Contacts of the helix formed by residues 256 - 271 (chain B) in PDB entry 2RG8
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 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A GLU* 5.1 4.9 + - - -
186A GLU* 3.6 32.9 + - - +
187A MSE 4.9 9.2 - - - -
190A ASP* 2.9 33.0 + - - -
216B ARG* 3.9 11.1 - - - +
254B THR* 3.1 4.8 + - + +
255B PRO* 1.3 78.9 - - + +
257B ALA* 1.3 64.8 + - - +
258B PRO* 3.2 4.0 - - - -
259B GLN* 3.1 27.1 + - + +
260B LEU* 2.9 44.1 + - + +
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Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 4.3 9.6 - - + -
247B LEU* 3.8 14.8 - - + -
250B LEU* 4.1 10.8 - - + +
251B ALA* 3.9 16.2 - - - +
254B THR* 2.9 29.5 + - - +
256B ARG* 1.3 75.4 - - - +
258B PRO* 1.3 64.0 - - + +
260B LEU* 3.7 4.8 - - - -
261B VAL* 2.8 35.2 + - - +
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Residues in contact with PRO 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 3.9 13.5 - - + -
251B ALA* 4.4 4.7 - - + -
255B PRO 3.5 12.1 - - - +
256B ARG 3.4 4.3 - - - -
257B ALA* 1.3 93.5 - - + +
259B GLN* 1.3 64.6 + - - +
262B GLY 3.0 22.5 + - - -
290B GLN* 3.8 45.1 - - + +
293B ALA* 4.1 14.1 - - + -
294B ALA* 3.3 19.0 - - + +
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Residues in contact with GLN 259 (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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190A ASP* 4.2 19.2 - - - +
255B PRO 3.9 2.7 + - - +
256B ARG* 3.1 37.7 + - + +
258B PRO* 1.3 92.7 - - + +
260B LEU* 1.3 64.8 + - + +
262B GLY* 3.1 2.8 + - - -
263B GLN* 3.1 19.9 + - - +
293B ALA* 5.9 2.1 - - + +
297B LYS* 3.7 34.0 - - + +
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Residues in contact with LEU 260 (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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186A GLU* 3.7 33.4 - - + +
189A ARG* 6.3 0.4 - - - +
190A ASP* 5.9 1.6 - - - +
5B NA 3.0 17.3 - - - -
209B LEU* 3.6 27.4 - - + -
216B ARG* 3.7 25.8 - - - +
254B THR* 4.2 10.8 - - + -
256B ARG* 2.9 47.4 + - + +
257B ALA 3.8 0.2 - - - +
259B GLN* 1.3 75.1 - - + +
261B VAL* 1.3 62.5 + - - +
263B GLN* 3.2 4.9 + - + +
264B PHE* 3.0 26.3 + - - -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 4.8 9.2 - - + -
209B LEU* 4.4 18.4 - - + -
240B PHE* 5.2 3.1 - - + -
243B LEU* 4.9 16.8 - - + -
244B LEU* 4.4 14.8 - - + -
247B LEU* 3.6 22.4 - - + -
250B LEU* 5.0 3.6 - - + -
257B ALA 2.8 21.9 + - - +
258B PRO 3.7 4.3 - - - +
260B LEU* 1.3 73.2 - - - +
262B GLY* 1.3 61.1 + - - +
264B PHE* 3.1 9.8 + - + +
265B ILE* 2.9 37.1 + - + +
294B ALA* 4.2 12.3 - - + -
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Residues in contact with GLY 262 (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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258B PRO 3.0 12.3 + - - -
259B GLN 3.1 6.2 + - - -
261B VAL* 1.3 78.0 - - - +
263B GLN* 1.3 55.8 + - - +
265B ILE* 3.3 2.0 + - - -
266B ALA* 3.0 25.6 + - - +
294B ALA* 3.4 26.4 + - - +
297B LYS* 4.1 2.2 - - - -
298B ALA* 3.4 16.5 - - - +
301B LEU* 4.1 6.1 - - - -
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Residues in contact with GLN 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 3.4 54.6 + - - +
229A THR* 5.6 1.2 - - - +
5B NA 3.5 16.2 - - - -
217B GLU* 5.0 4.2 + - - -
220B SER* 5.6 1.1 - - - +
259B GLN 3.1 11.8 + - - +
260B LEU* 3.5 11.2 - - + +
261B VAL 3.2 0.2 - - - -
262B GLY* 1.3 74.0 - - - +
264B PHE* 1.3 60.4 + - - +
266B ALA* 4.2 4.5 - - - +
267B ARG* 2.9 59.1 + - + +
301B LEU* 3.6 17.1 - - + +
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Residues in contact with PHE 264 (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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5B NA 3.4 12.8 - - - -
