Contacts of the helix formed by residues 267 - 282 (chain B) in PDB entry 2JDQ
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 ASP 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B LEU* 3.8 27.2 - - + +
230B ARG* 3.1 41.9 + - - -
265B VAL* 3.6 6.2 - - + +
266B SER* 1.3 77.9 + - - +
268B THR* 1.3 65.8 + - - +
269B ASP* 3.3 4.2 + - - +
270B VAL* 3.2 33.8 + - + +
271B LEU* 3.2 25.3 + - - +
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Residues in contact with THR 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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266B SER 3.2 6.1 + - - -
267B ASP* 1.3 75.6 + - - +
269B ASP* 1.3 65.2 + - - +
271B LEU* 3.8 4.4 - - - +
272B ALA* 3.0 29.0 + - + +
307B HIS* 4.0 15.2 + - - -
309B ASP* 3.4 28.2 + - + +
311B LYS* 4.6 9.9 - - + -
312B VAL* 3.7 21.4 - - + +
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Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ARG* 3.2 43.2 + - + +
267B ASP* 3.3 11.0 + - - +
268B THR* 1.3 83.5 - - - +
270B VAL* 1.3 63.4 + - - +
272B ALA* 3.9 3.9 - - - +
273B ASP* 3.2 32.5 + - - +
311B LYS* 5.2 10.9 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 4.6 4.5 - - + -
229B THR* 3.9 20.9 - - + -
230B ARG* 3.8 20.6 - - + +
233B VAL* 4.1 15.1 - - + +
262B LEU* 4.1 34.5 - - + +
265B VAL* 4.3 13.7 - - + -
267B ASP* 3.2 28.5 + - + +
269B ASP* 1.3 73.1 - - - +
271B LEU* 1.3 56.5 + - - +
273B ASP* 3.3 3.8 + - - +
274B ALA* 2.8 33.1 + - - +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU 3.8 17.3 - - - +
263B LEU* 3.8 18.2 - - + +
265B VAL* 3.2 27.6 - - + +
266B SER* 4.0 11.4 - - - +
267B ASP 3.2 18.5 + - - +
268B THR* 3.8 4.5 - - - +
270B VAL* 1.3 79.9 - - - +
272B ALA* 1.3 56.1 + - - +
274B ALA* 3.2 6.4 + - - +
275B CYS* 2.8 36.4 + - - -
300B ARG* 4.5 1.6 - - - +
304B LEU* 3.9 30.3 - - + -
307B HIS* 4.1 16.4 - - + +
312B VAL* 4.3 10.3 - - + -
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 3.0 20.2 + - + +
269B ASP* 3.9 5.8 - - - +
270B VAL 3.3 0.2 - - - -
271B LEU* 1.3 75.9 - - - +
273B ASP* 1.3 58.5 + - - +
275B CYS* 4.5 0.2 - - - -
276B TRP* 3.0 37.4 + - + -
311B LYS* 3.2 37.9 - - + +
312B VAL* 4.3 5.5 - - + +
315B PRO* 3.6 7.6 - - + +
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Residues in contact with ASP 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ARG* 4.0 6.6 - - - +
233B VAL* 3.9 19.7 - - + +
234B TRP* 3.7 37.9 + - - +
237B SER* 4.0 7.7 + - - +
269B ASP* 3.2 20.1 + - - +
270B VAL* 3.9 3.1 - - - +
272B ALA* 1.3 77.9 - - - +
274B ALA* 1.3 64.1 + - - +
275B CYS 3.2 0.2 - - - -
276B TRP* 3.8 14.4 - - - +
277B ALA* 3.0 25.3 + - - +
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Residues in contact with ALA 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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233B VAL* 3.7 14.5 - - + +
259B LEU* 4.1 10.0 - - + +
262B LEU* 4.4 18.2 - - + -
263B LEU* 4.0 19.5 - - + -
270B VAL 2.8 22.4 + - - +
271B LEU* 3.5 7.4 - - - +
273B ASP* 1.3 72.2 - - - +
275B CYS* 1.3 56.7 + - - +
277B ALA* 3.5 4.6 + - - +
278B LEU* 3.1 34.2 + - - +
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Residues in contact with CYS 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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263B LEU* 4.2 4.0 - - - -
271B LEU 2.8 21.1 + - - +
272B ALA 3.6 1.3 - - - +
274B ALA* 1.3 74.1 - - - +
276B TRP* 1.3 64.1 + - - +
278B LEU* 3.3 8.0 + - - +
279B SER* 2.9 23.2 + - - -
301B LEU* 3.9 13.5 - - + -
304B LEU* 3.8 27.8 - - - -
312B VAL* 4.6 3.8 - - - -
315B PRO* 3.6 24.6 - - + +
316B ALA* 3.7 22.4 - - - +
