4 + - - +
228B LEU* 1.3 74.4 - - - +
230B ASN* 1.3 72.1 + - - +
264B ASN* 2.9 32.8 + - - +
265B LYS* 3.6 18.1 + - + +
267B HIS* 4.8 2.5 - - - +
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Residues in contact with ASN 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 2.8 79.8 + - - +
228B LEU* 3.2 14.9 - - - +
229B VAL* 1.3 86.8 - - - +
231B VAL* 1.3 63.7 + - - +
232B THR* 3.2 29.1 + - - +
261B THR* 4.9 2.7 - - + +
262B PHE 3.1 21.1 - - - +
263B ASP* 4.1 4.5 - - - -
264B ASN* 4.0 4.3 - - - +
265B LYS* 4.0 5.1 + - - +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 4.5 11.4 - - + -
165B LEU* 4.3 25.6 - - + -
166B CYS 3.6 6.3 - - - +
167B GLN* 4.2 11.4 - - + -
221B LEU* 5.7 0.7 - - + -
223B LEU* 3.8 28.9 - - + -
228B LEU* 3.9 12.3 - - + -
230B ASN* 1.3 79.5 - - - +
232B THR* 1.3 70.3 + - - +
233B ILE* 4.8 1.1 - - + -
261B THR* 3.7 1.0 - - - -
262B PHE* 2.8 59.4 + - + -
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Residues in contact with THR 232 (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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164B ALA 3.4 4.9 - - - +
165B LEU* 3.4 1.2 - - - -
166B CYS* 2.8 46.6 + - - +
168B ARG* 5.1 9.8 + - - +
230B ASN* 3.2 23.7 + - - +
231B VAL* 1.3 75.5 - - - +
233B ILE* 1.3 60.1 + - - +
234B HIS* 3.4 25.9 + - + +
259B LEU* 3.9 18.4 - - + -
260B ILE 3.5 2.7 - - - -
261B THR* 4.0 13.0 - - + +
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Residues in contact with ILE 233 (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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129B ILE* 3.9 18.4 - - + +
132B ALA* 3.7 26.2 - - + -
133B VAL* 4.7 4.0 - - + -
163B LEU* 3.4 31.2 - - + -
165B LEU* 3.6 24.7 - - + +
231B VAL* 4.2 2.0 - - + -
232B THR* 1.3 70.1 - - - +
234B HIS* 1.3 59.4 + - - +
235B PHE* 3.8 14.1 - - + -
258B VAL 3.5 1.6 - - - +
259B LEU* 3.5 4.2 - - - -
260B ILE* 2.8 50.5 + - + +
262B PHE* 3.8 25.6 - - + -
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Residues in contact with HIS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PRO* 4.5 19.0 - - + +
157B TRP* 3.3 32.5 + + + -
163B LEU* 3.7 1.4 - - - +
164B ALA 3.1 35.3 + - - +
166B CYS* 4.5 6.0 - - - +
232B THR* 3.4 32.3 + - + -
233B ILE* 1.3 73.6 - - - +
235B PHE* 1.3 63.1 + - - +
258B VAL 3.5 4.5 + - - +
259B LEU* 3.4 37.4 - - + +
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Residues in contact with PHE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.6 31.2 - + - -
132B ALA 5.6 0.9 - - - -
136B TYR* 3.6 35.4 - + + -
157B TRP* 4.0 3.8 - - - -
162B GLY 3.7 11.0 - - - +
163B LEU* 3.3 20.9 - - + -
233B ILE* 3.8 7.0 - - + -
234B HIS* 1.3 74.1 - - - +
236B ARG* 1.3 63.1 + - - +
237B LEU* 3.7 27.6 - - + -
257B SER* 4.8 0.6 + - - -
258B VAL* 2.8 72.6 + - + +
260B ILE* 3.8 16.6 - - + -
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Residues in contact with ARG 236 (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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136B TYR* 5.1 2.4 + - - -
149B TYR* 4.4 0.5 - - - -
150B VAL* 3.1 58.3 + - + +
151B ARG 3.5 20.4 + - - -
152B GLY* 4.4 1.8 - - - -
153B GLY* 4.3 9.1 - - - +
154B GLY* 5.0 3.8 - - - +
157B TRP* 3.2 52.6 - - + +
161B SER 5.5 0.2 + - - -
162B GLY 4.6 0.6 + - - -
235B PHE* 1.3 78.0 - - - +
237B LEU* 1.3 71.5 + - - +
238B LYS 4.3 0.2 - - - -
255B THR* 4.2 16.2 - - + +
256B PHE 3.0 11.7 - - - +
257B SER* 3.7 22.4 - - - +
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Residues in contact with LEU 237 (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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101B PHE* 3.6 34.3 - - + -
105B PHE* 4.5 0.4 - - + -
139B LEU* 3.8 31.0 - - + -
147B TYR* 3.8 25.4 - - + -
148B ALA 3.5 11.2 - - - +
149B TYR* 4.1 16.4 - - + -
235B PHE* 3.7 27.1 - - + -
236B ARG* 1.3 83.7 - - - +
238B LYS* 1.3 61.9 + - - +
239B THR 3.9 0.3 + - - -
255B THR* 3.4 2.0 - - - -
256B PHE* 2.8 44.3 + - + +
258B VAL* 4.8 2.0 - - + +
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Residues in contact with LYS 238 (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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177A PRO* 3.4 35.6 + - + +
178A ALA* 4.9 6.0 - - + +
147B TYR* 3.5 6.4 - - - -
148B ALA* 2.8 38.8 + - + +
149B TYR 4.0 7.9 - - - +
150B VAL* 3.7 27.8 - - + -
237B LEU* 1.3 71.8 - - - +
239B THR* 1.3 60.0 + - - +
253B CYS* 5.3 9.9 + - - +
254B TYR 3.3 8.9 + - - +
255B THR* 3.6 20.9 + - + +
282B GLN* 5.4 7.4 - - - +
284B CYS* 5.9 2.0 - - - +
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Residues in contact with THR 239 (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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177A PRO* 3.9 5.6 - - - +
267A HIS 5.1 3.6 + - - -
93B PHE* 3.5 29.0 - - + -
97B ASN* 5.6 0.2 + - - -
146B ARG* 3.2 22.0 + - - +
147B TYR* 4.4 10.9 - - + -
238B LYS* 1.3 75.4 + - - +
240B ILE* 1.3 74.6 + - - +
253B CYS* 3.3 5.2 - - - +
254B TYR* 2.8 46.1 + - + +
256B PHE* 3.6 24.2 - - + -
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Residues in contact with ILE 240 (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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175A VAL* 3.8 15.5 - - + -
176A ASP 3.4 17.7 - - - +
177A PRO* 3.3 42.2 - - + +
182A PHE* 4.6 28.0 - - + -
267A HIS* 5.3 2.8 - - - +
93B PHE* 4.7 1.0 - - - -
146B ARG* 4.8 2.5 + - + +
239B THR* 1.3 85.5 + - - +
241B ASN* 1.3 61.3 + - - +
242B LEU* 3.0 37.7 + - + +
250B ILE 4.8 7.9 - - - +
252B ASP 3.9 5.6 - - - +
253B CYS* 4.4 2.5 - - + +
284B CYS* 4.7 15.5 - - - -
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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