Contacts of the helix formed by residues 215 - 233 (chain B) in PDB entry 2R7D
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 PRO 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PRO* 4.3 20.9 - - + +
90B PHE* 3.4 39.5 - - + -
104B VAL 5.1 0.2 - - - +
105B GLY* 4.9 3.1 - - - -
106B VAL* 3.7 28.9 - - + +
214B GLU* 1.3 88.6 - - + +
216B PHE* 1.3 63.0 + - + +
217B VAL 3.3 2.9 - - - -
218B THR* 3.2 3.1 + - - -
219B LEU* 2.8 44.7 + - + +
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Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 3.8 28.0 - + - -
92B ILE* 4.1 11.0 - - + -
200B LEU* 3.8 30.7 - - + -
205B ALA* 4.1 18.6 - - + -
208B ARG* 3.6 33.2 - - + -
209B LEU* 3.5 22.9 - - + +
213B GLU* 3.2 17.7 - - + +
214B GLU 3.3 15.1 - - - -
215B PRO* 1.3 81.5 - - + +
217B VAL* 1.3 63.0 + - - +
219B LEU* 3.7 9.4 - - + +
220B ALA* 3.0 25.5 + - - +
262B MSE 4.1 20.2 - - + +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.6 16.6 - - + -
212B GLY* 3.3 44.0 - - - +
213B GLU 3.1 5.0 + - - +
214B GLU* 3.8 17.7 - - - +
215B PRO 3.3 0.4 - - - -
216B PHE* 1.3 75.3 - - - +
218B THR* 1.3 63.8 + - - +
220B ALA* 3.3 3.6 + - - +
221B ARG* 3.1 21.1 + - + +
224B ARG* 4.7 1.6 + - - -
204C GLU* 4.1 9.2 - - - +
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Residues in contact with THR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 3.9 21.0 - - + +
114B THR* 3.8 21.5 - - + -
214B GLU* 2.6 33.4 + - - -
215B PRO 3.2 3.1 + - - -
217B VAL* 1.3 73.6 - - - +
219B LEU* 1.3 67.6 + - - +
221B ARG* 3.0 42.0 + - - +
222B LEU* 3.0 14.8 + - + +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 5.9 0.4 - - + -
92B ILE* 5.1 1.1 - - + -
104B VAL* 3.7 28.7 - - + -
105B GLY 4.5 1.6 - - - +
106B VAL* 3.7 22.9 - - + -
116B LEU* 3.8 19.5 - - + -
215B PRO* 2.8 43.0 + - + +
216B PHE* 3.7 12.3 - - + +
218B THR* 1.3 73.2 - - - +
220B ALA* 1.3 58.2 + - - +
222B LEU* 3.5 6.4 + - + +
223B ALA* 2.9 31.2 + - - +
262B MSE 4.5 11.0 - - + -
265B VAL* 3.4 13.4 - - + +
269B CYS* 4.0 16.1 - - - -
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 4.1 12.8 - - + -
216B PHE 3.0 18.6 + - - +
217B VAL 3.5 4.9 - - - +
218B THR 3.1 0.2 - - - -
219B LEU* 1.3 75.2 - - - +
221B ARG* 1.3 62.9 + - - +
223B ALA* 3.4 0.7 + - - +
224B ARG* 2.9 58.3 + - - +
261B GLU* 4.8 1.1 - - - +
262B MSE 4.8 0.7 - - - -
265B VAL* 3.8 23.3 - - + +
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Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLY 5.5 1.0 + - - -
114B THR* 3.0 26.7 + - - -
180B ASP 5.3 0.4 - - - -
181B PRO* 4.2 26.0 + - - +
217B VAL* 3.1 13.1 + - + +
218B THR* 3.0 30.3 + - - +
220B ALA* 1.3 77.4 - - - +
222B LEU* 1.3 79.7 + - - +
224B ARG* 3.2 16.7 + - - +
225B ALA* 3.1 24.3 + - + +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 4.2 12.8 - - + -
114B THR* 3.7 34.5 - - + +
116B LEU* 4.2 22.9 - - + -
179B LEU* 4.2 29.7 - - + +
180B ASP 5.2 3.1 - - - +
183B GLY* 6.6 0.2 - - - -
218B THR* 3.0 25.6 + - + +
219B LEU* 3.8 5.2 - - - +
221B ARG* 1.3 96.9 - - - +
223B ALA* 1.3 57.0 + - - +
225B ALA* 3.3 6.6 + - + +
226B SER* 2.9 32.7 + - - -
269B CYS* 6.4 1.1 - - - -
272B LEU* 4.8 5.1 - - + +
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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
----------------------------------------------------------
219B LEU 2.9 18.9 + - - +
220B ALA 3.7 3.6 - - - +
221B ARG 3.2 0.2 - - - -
222B LEU* 1.3 78.2 - - - +
224B ARG* 1.3 61.6 + - + +
226B SER* 4.5 0.2 - - - -