319B ALA* 4.3 1.6 - - - +
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Residues in contact with TRP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B SER* 4.7 4.7 - - - +
272B ALA* 3.0 33.5 + - + +
273B ASP* 3.4 16.6 + - - +
275B CYS* 1.3 74.9 - - - +
277B ALA* 1.3 64.5 + - - +
279B SER* 2.8 31.9 + - - -
280B TYR* 3.0 44.1 + + + +
311B LYS 4.6 3.4 + - - -
314B SER* 4.7 9.6 - - - -
315B PRO* 3.5 35.6 - - + +
318B ARG* 4.2 34.8 - - + -
748D GLN* 4.8 11.0 - - + -
749D THR* 3.6 36.3 - - + +
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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
----------------------------------------------------------
233B VAL* 5.2 1.6 - - + +
236B LEU* 4.9 1.3 - - + +
237B SER* 4.0 20.3 - - - +
240B CYS* 4.0 7.5 - - - +
259B LEU* 3.9 23.8 - - + -
273B ASP 3.0 17.9 + - - +
274B ALA 3.5 5.8 - - - +
276B TRP* 1.3 75.0 - - - +
278B LEU* 1.3 62.4 + - - +
280B TYR* 3.0 15.9 + - - +
281B LEU* 3.0 27.0 + - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 3.9 28.3 - - + -
259B LEU* 3.9 21.3 - - + -
263B LEU* 3.8 23.6 - - + -
274B ALA 3.1 20.8 + - - +
275B CYS 3.7 4.7 - - - +
276B TRP 3.3 0.2 - - - -
277B ALA* 1.3 76.0 - - - +
279B SER* 1.3 52.3 + - - +
281B LEU* 3.3 5.0 + - + +
282B SER* 2.6 39.4 + - - -
292B VAL* 4.2 7.5 - - + +
297B VAL* 3.9 25.6 - - + -
301B LEU* 3.7 26.0 - - + -
319B ALA* 4.3 10.3 - - + -
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Residues in contact with SER 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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275B CYS 2.9 13.6 + - - -
276B TRP* 2.8 27.5 + - - -
278B LEU* 1.3 76.7 - - - +
280B TYR* 1.3 70.5 + - - +
282B SER* 3.4 8.7 + - - -
283B ASP* 3.4 6.1 + - - +
315B PRO 4.0 1.8 - - - -
318B ARG* 3.8 18.9 + - - +
319B ALA* 3.7 25.1 - - - +
322B ASN* 2.9 23.2 + - - -
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Residues in contact with TYR 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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237B SER* 3.3 31.4 - - - -
240B CYS* 3.3 23.1 - - + +
241B ARG* 3.4 48.9 + - + -
242B GLY 5.1 1.3 - - - -
276B TRP* 3.0 49.4 + + + +
277B ALA* 3.4 7.6 - - - +
279B SER* 1.3 91.1 + - - +
281B LEU* 1.3 64.0 + - - +
282B SER 3.4 0.3 + - - -
283B ASP* 3.5 21.2 + - - +
288B LYS* 6.0 0.3 - - - +
318B ARG* 6.2 0.9 - - - -
748D GLN* 5.1 10.0 + - - +
749D THR* 3.9 7.8 + - - -
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Residues in contact with LEU 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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240B CYS* 3.8 18.6 - - + +
249B PHE* 3.5 34.2 - - + -
252B VAL* 3.4 37.5 - - + +
253B SER* 4.7 1.8 - - - +
255B CYS* 4.0 5.2 - - - -
256B LEU* 3.9 16.2 - - + -
259B LEU* 3.6 31.4 - - + -
277B ALA 3.0 16.6 + - - +
278B LEU* 3.3 5.8 + - - +
280B TYR* 1.3 75.7 - - - +
282B SER* 1.3 59.3 + - - +
283B ASP 3.7 0.6 + - - -
288B LYS* 3.6 14.4 - - - +
292B VAL* 3.9 16.6 - - + +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU 2.6 22.3 + - - -
279B SER* 3.4 12.5 + - - -
280B TYR 3.2 0.2 - - - -
281B LEU* 1.3 75.6 - - - +
283B ASP* 1.3 61.4 + - - +
284B GLY* 3.4 3.7 + - - -
288B LYS* 5.4 0.7 - - - -
289B ILE* 3.5 26.2 - - - +
292B VAL* 4.2 16.2 - - - -
319B ALA* 4.0 4.9 + - - +
322B ASN* 3.6 25.1 - - - +
323B ILE* 4.2 19.3 - - - -
325B THR* 5.1 0.3 + - - -
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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
------------------------------------------------------------
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