Contacts of the helix formed by residues 213 - 229 (chain B) in PDB entry 4OBP
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 ARG 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASP* 2.9 29.7 + - - +
212B TYR* 1.3 109.1 + - + +
214B SER* 1.4 62.7 + - - +
215B ASP 3.2 2.2 - - - -
216B LEU* 3.0 21.2 + - + +
217B TRP 3.3 4.7 + - - -
274B TYR* 3.2 36.9 + - + +
275B MET* 3.3 29.3 + - - +
277B ARG* 3.0 51.2 + - - +
278B PRO 3.7 14.1 - - - +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ILE* 5.2 0.2 - - - -
196B ALA* 4.0 10.5 - - - +
198B GLU* 2.9 28.7 + - - +
199B VAL* 4.0 6.0 - - - +
210B TYR* 4.1 20.9 - - - -
211B ASP* 2.9 30.6 + - - +
213B ARG* 1.4 76.4 - - - +
215B ASP* 1.4 59.2 + - - +
217B TRP* 3.4 5.9 + - - +
218B SER* 3.1 25.5 + - - -
277B ARG* 3.7 2.8 - - - +
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Residues in contact with ASP 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.7 18.0 - - + +
145B HIS* 2.8 26.5 + - + +
150B ILE* 3.5 11.4 - - - +
151B HIS* 2.9 31.9 + - - +
152B ARG* 2.9 27.6 + - - -
154B ILE* 4.2 7.2 - - + +
212B TYR 3.3 7.1 + - - +
213B ARG 3.2 0.6 - - - -
214B SER* 1.4 76.2 - - - +
216B LEU* 1.3 59.0 + - - +
218B SER* 3.4 8.8 + - - -
219B CYS* 2.8 27.9 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 3.7 27.8 - - + -
141B LEU* 4.3 9.0 - - + -
145B HIS* 4.4 1.6 - - + -
212B TYR* 4.2 3.8 - - + +
213B ARG* 3.0 25.9 + - + +
215B ASP* 1.3 73.2 - - - +
217B TRP* 1.3 63.7 + - - +
219B CYS* 3.3 6.4 + - - +
220B GLY 3.0 17.3 + - - -
269B CYS* 3.4 13.6 - - - +
277B ARG* 4.3 7.0 - - - -
278B PRO 3.0 26.9 - - - +
279B SER* 3.6 3.6 - - - +
280B THR* 3.5 40.6 - - + +
283B LEU* 4.0 14.4 - - + -
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Residues in contact with TRP 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR 5.1 1.0 + - - -
194B TRP 3.6 11.0 - - - -
195B MET 3.3 11.9 + - - -
196B ALA* 3.5 24.0 - - + -
197B PRO* 3.7 34.3 - - + -
213B ARG 3.3 3.8 + - - -
214B SER 3.6 8.7 - - - +
216B LEU* 1.3 77.1 - - - +
218B SER* 1.3 59.4 + - - +
220B GLY 3.0 16.3 + - - -
221B ILE* 3.0 25.1 + - + +
245B ILE* 4.3 12.1 - - + +
251B PRO* 3.6 35.4 - - + -
269B CYS 3.6 11.0 + - - -
270B LEU* 3.3 46.2 - - + +
271B VAL 3.7 18.2 - - - -
272B LYS* 4.0 15.3 - - + -
277B ARG* 3.8 10.1 - - - +
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ARG 5.5 2.9 + - - -
154B ILE* 3.4 32.0 + - - -
194B TRP* 2.8 26.8 + - - -
195B MET* 4.9 0.5 - - - -
196B ALA 4.8 1.6 + - - -
214B SER 3.1 14.0 + - - -
215B ASP* 3.5 10.5 + - - -
216B LEU 3.3 0.2 - - - -
217B TRP* 1.3 78.3 - - - +
219B CYS* 1.4 48.1 + - - +
221B ILE* 3.3 6.0 + - - +
222B THR* 2.7 39.4 + - - -
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Residues in contact with CYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 4.3 10.7 + - - -
137B ILE* 4.0 24.9 - - + +
138B LEU* 4.1 25.1 - - + -
141B LEU* 4.5 3.4 - - + -
154B ILE* 3.7 12.7 - - + +
215B ASP 2.8 15.2 + - - +
216B LEU* 3.4 14.1 - - - +
218B SER* 1.4 72.2 - - - +
220B GLY* 1.3 57.5 - - - +
222B THR* 3.3 5.9 + - - -
223B ALA* 3.0 26.2 + - - +
226B MET* 5.7 0.2 - - - +
265B PHE* 4.4 15.3 - - - -
269B CYS* 4.7 1.3 - - - -
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Residues in contact with GLY 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU 3.0 7.3 + - - -
217B TRP 3.0 8.4 + - - -
219B CYS* 1.3 72.9 - - - +
221B ILE* 1.3 62.9 + - - +
223B ALA* 3.3 8.7 + - - +
224B ILE* 3.2 25.5 + - - +
266B ILE* 3.8 7.2 - - - +
269B CYS* 3.6 26.2 - - - +
270B LEU* 4.0 9.4 - - - -
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Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR 3.5 22.2 - - - +
