Contacts of the helix formed by residues 251 - 264 (chain R) in PDB entry 6CNB
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 ALA 251 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245R VAL* 4.4 1.8 - - - -
250R VAL* 1.3 77.1 - - - +
252R GLU* 1.3 55.3 + - - +
253R GLU* 4.3 4.5 - - + +
254R THR* 3.0 18.4 + - - +
255R LEU* 2.6 35.9 + - - +
407S ASN* 3.5 9.2 - - - +
61Y T 2.9 34.1 + - + +
62Y G 4.5 11.0 - - - +
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Residues in contact with GLU 252 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241R HIS* 4.7 16.8 - - + -
242R THR* 3.2 31.6 - - + +
245R VAL* 4.4 12.9 - - + +
250R VAL 3.9 1.6 + - - -
251R ALA* 1.3 70.8 - - - +
253R GLU* 1.3 65.0 - - - +
255R LEU* 2.9 21.4 + - - +
256R GLN* 2.9 21.0 + - - +
405S LEU* 5.4 3.9 - - + +
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Residues in contact with GLU 253 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251R ALA* 3.3 4.6 - - + +
252R GLU* 1.3 78.1 - - - +
254R THR* 1.3 65.0 + - - +
256R GLN* 4.5 7.2 - - - +
257R GLN* 2.8 60.2 + - + +
5X C 6.1 0.7 - - - -
6X A 5.0 8.4 + - - +
7X A 4.7 8.8 + - - -
61Y T 5.0 7.3 - - + +
62Y G 3.8 24.0 - - - +
63Y T 3.9 15.7 - - + +
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Residues in contact with THR 254 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218R ARG* 4.8 6.5 + - - +
219R ARG* 6.4 0.4 - - + -
222R GLY* 5.3 7.9 - - - -
250R VAL* 4.5 11.4 - - + -
251R ALA* 3.0 22.1 + - - +
253R GLU* 1.3 77.3 - - - +
255R LEU* 1.3 65.4 + - - +
257R GLN* 3.7 18.3 + - - +
258R ARG* 3.8 11.8 + - - +
60Y A 3.5 43.5 - - - +
61Y T 3.1 22.3 + - - +
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Residues in contact with LEU 255 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222R GLY* 4.3 6.7 - - - +
225R GLY* 3.9 6.5 - - - +
226R ALA* 3.6 40.4 - - + +
229R LEU* 3.9 15.5 - - + -
241R HIS* 3.6 43.7 - - + +
244R ILE* 4.5 13.0 - - + -
245R VAL* 4.8 4.3 - - + -
250R VAL* 4.8 11.8 - - + +
251R ALA 2.6 15.4 + - - +
252R GLU* 2.9 11.1 + - - +
254R THR* 1.3 77.6 - - - +
256R GLN* 1.3 66.0 + - - +
257R GLN 3.1 0.3 + - - -
258R ARG* 3.4 3.5 + - - +
259R LEU* 3.3 17.1 + - + +
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Residues in contact with GLN 256 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241R HIS* 3.0 48.9 + - + +
252R GLU* 2.9 19.0 + - - +
253R GLU* 4.2 6.6 - - - +
255R LEU* 1.3 74.1 - - + +
257R GLN* 1.3 57.6 + - - +
259R LEU* 3.1 20.6 - - + +
260R ASN* 2.9 37.9 + - - +
4X T 5.5 2.6 + - - -
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Residues in contact with GLN 257 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218R ARG* 5.7 2.6 + - - +
253R GLU* 2.8 56.0 + - + +
254R THR* 3.8 17.4 + - - +
255R LEU 3.1 0.4 + - - -
256R GLN* 1.3 76.0 - - - +
258R ARG* 1.3 59.5 + - - +
260R ASN* 2.7 29.7 + - - +
261R GLU* 2.9 11.1 + - - +
61Y T 4.5 15.8 - - - +
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Residues in contact with ARG 258 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209R MET* 3.8 20.9 + - + +
214R MET* 2.3 60.2 + - - +
215R PHE* 3.3 8.1 - - - +
218R ARG* 3.1 38.7 - - - +
222R GLY 5.3 1.8 - - - -
223R ILE* 3.2 55.3 - - - +
226R ALA* 5.3 6.3 - - + -
254R THR 3.8 3.7 + - - +
255R LEU 3.4 6.9 + - - +
257R GLN* 1.3 77.7 - - - +
259R LEU* 1.3 57.8 + - - +
261R GLU* 3.1 24.3 + - + +
262R PHE* 2.9 26.5 + - - +
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Residues in contact with LEU 259 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226R ALA* 5.5 6.3 - - + +
229R LEU* 4.8 17.0 - - + -
230R LEU* 3.5 34.1 - - + -
241R HIS* 5.3 2.2 - - - +
255R LEU* 3.3 9.2 + - + +
256R GLN* 3.1 34.8 - - + +
257R GLN 3.1 0.4 - - - -
258R ARG* 1.3 77.0 - - - +
260R ASN* 1.3 63.8 + - - +
262R PHE* 2.9 16.3 + - + +
263R LYS* 2.9 23.7 + - + +
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Residues in contact with ASN 260 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256R GLN* 2.9 25.5 + - - +
257R GLN* 2.7 16.1 + - - +
259R LEU* 1.3 80.4 - - - +
261R GLU* 1.3 56.5 + - - +
263R LYS* 2.8 38.6 + - + +
264R ASN* 3.4 9.0 + - - +
4X T 6.0 0.2 + - - -
5X C 5.0 9.3 + - - -
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Residues in contact with GLU 261 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214R MET* 3.3 27.9 - - + +
218R ARG* 3.7 15.4 + - - -
257R GLN 2.9 6.5 + - - +
258R ARG* 3.3 44.1 + - + +
260R ASN* 1.3 75.8 - - - +
262R PHE* 1.3 54.4 + - - +
264R ASN* 2.6 24.6 - - - +
265R THR* 3.1 11.1 - - - +
288R PRO* 3.1 40.4 - - + +
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Residues in contact with PHE 262 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205R LEU* 4.4 15.7 - - + -
208R ARG* 3.5 29.8 - - - -
209R MET* 4.3 37.7 - - + -
212R ASP* 4.8 2.0 - - - -
214R MET* 6.3 0.2 - - - -
230R LEU* 4.7 24.7 - - + -
258R ARG 2.9 11.2 + - - +
259R LEU* 2.9 16.4 + - + +
261R GLU* 1.3 76.6 - - - +
263R LYS* 1.3 63.1 + - - +
264R ASN 3.2 0.9 - - - -
265R THR* 2.6 39.8 + - + -
268R ALA* 3.2 20.8 - - - +
272R VAL* 5.7 6.1 - - + -
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Residues in contact with LYS 263 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259R LEU* 2.9 7.3 + - + +
260R ASN* 2.8 31.0 + - + +
262R PHE* 1.3 80.8 - - - +
264R ASN* 1.3 56.0 + - + +
268R ALA* 3.1 14.8 - - - +
269R LYS* 2.9 58.1 + - + +
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Residues in contact with ASN 264 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260R ASN 3.4 6.7 + - - +
261R GLU* 2.6 33.7 - - - +
263R LYS* 1.3 76.8 - - + +
265R THR* 1.3 70.3 + - - +
269R LYS* 4.9 2.2 - - - +
288R PRO* 5.8 4.8 - - - +
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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