Contacts of the helix formed by residues 247 - 257 (chain B) in PDB entry 4J1O
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 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B ASN* 4.4 11.0 - - - +
245B GLY 3.4 1.4 + - - -
246B GLU* 1.3 87.0 - - - +
248B LEU* 1.3 66.1 + - - +
249B SER* 3.5 12.1 + - - +
250B THR* 2.8 50.2 + - - -
251B VAL* 3.2 14.6 + - - +
270B ILE* 3.4 13.5 - - - -
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Residues in contact with LEU 248 (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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281A ASP* 3.6 29.6 - - + +
282A ILE 4.4 1.6 - - - +
285A ALA* 4.2 10.5 - - + -
247B ASP* 1.3 74.8 - - - +
249B SER* 1.3 58.0 + - - +
251B VAL* 3.1 7.0 + - + +
252B ILE* 2.9 37.8 + - + +
270B ILE* 3.6 8.9 + - + +
275B GLN* 3.6 34.9 + - - +
278B ALA* 3.9 17.0 - - + -
279B PHE* 3.7 34.8 - - + +
282B ILE* 3.7 21.1 - - + -
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Residues in contact with SER 249 (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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285A ALA* 4.1 19.2 + - - +
286A ARG* 2.8 53.5 + - - +
247B ASP* 3.5 12.5 + - - +
248B LEU* 1.3 79.6 - - - +
250B THR* 1.3 61.8 + - - +
252B ILE* 3.3 7.6 + - - +
253B ARG* 3.1 6.2 + - - +
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Residues in contact with THR 250 (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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225B LEU* 3.9 24.4 - - + +
241B LEU* 5.4 3.8 - - + -
244B SER 3.3 27.9 + - - +
245B GLY* 4.5 2.7 - - - -
246B GLU* 4.4 3.8 + - - +
247B ASP* 2.8 37.0 + - - -
249B SER* 1.3 70.6 - - - +
251B VAL* 1.3 60.8 + - - +
253B ARG* 3.2 8.0 + - + +
254B ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 251 (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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245B GLY* 4.9 4.3 - - - -
247B ASP 3.2 13.1 + - - +
248B LEU* 3.1 11.8 + - + +
250B THR* 1.3 74.1 - - - +
252B ILE* 1.3 58.8 + - - +
254B ALA* 3.3 5.6 + - - +
255B ALA* 2.8 29.6 + - - +
263B PHE* 4.0 20.1 - - + -
265B MET* 3.8 18.6 - - + -
270B ILE* 4.4 4.3 - - + -
279B PHE* 3.7 35.9 - - + -
282B ILE* 4.1 27.6 - - + -
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Residues in contact with ILE 252 (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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252A ILE* 4.5 10.8 - - + +
255A ALA* 4.0 13.0 - - + -
256A GLY* 3.7 24.0 - - - +
282A ILE* 3.9 40.4 - - + +
285A ALA* 3.9 16.2 - - + -
286A ARG* 4.0 13.9 - - + +
248B LEU* 2.9 24.6 + - + +
249B SER* 3.5 8.3 - - - +
250B THR 3.2 0.2 - - - -
251B VAL* 1.3 78.1 - - - +
253B ARG* 1.3 56.8 + - - +
255B ALA* 4.3 3.1 - - - +
256B GLY* 2.9 28.9 + - - -
282B ILE* 3.8 17.9 - - + -
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Residues in contact with ARG 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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256A GLY* 4.6 6.3 - - - -
286A ARG* 3.4 18.2 - - - +
225B LEU* 3.7 24.3 - - - +
226B GLU* 2.7 32.5 + - - -
229B ALA* 5.2 5.7 - - - +
249B SER 3.1 8.2 + - - +
250B THR* 3.2 11.6 + - - +
252B ILE* 1.3 75.5 - - - +
254B ALA* 1.3 59.7 + - - +
257B GLN* 2.9 65.0 + - - +
259B LEU* 3.8 18.5 - - + +
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Residues in contact with ALA 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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225B LEU* 5.2 2.0 - - + +
241B LEU* 3.8 28.7 - - + -
250B THR 2.9 16.5 + - - +
251B VAL 3.8 3.1 - - - +
253B ARG* 1.3 77.2 - - - +
255B ALA* 1.3 62.2 + - - +
258B GLY* 3.1 2.8 + - - -
259B LEU* 2.8 43.0 + - + -
260B CYS* 4.0 16.9 + - - +
263B PHE* 4.2 6.3 - - + -
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Residues in contact with ALA 255 (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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252A ILE* 4.0 16.8 - - + -
251B VAL* 2.8 21.7 + - + +
254B ALA* 1.3 73.4 - - - +
256B GLY* 1.3 62.3 + - - +
258B GLY* 3.4 11.0 + - - -
260B CYS 6.0 0.4 - - - -
263B PHE* 5.0 1.9 - - + -
282B ILE* 4.0 14.4 - - + -
286B ARG* 3.1 23.7 + - + +
288B LEU* 3.9 29.3 - - + +
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Residues in contact with GLY 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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252A ILE* 3.7 26.6 - - - +
253A ARG* 4.7 2.6 - - - +
256A GLY* 4.2 2.5 - - - -
257A GLN* 3.1 28.4 + - - +
252B ILE 2.9 18.2 + - - -
255B ALA* 1.3 77.9 - - - +
257B GLN* 1.3 62.6 + - - +
286B ARG* 4.3 5.5 + - - -
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Residues in contact with GLN 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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256A GLY 3.1 26.2 + - - +
257A GLN* 4.5 13.2 - - + +
232B ARG* 4.9 3.6 + - - -
253B ARG* 2.9 48.6 + - - +
256B GLY* 1.3 76.9 - - - +
258B GLY* 1.3 64.4 + - - +
259B LEU* 3.4 23.1 + - + +
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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