Contacts of the helix formed by residues 258 - 269 (chain B) in PDB entry 2O1S
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 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B ASP* 3.7 27.6 + - + +
256B GLY 3.4 3.0 - - - -
257B HIS* 1.3 76.0 - - - +
259B VAL* 1.3 55.0 + - - +
260B LEU* 3.4 8.1 + - - +
261B GLY* 2.7 55.2 + - - +
262B LEU* 2.8 17.7 + - - +
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Residues in contact with VAL 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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28B LEU* 4.0 22.4 - - + -
29B PRO* 4.1 21.5 - - + -
32B CYS* 3.2 37.0 - - + -
58B GLU* 3.5 26.2 - - + +
61B VAL* 4.3 9.2 - - + -
62B ALA* 4.2 1.6 - - - +
257B HIS 3.7 2.1 + - - +
258B ASP* 1.3 71.6 + - - +
260B LEU* 1.3 61.7 + - - +
262B LEU* 3.4 9.1 + - - +
263B ILE* 3.1 32.8 + - + +
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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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25B LYS* 3.8 45.3 - - + +
26B GLU* 5.1 7.6 - - + -
28B LEU* 4.7 1.3 - - + -
29B PRO* 4.1 23.8 - - + -
258B ASP* 3.3 5.8 + - - +
259B VAL* 1.3 79.9 - - - +
261B GLY* 1.3 62.1 + - - +
263B ILE* 3.5 17.4 + - + +
264B THR* 3.1 27.4 + - - +
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Residues in contact with GLY 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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258B ASP* 2.7 28.9 + - - -
260B LEU* 1.3 74.7 - - - +
262B LEU* 1.3 64.5 + - - -
264B THR* 3.4 6.8 + - - -
265B THR* 3.1 26.1 + - - -
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Residues in contact with LEU 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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58B GLU* 4.3 7.4 - - + +
59B LEU* 4.8 13.0 - - + -
62B ALA* 3.7 16.6 - - + -
254B VAL* 4.0 21.5 - - + -
255B ASP 3.1 22.4 - - - +
256B GLY* 3.6 24.9 - - - +
258B ASP 2.8 42.1 + - - +
259B VAL* 3.9 4.9 - - - +
261B GLY* 1.3 70.2 - - - -
263B ILE* 1.3 61.7 + - - +
265B THR* 3.2 6.3 + - - +
266B LEU* 2.8 39.8 + - + +
278B LEU* 5.4 3.8 - - + -
280B ILE* 4.2 8.5 - - + -
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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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25B LYS* 3.6 16.6 - - + +
28B LEU* 3.2 35.2 - - + -
62B ALA* 3.8 21.3 - - - -
65B TYR* 3.5 11.9 - - + -
66B VAL* 3.9 15.8 - - + +
259B VAL* 3.1 21.0 + - + +
260B LEU* 3.6 16.6 - - + +
261B GLY 3.2 0.2 - - - -
262B LEU* 1.3 76.0 - - - +
264B THR* 1.3 66.5 + - - +
266B LEU* 3.2 1.8 + - - +
267B LYS* 2.9 47.0 + - - +
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Residues in contact with THR 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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260B LEU 3.1 16.6 + - - -
261B GLY* 3.6 6.5 - - - -
263B ILE* 1.3 80.6 - - - +
265B THR* 1.3 59.7 + - - +
267B LYS* 3.3 7.5 + - - +
268B ASN* 2.8 49.9 + - - +
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Residues in contact with THR 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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251B ILE* 4.6 8.3 - - + -
254B VAL* 4.9 14.5 - - + +
261B GLY 3.1 13.2 + - - -
262B LEU* 3.6 11.1 - - - -
264B THR* 1.3 76.7 - - - +
266B LEU* 1.3 66.3 + - - +
268B ASN* 3.0 20.0 + - + +
269B MSE 3.0 40.2 + - + +
278B LEU* 4.1 16.2 - - + -
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Residues in contact with LEU 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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59B LEU* 5.2 2.7 - - + -
62B ALA* 3.9 37.7 - - + +
63B LEU* 3.9 24.2 - - + -
66B VAL* 4.2 19.1 - - + +
67B TYR* 4.4 10.7 + - + -
175B LEU* 3.9 20.6 - - + -
177B ILE* 4.4 2.5 - - + -
262B LEU* 2.8 28.0 + - + +
263B ILE 3.7 3.1 - - - +
265B THR* 1.3 72.6 - - - +
267B LYS* 1.3 62.2 + - - +
269B MSE 3.1 31.6 + - + +
270B ARG* 3.3 10.4 + - - +
278B LEU* 4.1 11.4 - - + -
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Residues in contact with LYS 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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25B LYS* 3.8 15.8 - - - +
65B TYR* 5.7 1.2 - - - -
66B VAL* 4.2 18.8 - - + +
263B ILE* 2.9 41.6 + - - +
264B THR* 3.6 7.2 - - - +
266B LEU* 1.3 79.3 - - - +
268B ASN* 1.3 62.7 + - - +
270B ARG* 3.2 29.6 + - + +
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Residues in contact with ASN 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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264B THR* 2.8 45.9 + - - +
265B THR* 3.0 12.0 + - + +
267B LYS* 1.3 78.1 - - - +
269B MSE 1.3 61.7 + - + +
270B ARG 3.3 1.4 + - - -
271B ASP 4.8 2.3 + - - -
272B LEU* 4.4 8.3 - - - +
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Residues in contact with MSE 269 (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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175B LEU* 4.5 16.2 - - + -
251B ILE* 4.0 27.6 - - + -
265B THR* 3.0 47.0 + - + +
266B LEU* 3.1 18.8 + - + +
268B ASN* 1.3 78.9 - - + +
270B ARG* 1.3 65.3 + - - +
271B ASP 3.3 2.7 - - - -
272B LEU* 3.1 41.5 + - + +
276B GLN* 5.4 7.0 - - + +
278B LEU* 3.5 29.8 - - + -
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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