Contacts of the strand formed by residues 275 - 281 (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 PRO 275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B ALA* 4.0 19.7 - - + +
168B GLY* 4.5 0.2 - - - -
171B ARG* 3.6 29.8 + - - +
172B PRO 3.2 13.9 - - - +
174B MSE 3.7 8.3 - - + +
247B GLY 3.7 20.2 - - - +
248B PHE* 3.6 30.5 - - + -
249B ASN* 3.1 27.5 + - - +
274B GLY* 1.3 82.3 - - - +
276B GLN* 1.3 60.9 + - - +
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B MSE 2.9 14.5 + - - +
175B LEU* 3.4 17.7 - - + -
176B VAL 2.7 31.0 + - - -
248B PHE* 3.6 6.7 - - - -
249B ASN* 2.7 40.3 + - - +
251B ILE* 4.5 4.1 - - + +
269B MSE 5.4 8.2 - - + +
272B LEU* 3.4 40.7 - - + +
273B LYS 2.6 26.9 + - - -
274B GLY 3.7 8.9 + - - +
275B PRO* 1.3 75.1 + - - +
277B PHE* 1.3 56.3 + - - +
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Residues in contact with PHE 277 (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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155B ILE* 5.5 4.0 - - + -
164B MSE 3.9 22.4 - - + -
175B LEU* 4.4 0.4 - - - -
176B VAL* 3.2 29.6 - - + -
178B LEU* 3.4 35.7 - - + -
243B PHE* 3.4 51.6 - + + -
248B PHE* 3.9 14.8 - + + -
249B ASN 3.0 13.0 + - - +
250B TYR* 3.9 16.4 - + - -
251B ILE* 2.8 31.9 + - - +
276B GLN* 1.3 75.7 - - - +
278B LEU* 1.3 63.6 + - - +
279B HIS* 4.2 9.4 - - + -
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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
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59B LEU* 6.1 1.1 - - + -
175B LEU* 3.9 15.8 - - + +
176B VAL 2.7 9.3 + - - -
177B ILE* 3.2 17.0 - - + +
178B LEU 2.8 26.5 + - - -
251B ILE* 3.8 31.0 - - + +
254B VAL* 4.2 15.5 - - + -
262B LEU* 5.4 4.7 - - + -
265B THR* 4.1 11.0 - - + -
266B LEU* 4.1 15.5 - - + -
269B MSE 3.5 26.5 - - + -
277B PHE* 1.3 73.4 - - - +
279B HIS* 1.3 61.8 - - - +
280B ILE* 4.0 20.0 - - + -
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Residues in contact with HIS 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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178B LEU* 3.8 23.9 - - + +
180B ASP* 2.9 35.6 + - + +
243B PHE* 5.1 3.3 - + - -
250B TYR* 3.0 43.5 + - + +
251B ILE 3.1 11.5 + - - +
253B PRO* 3.3 9.5 - - + +
254B VAL* 2.9 26.0 + - - +
277B PHE* 3.9 4.4 + - + -
278B LEU* 1.3 70.5 - - - +
280B ILE* 1.3 75.5 + - - +
281B MSE 3.7 13.2 - - - -
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Residues in contact with ILE 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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59B LEU* 3.6 37.2 - - + -
177B ILE* 4.1 8.1 - - + -
178B LEU 3.0 18.3 + - - +
179B ASN* 3.7 22.2 - - - +
180B ASP* 3.1 30.7 + - - +
254B VAL* 3.3 27.4 - - + +
256B GLY* 4.0 10.8 - - - -
262B LEU* 4.2 8.5 - - + -
278B LEU* 4.0 20.4 - - + -
279B HIS* 1.3 76.4 - - - +
281B MSE 1.3 62.1 + - - +
282B THR* 4.1 10.5 - - + -
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Residues in contact with MSE 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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180B ASP* 3.0 49.6 - - + +
181B ASN* 5.2 1.1 - - - -
253B PRO* 4.1 21.5 - - + -
254B VAL 2.9 17.7 + - - +
255B ASP* 4.1 4.2 - - - +
256B GLY* 2.8 26.6 + - - +
257B HIS* 4.1 3.6 + - - -
279B HIS* 3.7 21.5 - - - -
280B ILE* 1.3 73.3 - - - +
282B THR* 1.3 63.1 + - - +
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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