Contacts of the strand formed by residues 174 - 180 (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 MSE 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B ILE* 4.4 2.0 - - + +
130B GLY 3.9 15.9 - - - +
131B ILE* 3.8 33.4 - - + +
134B ALA* 3.9 8.1 - - + -
146B THR* 3.6 14.4 - - + +
148B CYS* 3.7 29.4 - - - -
167B ALA* 4.5 8.1 - - - -
172B PRO* 3.3 21.7 + - + +
173B ASP* 1.3 77.9 - - - +
175B LEU* 1.3 63.4 + - - +
176B VAL* 3.9 17.0 - - + -
248B PHE* 4.8 7.2 - - + -
274B GLY 3.5 4.9 + - - +
275B PRO* 4.3 8.3 - - + -
276B GLN* 2.9 29.4 + - - +
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Residues in contact with LEU 175 (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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67B TYR* 3.5 25.4 - - - +
146B THR 3.1 10.8 + - - +
147B VAL* 3.3 6.8 - - + -
148B CYS* 2.8 27.9 + - - +
174B MSE 1.3 79.3 - - - +
176B VAL* 1.3 76.6 + - - +
177B ILE* 3.8 19.1 - - + -
266B LEU* 3.9 23.1 - - + -
269B MSE 4.5 15.9 - - + -
276B GLN* 3.4 26.2 - - + +
277B PHE 4.4 0.2 - - - -
278B LEU* 3.9 16.4 - - + +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 4.0 33.9 - - + -
148B CYS* 3.4 7.4 - - + +
150B ILE* 4.1 13.2 - - + -
164B MSE 5.5 0.2 - - - -
174B MSE 3.9 19.5 - - + -
175B LEU* 1.3 76.2 - - - +
177B ILE* 1.3 58.2 + - - +
248B PHE* 3.5 29.4 - - + -
276B GLN 2.7 12.7 + - - +
277B PHE* 3.2 26.2 - - + -
278B LEU 2.7 32.6 + - - +
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Residues in contact with ILE 177 (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* 4.1 19.1 - - + -
63B LEU* 3.9 18.8 - - + -
147B VAL* 3.7 22.0 - - + -
148B CYS 2.6 15.0 + - - +
149B VAL* 3.4 8.9 - - + +
150B ILE* 2.9 29.1 + - - +
175B LEU* 3.8 22.7 - - + -
176B VAL* 1.3 79.1 - - - +
178B LEU* 1.3 61.7 + - - +
179B ASN 3.6 1.0 + - - +
266B LEU* 4.4 6.1 - - + -
278B LEU* 3.2 18.2 - - + +
280B ILE* 4.1 32.3 - - + -
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Residues in contact with LEU 178 (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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150B ILE* 3.4 14.8 - - + +
151B GLY 3.8 2.0 - - - +
152B ASP* 3.8 18.2 - - + +
155B ILE* 3.5 31.2 - - + -
176B VAL 4.0 1.4 + - - -
177B ILE* 1.3 70.1 - - - +
179B ASN* 1.3 59.8 + - - +
180B ASP* 3.2 11.0 + - + +
243B PHE* 3.9 16.8 - - + -
277B PHE* 3.4 35.4 - - + -
278B LEU 2.8 9.0 + - - +
279B HIS* 3.8 29.4 - - + +
280B ILE* 3.0 28.1 + - - +
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Residues in contact with ASN 179 (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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55B GLY 4.6 1.1 + - - +
56B THR* 3.8 11.6 - - - +
59B LEU* 5.3 0.4 - - - -
81B GLN* 3.2 33.3 + - - +
149B VAL* 4.4 15.9 - - + +
150B ILE 2.8 15.1 + - - +
151B GLY* 3.8 1.3 - - - -
152B ASP* 3.3 17.2 + - - +
177B ILE 3.6 1.2 + - - -
178B LEU* 1.3 70.7 - - - +
180B ASP* 1.3 58.0 + - - +
181B ASN* 3.4 3.9 + - - +
280B ILE* 3.7 14.9 - - + +
282B THR* 2.6 40.8 + - - +
1002B MG 3.3 13.6 - - - -
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Residues in contact with ASP 180 (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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152B ASP* 3.8 18.1 - - - +
178B LEU* 3.2 8.2 + - + +
179B ASN* 1.3 70.9 + - - +
181B ASN* 1.3 71.4 + - - +
279B HIS* 2.9 38.2 + - + +
280B ILE 3.1 11.6 + - - +
281B MSE 3.0 25.0 - - + +
282B THR 2.9 21.8 + - - -
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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