Contacts of the helix formed by residues 270 - 284 (chain B) in PDB entry 4CRU
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 THR 270 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B LYS 5.3 0.2 + - - -
268B ASP* 3.3 9.1 + - - -
269B ASP* 1.3 73.7 - - - +
271B THR* 1.3 59.1 + - - +
273B LYS* 3.5 18.2 + - - +
274B ARG* 2.9 44.1 + - + +
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Residues in contact with THR 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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230B LYS* 4.0 17.3 + - - +
269B ASP* 3.2 7.1 + - - -
270B THR* 1.3 78.6 - - - +
272B THR* 1.3 58.5 + - - +
274B ARG* 3.1 28.5 + - - +
275B TRP* 2.9 64.9 + - + -
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Residues in contact with THR 272 (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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226B ALA 5.9 0.2 - - - +
229B LEU* 4.7 1.3 - - + -
230B LYS* 3.2 40.7 - - - +
233B VAL* 3.9 21.9 - - + +
266B LEU* 3.4 22.0 - - + -
269B ASP* 2.6 31.8 + - - +
271B THR* 1.3 76.5 - - - +
273B LYS* 1.3 58.5 + - - +
275B TRP* 3.2 10.4 + - - +
276B LEU* 2.9 28.4 + - - +
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Residues in contact with LYS 273 (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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263B ALA 5.5 1.8 - - - +
266B LEU* 3.1 44.4 + - + +
267B LYS* 2.6 33.9 + - - +
269B ASP 3.0 9.6 + - - +
270B THR* 3.6 23.7 + - - +
272B THR* 1.3 77.6 - - - +
274B ARG* 1.3 61.6 + - - +
276B LEU* 3.4 7.0 + - - +
277B ALA* 3.0 24.6 + - - +
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Residues in contact with ARG 274 (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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270B THR* 2.9 42.4 + - + +
271B THR* 3.1 30.8 + - - +
273B LYS* 1.3 75.8 - - - +
275B TRP* 1.3 69.2 + - + +
277B ALA* 3.3 7.2 + - - +
278B GLN* 3.0 29.4 + - + +
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Residues in contact with TRP 275 (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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187B GLN* 5.2 6.3 - - - -
230B LYS* 3.6 45.1 - - + -
231B HIS* 6.1 0.2 - - - -
233B VAL* 3.8 11.2 - - + -
234B ARG* 3.7 48.0 - - + +
237B LEU* 3.9 28.0 - - + +
271B THR* 2.9 29.2 + - + +
272B THR* 3.5 17.5 - - - +
274B ARG* 1.3 91.1 - - + +
276B LEU* 1.3 57.2 + - - +
278B GLN* 3.2 6.0 + - + +
279B LEU* 2.9 27.4 + - - +
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Residues in contact with LEU 276 (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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233B VAL* 3.7 16.3 - - + +
257B LEU* 3.6 52.7 - - + +
259B ASP 6.1 0.9 - - - +
262B PHE* 5.6 3.1 - - + -
266B LEU* 3.9 24.2 - - + -
272B THR 2.9 20.7 + - - +
273B LYS* 3.7 6.3 - - - +
275B TRP* 1.3 71.7 - - - +
277B ALA* 1.3 58.4 + - - +
279B LEU* 3.1 20.4 + - + +
280B VAL* 3.0 33.5 + - + +
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Residues in contact with ALA 277 (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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273B LYS 3.0 17.1 + - - +
274B ARG* 3.7 6.7 - - - +
276B LEU* 1.3 76.7 - - - +
278B GLN* 1.3 57.7 + - - +
280B VAL* 3.4 8.6 + - - +
281B LYS* 3.0 28.8 + - - +
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Residues in contact with GLN 278 (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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237B LEU* 3.7 19.5 - - + -
274B ARG* 3.0 15.9 + - + +
275B TRP* 3.2 10.3 + - + +
277B ALA* 1.3 76.0 - - - +
279B LEU* 1.3 59.6 + - - +
281B LYS* 3.3 30.1 + - - +
282B ASN* 2.8 59.5 + - - +
285B GLU* 4.9 2.0 + - - -
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Residues in contact with LEU 279 (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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233B VAL* 4.9 4.3 - - + +
236B TYR* 3.6 47.6 - - + +
237B LEU* 3.6 14.5 - - + +
240B SER* 3.8 16.4 - - - +
249B LEU* 4.7 3.8 - - + -
253B LEU* 4.0 19.1 - - + -
257B LEU* 4.8 3.1 - - + -
275B TRP 2.9 12.9 + - - +
276B LEU* 3.1 27.6 + - + +
278B GLN* 1.3 75.2 - - - +
280B VAL* 1.3 66.4 + - + +
282B ASN* 3.1 13.3 + - - +
283B LEU* 3.1 34.5 + - + +
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Residues in contact with VAL 280 (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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253B LEU* 5.2 8.5 - - + -
257B LEU 4.3 17.3 - - - +
258B LYS* 5.2 8.3 - - + -
276B LEU* 3.0 25.1 + - + +
277B ALA* 3.8 7.4 - - - +
279B LEU* 1.3 78.8 - - + +
281B LYS* 1.3 63.9 + - - +
283B LEU* 3.3 17.1 + - - +
284B GLN* 3.5 18.0 + - - +
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Residues in contact with LYS 281 (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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277B ALA 3.0 18.2 + - - +
278B GLN* 3.5 27.4 + - - +
279B LEU 3.2 0.2 - - - -
280B VAL* 1.3 78.2 - - - +
282B ASN* 1.3 60.2 + - - +
284B GLN* 2.9 37.7 - - - +
285B GLU* 3.1 33.1 - - + +
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Residues in contact with ASN 282 (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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237B LEU* 3.7 19.0 - - - +
240B SER* 3.0 27.7 + - - +
241B ASP* 4.2 9.5 + - - -
246B ARG* 3.2 47.8 + - - +
278B GLN* 2.8 36.5 + - - +
279B LEU 3.1 8.0 + - - +
281B LYS* 1.3 76.1 - - - +
283B LEU* 1.3 61.1 - - - +
285B GLU* 3.4 22.0 + - - +
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Residues in contact with LEU 283 (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 SER* 4.2 14.8 - - - -
246B ARG* 3.7 34.1 - - + +
249B LEU* 3.8 27.8 - - + +
250B ARG* 3.1 39.7 + - + +
253B LEU* 3.8 30.5 - - + -
279B LEU* 3.1 23.6 + - + +
280B VAL* 3.7 9.6 - - - +
281B LYS 3.2 0.8 - - - -
282B ASN* 1.3 76.7 - - - +
284B GLN* 1.3 57.5 + - - +
285B GLU 3.4 0.2 - - - -
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Residues in contact with GLN 284 (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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250B ARG* 5.2 0.2 - - - -
280B VAL* 3.5 16.2 + - - +
281B LYS* 2.9 37.4 + - - +
283B LEU* 1.3 77.1 - - - +
285B GLU* 1.3 70.5 + - - +
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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