Contacts of the helix formed by residues 252 - 263 (chain B) in PDB entry 2J25
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 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B LEU* 3.7 25.6 - - + +
251B PHE* 1.3 74.8 - - - +
253B PRO* 1.3 66.3 - - + +
254B GLU* 3.5 10.7 + - - +
255B HIS* 2.9 23.1 + - - +
256B GLN* 2.8 31.5 + - - +
291B TRP* 3.8 1.1 - - - -
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Residues in contact with PRO 253 (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 LEU* 5.7 1.1 - - + -
252B THR* 1.3 91.3 - - + +
254B GLU* 1.3 59.2 + - - +
256B GLN* 3.2 3.1 + - - +
257B ARG* 2.5 35.7 + - - +
290B HIS* 4.4 16.6 - - + +
291B TRP* 3.3 53.4 - - + +
294B VAL* 3.7 26.9 - - + -
295B VAL* 3.9 3.7 - - + +
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Residues in contact with GLU 254 (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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252B THR* 3.5 11.7 + - - +
253B PRO* 1.3 88.4 - - - +
255B HIS* 1.3 64.3 + - - +
257B ARG* 3.1 38.8 - - - +
258B ASP* 2.9 31.5 + - - +
290B HIS* 4.4 8.0 + - - -
294B VAL* 3.7 19.6 - - + +
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Residues in contact with HIS 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 3.9 30.7 + - - -
197B LEU* 4.2 9.8 - - + +
199B GLY 5.0 3.8 - - - -
200B GLN* 5.6 1.1 - - + -
201B PRO* 4.3 12.9 - - + +
206B HIS* 2.8 34.5 + + - -
250B GLY 4.3 5.5 + - - -
251B PHE* 3.8 18.8 - + - -
252B THR* 2.9 27.3 + - - +
254B GLU* 1.3 80.7 - - - +
256B GLN* 1.3 52.1 + - - +
258B ASP* 3.7 4.2 - - - +
259B PHE* 2.7 32.9 + - + +
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Residues in contact with GLN 256 (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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232B ALA* 3.3 31.9 + - - +
233B GLU* 4.5 5.1 - - - +
236B PRO* 4.5 4.2 - - - +
251B PHE* 3.7 24.0 - - + -
252B THR 2.8 15.8 + - - +
253B PRO 3.4 6.7 - - - +
255B HIS* 1.3 72.4 - - - +
257B ARG* 1.3 66.2 + - - +
259B PHE* 3.1 2.4 + - - +
260B ILE* 2.9 36.1 + - + +
280B MET* 3.6 8.8 - - - +
281B LEU 3.1 28.8 + - - +
291B TRP* 3.1 27.0 - - + -
295B VAL* 4.2 6.3 - - + -
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Residues in contact with ARG 257 (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 PRO 2.5 17.8 + - - +
254B GLU* 3.1 43.2 - - - +
256B GLN* 1.3 74.6 - - - +
258B ASP* 1.3 87.3 + - - +
260B ILE* 3.3 4.2 + - - +
261B ALA* 3.0 24.3 + - - +
294B VAL* 3.6 27.3 + - - +
295B VAL* 4.0 18.8 - - + -
298B ASP* 3.6 29.6 + - - +
301B ALA* 3.7 11.8 - - + +
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Residues in contact with ASP 258 (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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201B PRO* 3.3 25.5 - - + +
254B GLU* 2.9 19.0 + - - +
255B HIS* 4.7 1.4 - - - -
257B ARG* 1.3 108.6 + - - +
259B PHE* 1.3 67.1 + - - +
260B ILE 3.1 2.0 - - - -
261B ALA* 4.1 6.8 - - - +
262B ARG* 2.8 33.1 + - + +
298B ASP* 4.6 4.3 - - - +
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Residues in contact with PHE 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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197B LEU* 4.2 3.1 - - + -
201B PRO* 3.8 4.2 - - - +
206B HIS* 3.6 45.1 - + + -
209B TRP* 3.4 32.8 - + - -
210B ALA* 4.1 9.0 - - - -
213B PHE* 4.4 2.7 - + - -
232B ALA* 4.3 13.5 - - + -
251B PHE* 3.7 24.0 - + + -
255B HIS* 2.7 21.5 + - + +
256B GLN* 3.1 4.0 + - - +
258B ASP* 1.3 72.7 - - - +
260B ILE* 1.3 63.5 + - + +
263B ASP* 3.0 39.4 + - + -
264B LEU* 3.1 43.8 + - + -
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Residues in contact with ILE 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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232B ALA* 3.9 21.3 - - + -
256B GLN* 2.9 40.9 + - + +
257B ARG 3.6 4.0 - - - +
259B PHE* 1.3 83.9 - - + +
261B ALA* 1.3 61.9 + - - +
264B LEU* 4.3 3.8 - - + -
265B GLY* 2.9 33.1 + - - +
278B LEU* 3.4 31.2 - - + -
280B MET* 4.3 8.1 - - + -
295B VAL* 4.6 5.4 - - + -
301B ALA* 3.8 23.6 - - + +
304B TYR* 4.0 5.7 - - + -
305B VAL* 4.0 15.9 - - + -
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Residues in contact with ALA 261 (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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257B ARG 3.0 17.1 + - - +
258B ASP* 3.7 9.2 - - - +
260B ILE* 1.3 77.7 - - - +
262B ARG* 1.3 67.7 + - + +
266B PRO* 3.3 19.1 - - - +
298B ASP* 4.7 6.5 - - - +
300B GLU* 4.0 19.9 - - + +
301B ALA* 4.0 18.8 - - + +
304B TYR* 4.0 6.4 - - - -
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Residues in contact with ARG 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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201B PRO* 4.0 20.9 + - + +
202B GLY* 3.9 21.9 - - - +
207B GLN* 3.9 6.2 + - - -
258B ASP* 2.8 24.8 + - + +
261B ALA* 1.3 79.9 - - + +
263B ASP* 1.3 72.5 + - - +
266B PRO* 3.3 14.7 - - - +
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Residues in contact with ASP 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO* 3.3 10.9 - - - +
202B GLY* 3.0 36.6 + - - -
206B HIS* 3.1 26.3 - - - +
207B GLN* 2.8 31.5 + - - +
210B ALA* 3.7 1.8 - - + -
259B PHE* 3.0 27.2 + - + +
261B ALA 3.5 1.0 - - - -
262B ARG* 1.3 77.9 - - - +
264B LEU* 1.3 57.8 + - - +
265B GLY 3.3 1.6 - - - -
266B PRO* 3.3 2.0 - - - +
267B THR* 2.2 39.0 + - - +
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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