Contacts of the helix formed by residues 256 - 267 (chain B) in PDB entry 4OSI
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 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B ARG* 3.5 9.0 - - - +
254B GLN 4.1 4.7 - - - +
255B LEU* 1.3 76.5 - - - +
257B THR* 1.3 67.4 + - - +
258B GLY* 3.6 14.0 + - - -
259B GLN* 3.0 32.8 + - - +
260B LEU* 2.6 38.3 + - - +
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Residues in contact with THR 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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249B ARG* 2.3 40.2 + - - +
256B ASP* 1.3 79.7 + - - +
258B GLY* 1.3 65.3 + - - -
260B LEU* 3.8 3.6 - - - +
261B LEU* 3.0 30.9 + - + +
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Residues in contact with GLY 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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256B ASP* 3.5 7.9 + - - -
257B THR* 1.3 80.1 + - - +
259B GLN* 1.3 52.9 + - - +
261B LEU* 2.9 9.4 + - - +
262B LYS* 2.7 36.7 + - - +
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Residues in contact with GLN 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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254B GLN 4.2 1.8 - - - +
255B LEU* 2.3 54.5 - - + +
256B ASP* 3.0 32.7 + - - +
257B THR 3.4 0.4 - - - -
258B GLY* 1.3 71.7 - - - +
260B LEU* 1.3 65.8 + - - +
261B LEU 2.9 1.2 + - - -
262B LYS* 3.0 11.3 + - - +
263B ILE* 2.9 27.2 + - - +
291B PRO* 4.8 3.9 - - - +
292B GLU* 4.6 19.6 - - - +
295B VAL* 4.1 13.8 - - + +
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Residues in contact with LEU 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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241B LEU* 4.2 20.5 - - + +
245B ALA* 4.5 17.0 - - + +
248B LEU* 4.0 16.2 - - + -
249B ARG* 3.8 34.1 - - + +
255B LEU* 3.0 40.4 - - + -
256B ASP 2.6 27.5 + - - +
257B THR* 3.8 3.6 - - - +
259B GLN* 1.3 72.9 - - - +
261B LEU* 1.3 57.2 + - + +
263B ILE* 4.0 7.7 - - + +
264B ALA* 3.0 29.5 + - - +
272B VAL* 5.1 0.9 - - - +
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Residues in contact with LEU 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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241B LEU* 5.0 12.3 - - + -
257B THR* 3.0 19.0 + - + +
258B GLY* 2.9 12.1 + - - +
259B GLN 2.9 1.2 + - - -
260B LEU* 1.3 75.1 - - + +
262B LYS* 1.3 67.1 + - - +
264B ALA* 3.0 8.2 + - + +
265B LYS* 2.8 50.0 + - + +
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Residues in contact with LYS 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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258B GLY 2.7 14.6 + - - +
259B GLN* 3.2 13.0 - - - +
261B LEU* 1.3 74.0 - - - +
263B ILE* 1.3 64.9 + - - +
265B LYS* 3.0 9.0 + - - +
266B ARG* 3.0 38.7 + - - +
267B GLY 4.2 0.3 + - - -
295B VAL* 3.9 19.3 - - + +
296B ALA* 4.6 13.1 - - - +
299B SER* 3.4 25.7 + - - +
7H A 4.8 13.7 + - - -
8H A 3.2 32.5 + - - +
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Residues in contact with ILE 263 (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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248B LEU* 5.9 1.3 - - + -
255B LEU* 4.1 19.1 - - + -
259B GLN 2.9 22.6 + - - +
260B LEU* 4.0 6.1 - - + +
262B LYS* 1.3 74.2 - - - +
264B ALA* 1.3 58.8 + - - +
267B GLY* 3.2 6.2 + - - -
268B GLY 3.1 21.3 + - - -
271B ALA* 4.1 3.1 - - + -
272B VAL* 3.8 22.4 - - + +
275B VAL* 3.9 35.0 - - + -
295B VAL* 3.6 33.4 - - + -
298B ALA* 4.1 10.8 - - + -
299B SER* 3.4 18.2 - - - +
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Residues in contact with ALA 264 (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 ALA* 4.4 14.6 - - + +
241B LEU* 3.7 29.6 - - + -
260B LEU 3.0 20.0 + - - +
261B LEU* 3.0 7.2 + - + +
263B ILE* 1.3 78.1 - - - +
265B LYS* 1.3 58.2 + - + +
268B GLY* 3.3 20.2 - - - -
272B VAL* 3.6 13.7 - - + -
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Residues in contact with LYS 265 (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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261B LEU* 2.8 41.1 + - + +
262B LYS* 3.0 2.0 + - - +
264B ALA* 1.3 77.9 - - + +
266B ARG* 1.3 109.0 + - + +
268B GLY* 4.3 2.4 + - - -
9H A 3.4 21.0 + - - -
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Residues in contact with ARG 266 (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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262B LYS* 3.0 35.2 + - - +
265B LYS* 1.3 125.5 - - + +
267B GLY* 1.3 64.6 + - - +
268B GLY* 3.4 0.4 - - - -
299B SER* 3.5 23.7 + - - +
300B HIS* 3.5 9.4 - - - +
301B ASP* 3.2 24.6 - - - +
8H A 3.1 52.3 + - + +
9H A 3.1 18.2 + - - +
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Residues in contact with GLY 267 (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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262B LYS 4.2 0.2 + - - -
263B ILE 3.2 9.7 + - - -
266B ARG* 1.3 80.8 - - - +
268B GLY* 1.3 66.8 + - - +
270B THR* 3.9 6.6 + - - -
271B ALA* 3.1 30.2 + - - +
298B ALA 3.6 6.1 - - - -
299B SER 4.2 0.4 - - - -
300B HIS 3.4 17.0 - - - +
301B ASP* 5.8 0.3 - - - -
302B GLY 5.5 0.5 + - - -
303B GLY 5.6 0.5 + - - -
3G T 4.9 5.0 + - - -
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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