227B ARG* 3.0 27.1 + - - +
265B VAL* 3.6 35.9 - - + +
268B GLU* 3.4 26.4 - - + +
269B CYS* 5.3 2.7 - - - -
272B LEU* 5.3 2.7 - - - +
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 4.9 7.9 - - - +
217B VAL 4.7 1.6 + - - -
220B ALA* 2.9 57.9 + - - +
221B ARG* 3.5 15.0 - - - +
223B ALA* 1.3 77.2 - - + +
225B ALA* 1.3 62.6 + - - +
227B ARG* 3.8 9.0 - - - +
228B ARG* 3.1 30.2 + - + +
261B GLU* 2.8 38.6 + - - +
265B VAL* 5.8 1.3 - - + -
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PRO 4.8 7.9 - - - +
182B ASP 4.7 6.7 - - - +
183B GLY* 4.6 17.5 - - - +
221B ARG* 3.1 17.1 + - + +
222B LEU* 3.7 7.0 - - + +
224B ARG* 1.3 75.3 - - - +
226B SER* 1.3 66.4 + - - +
228B ARG* 3.1 12.8 + - - +
229B LEU* 3.1 25.1 + - - +
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 5.9 1.6 - - - -
183B GLY* 5.2 5.1 - - - -
222B LEU 2.9 18.1 + - - -
223B ALA 3.8 2.5 - - - -
225B ALA* 1.3 76.5 - - - +
227B ARG* 1.3 62.3 + - - +
229B LEU* 3.1 23.1 + - - +
230B ARG* 3.1 18.5 + - - +
268B GLU* 2.6 24.7 + - - -
272B LEU* 3.1 35.1 - - - +
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Residues in contact with ARG 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ALA* 3.0 22.6 + - - +
224B ARG* 3.8 8.1 - - - +
226B SER* 1.3 75.9 - - - +
228B ARG* 1.3 57.6 + - + +
230B ARG* 3.2 16.9 + - - +
231B GLU* 2.8 55.7 + - + +
264B THR* 3.0 50.6 + - - +
265B VAL* 4.2 1.0 - - - +
267B GLN* 4.5 8.3 + - - -
268B GLU* 2.4 48.2 + - - +
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Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 3.1 16.2 + - - +
225B ALA* 3.1 13.1 + - - +
227B ARG* 1.3 78.3 - - + +
229B LEU* 1.3 63.7 + - + +
231B GLU* 3.4 16.1 + - - +
232B GLY* 3.0 19.2 + - - -
250C THR* 5.6 10.3 - - - +
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Residues in contact with LEU 229 (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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182B ASP 4.0 10.1 - - - +
183B GLY* 3.6 39.3 - - - +
184B ASN* 4.1 13.0 - - - +
225B ALA 3.1 12.9 + - - +
226B SER* 3.1 12.6 + - - +
228B ARG* 1.3 75.9 - - - +
230B ARG* 1.3 65.3 + - + +
232B GLY* 3.0 10.8 + - - -
233B GLU* 3.1 28.7 + - + +
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Residues in contact with ARG 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B SER* 3.1 11.3 + - - +
227B ARG* 3.6 20.5 + - - +
229B LEU* 1.3 79.8 - - + +
231B GLU* 1.3 59.9 + - - +
233B GLU* 2.9 25.4 + - - +
235B ALA* 3.1 25.3 + - - +
236B LEU 5.8 0.8 + - - -
268B GLU* 3.2 38.6 + - - -
271B THR* 3.9 15.5 + - - +
272B LEU* 6.2 0.4 - - - -
329B GLY 4.4 1.8 + - - -
330B MSE 2.8 48.4 + - - +
331B GLY* 3.9 3.1 - - - +
332B LEU* 3.5 28.0 - - + +
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ARG* 2.8 53.9 + - + +
228B ARG* 3.7 20.7 + - - +
230B ARG* 1.3 74.1 - - + +
232B GLY* 1.3 60.6 + - - +
234B GLY* 3.2 10.9 + - - -
235B ALA* 3.6 27.6 + - + +
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Residues in contact with GLY 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG 3.0 15.2 + - - -
229B LEU* 3.0 5.1 + - - -
231B GLU* 1.3 77.5 - - - +
233B GLU* 1.3 65.7 + - - +
234B GLY 3.1 3.4 + - - -
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 3.1 28.6 - - + +
230B ARG* 2.9 9.6 + - - +
232B GLY* 1.3 83.5 - - - +
234B GLY* 1.3 57.2 + - - -
235B ALA 3.9 0.2 + - - -
328B HIS 5.1 0.9 - - - +
331B GLY* 3.4 30.0 - - - +
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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