205B VAL* 3.7 35.9 - - + -
208B ALA* 4.2 4.3 - - + -
209B LEU* 4.3 6.1 - - + -
216B ARG* 3.4 51.1 - - + -
219B THR* 3.8 25.1 - - + -
220B SER* 3.3 20.9 - - - -
223B LEU* 4.9 6.4 - - + +
240B PHE* 3.8 16.9 - - + -
260B LEU 3.0 24.3 + - - -
261B VAL* 3.4 10.5 - - + +
263B GLN* 1.3 77.3 - - - +
265B ILE* 1.3 57.1 + - - +
267B ARG* 3.5 2.3 + - - +
268B ALA* 3.0 29.6 + - - +
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Residues in contact with ILE 265 (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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240B PHE* 3.0 42.8 - - + -
244B LEU* 5.3 8.7 - - + -
261B VAL* 2.9 24.8 + - + +
262B GLY* 3.5 9.0 - - - +
263B GLN 3.2 0.2 - - - -
264B PHE* 1.3 76.8 - - - +
266B ALA* 1.3 64.4 + - - +
268B ALA* 3.1 3.6 + - - +
269B VAL* 2.9 27.3 + - + +
274B LEU* 3.7 14.8 - - + -
278B TYR* 3.8 15.7 - - + +
279B ILE* 3.4 32.8 - - + -
294B ALA* 5.6 1.8 - - + +
295B LEU* 5.7 1.8 - - + -
298B ALA* 3.6 10.1 - - + -
302B LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLY 3.0 16.9 + - - +
263B GLN* 3.7 7.4 - - - +
265B ILE* 1.3 77.9 - - - +
267B ARG* 1.3 57.9 + - - +
269B VAL 3.4 0.7 + - - -
270B GLY* 2.9 24.3 + - - -
298B ALA 4.2 2.2 - - - +
301B LEU* 3.8 30.7 - - + -
302B LEU* 3.7 31.0 - - + +
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Residues in contact with ARG 267 (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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229A THR* 6.4 1.8 - - - -
3B NA 3.9 3.8 - - - -
217B GLU* 3.1 34.5 + - - +
220B SER* 3.6 30.6 - - - +
221B LYS* 4.3 11.5 - - - +
263B GLN* 2.9 47.7 + - + +
264B PHE 3.8 3.6 - - - +
266B ALA* 1.3 73.8 - - + +
268B ALA* 1.3 61.1 + - - +
270B GLY* 3.3 2.0 + - - +
271B ASP* 2.7 74.3 + - - +
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Residues in contact with ALA 268 (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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3B NA 3.8 6.7 - - - -
223B LEU* 5.6 0.7 - - + -
240B PHE* 3.7 24.9 - - + -
264B PHE 3.0 17.9 + - - +
265B ILE 3.1 4.9 + - - +
267B ARG* 1.3 73.4 - - - +
269B VAL* 1.3 65.7 + - - +
271B ASP* 3.3 0.6 + - - -
272B GLY 3.1 4.0 + - - -
273B ILE* 3.1 49.7 + - + +
274B LEU* 3.3 10.3 + - + -
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Residues in contact with VAL 269 (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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265B ILE* 2.9 23.3 + - + +
266B ALA 3.7 3.8 - - - +
268B ALA* 1.3 76.5 - - - +
270B GLY* 1.3 66.1 + - - +
272B GLY* 3.1 13.5 + - - -
274B LEU* 3.4 31.8 - - + +
275B CYS 3.9 10.5 - - - +
276B ASN* 3.2 32.6 + - - +
278B TYR* 5.4 0.4 - - + -
279B ILE* 5.3 4.3 - - + -
302B LEU* 4.0 31.9 - - + -
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Residues in contact with GLY 270 (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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266B ALA 2.9 15.2 + - - -
267B ARG* 3.3 4.5 + - - -
268B ALA 3.2 0.2 - - - -
269B VAL* 1.3 80.0 - - - +
271B ASP* 1.3 61.6 + - - +
272B GLY 3.4 0.7 + - - -
302B LEU* 4.8 3.5 - - - +
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Residues in contact with ASP 271 (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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3B NA 2.6 27.2 - - - -
224B SER* 3.9 28.1 + - - +
267B ARG* 2.7 40.6 + - - +
268B ALA 3.8 4.0 - - - +
269B VAL 3.2 0.4 - - - -
270B GLY* 1.3 77.4 - - - +
272B GLY* 1.3 61.5 + - - +
273B ILE* 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