194B TRP* 3.4 24.9 - - + -
217B TRP* 3.0 39.3 + - + +
218B SER 3.3 7.2 + - - +
220B GLY* 1.3 71.3 - - - +
222B THR* 1.4 60.6 + - - +
224B ILE* 3.2 7.9 + - + +
225B GLU* 2.9 26.2 + - - +
231B PRO* 3.7 16.3 - - + +
232B PRO* 3.9 14.1 - - + -
251B PRO* 4.0 22.2 - - + -
270B LEU* 3.8 15.7 - - + -
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 5.2 1.3 - - + -
137B ILE* 4.1 24.0 - - + -
154B ILE* 3.8 2.5 - - + +
155B LYS* 3.3 24.8 + - - +
156B GLY* 3.6 26.9 - - - +
159B VAL* 4.7 2.7 - - + -
194B TRP* 3.5 1.5 - - - +
218B SER 2.7 21.8 + - - -
219B CYS* 3.3 10.3 + - - -
221B ILE* 1.4 75.2 - - - +
223B ALA* 1.4 56.7 + - - +
225B GLU* 3.3 9.8 - - - +
226B MET* 3.0 34.4 + - + +
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 4.0 9.1 - - + +
134B SER* 4.0 17.3 - - - +
219B CYS 3.0 12.7 + - - +
220B GLY 3.6 8.3 - - - +
221B ILE 3.2 0.4 - - - -
222B THR* 1.4 72.1 - - - +
224B ILE* 1.3 64.7 + - - +
226B MET* 3.4 13.8 + - - +
227B ALA* 3.1 22.3 + - - +
262B PHE* 3.8 9.3 - - + -
265B PHE* 4.1 7.9 - - + -
266B ILE* 3.7 17.0 - - + -
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Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLY 3.2 10.5 + - - +
221B ILE* 3.2 10.0 + - + +
223B ALA* 1.3 75.0 - - - +
225B GLU* 1.3 53.9 + - - +
227B ALA* 3.0 2.8 + - - +
228B GLU* 2.8 58.3 + - - +
230B ALA 4.1 4.0 - - - +
232B PRO* 3.8 36.8 - - + -
251B PRO* 4.1 10.1 - - + -
252B ARG 4.4 8.7 - - - +
253B LEU* 4.1 14.6 - - + -
266B ILE* 3.9 19.5 - - + -
270B LEU* 3.8 28.7 - - + -
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 6.3 0.9 - - - -
114B THR* 2.8 36.5 + - - +
117B VAL* 3.9 7.9 - - + +
156B GLY* 2.9 27.3 + - - -
194B TRP* 3.0 30.9 + - - +
221B ILE 2.9 13.2 + - - +
222B THR* 3.3 10.4 - - - +
224B ILE* 1.3 76.5 - - - +
226B MET* 1.4 54.6 + - + +
229B GLY* 2.7 34.1 + - - +
230B ALA* 3.7 30.0 + - - +
231B PRO* 4.2 2.6 - - - +
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Residues in contact with MET 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 3.6 24.2 - - + -
117B VAL* 3.3 18.0 - - + +
125B LEU* 3.0 40.8 + - + +
130B ILE* 3.8 22.9 - - + +
133B ILE* 3.6 37.2 - - + -
134B SER* 3.5 25.1 - - - +
137B ILE* 4.4 8.7 - - + -
219B CYS 5.7 0.2 - - - +
222B THR* 3.0 25.4 + - + +
223B ALA* 3.7 13.5 - - - +
224B ILE 3.3 0.2 - - - -
225B GLU* 1.4 75.0 - - + +
227B ALA* 1.3 59.2 + - - +
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Residues in contact with ALA 227 (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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124B THR* 2.9 23.7 + - - -
130B ILE* 3.8 11.6 - - + +
223B ALA 3.1 12.8 + - - +
224B ILE 3.0 8.2 + - - +
226B MET* 1.3 78.1 - - - +
228B GLU* 1.3 60.1 + - + +
253B LEU* 3.7 20.9 - - + -
258B TRP* 3.5 31.1 - - + -
262B PHE* 3.9 2.7 - - + -
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Residues in contact with GLU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLY 5.2 0.5 - - - +
123B ASN* 3.2 13.9 - - - +
124B THR* 5.2 0.2 - - - -
224B ILE* 2.8 34.4 + - - +
227B ALA* 1.3 78.9 - - + +
229B GLY* 1.3 60.1 + - - +
230B ALA* 3.3 13.9 + - + +
232B PRO* 5.5 3.5 - - - +
252B ARG 4.9 1.7 - - - +
253B LEU* 3.3 13.1 - - - +
254B LYS* 2.8 65.1 + - + +
255B SER* 4.4 2.2 + - - -
258B TRP* 5.0 3.5 + - + +
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Residues in contact with GLY 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 5.7 0.5 - - - +
117B VAL* 4.0 14.6 - - - +
118B LYS* 3.4 27.5 + - - +
123B ASN* 3.2 21.5 + - - -
225B GLU* 2.7 28.0 + - - +
228B GLU* 1.3 71.9 - - - +
230B ALA* 1.3 60.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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