Contacts of the strand formed by residues 174 - 180 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C ILE* 4.1 10.3 - - + +
130C GLY 4.0 14.4 - - - -
131C ILE* 3.7 20.0 - - - +
134C ALA* 4.2 7.9 - - + -
146C THR* 3.4 16.8 - - + +
148C CYS* 3.8 23.6 - - - -
167C ALA* 4.7 7.0 - - - -
172C PRO* 3.3 31.8 + - + +
173C ASP* 1.3 76.2 - - - +
175C LEU* 1.3 63.4 + - - +
176C VAL* 3.7 28.0 - - + -
248C PHE* 5.1 2.0 - - + -
269C MSE 6.2 0.2 - - - -
272C LEU 5.7 0.6 + - - -
274C GLY 3.6 2.9 + - - +
275C PRO* 4.7 6.7 - - + -
276C GLN* 2.9 30.4 + - - +
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TYR* 3.4 28.0 - - - +
146C THR 2.9 9.3 + - - +
147C VAL* 3.1 4.7 - - + +
148C CYS* 2.7 34.0 + - - +
174C MSE 1.3 75.9 - - - +
176C VAL* 1.3 70.0 + - - +
177C ILE* 3.6 18.2 - - + -
266C LEU* 3.5 31.0 - - + +
269C MSE 4.3 22.2 - - + +
270C ARG* 5.9 0.2 - - - -
276C GLN* 3.7 25.6 - - + +
277C PHE 4.1 0.2 - - - +
278C LEU* 4.0 14.8 - - + +
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ILE* 4.1 25.6 - - + -
148C CYS* 3.4 7.2 - - + +
150C ILE* 4.0 22.4 - - + -
164C MSE 5.6 0.2 - - - -
174C MSE 3.7 26.0 - - + -
175C LEU* 1.3 71.9 - - - +
177C ILE* 1.3 64.4 + - - +
248C PHE* 3.7 24.9 - - + -
276C GLN 2.9 11.6 + - - +
277C PHE* 3.3 27.0 - - + -
278C LEU 2.9 24.4 + - - +
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Residues in contact with ILE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LEU* 4.4 17.0 - - + -
63C LEU* 3.8 11.2 - - + -
147C VAL* 3.7 13.9 - - + -
148C CYS 2.6 15.3 + - - +
149C VAL* 3.4 9.2 - - + +
150C ILE* 2.8 32.1 + - - +
175C LEU* 3.6 34.1 - - + -
176C VAL* 1.3 73.4 - - - +
178C LEU* 1.3 66.5 + - - +
179C ASN 3.4 1.4 + - - +
266C LEU* 3.7 16.8 - - + -
278C LEU* 3.3 15.0 - - + +
280C ILE* 4.1 29.6 - - + -
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ILE* 3.3 17.5 - - + +
151C GLY 3.8 2.9 - - - +
152C ASP* 3.8 28.0 - - + +
155C ILE* 4.2 17.5 - - + -
176C VAL 4.0 1.8 + - - -
177C ILE* 1.3 68.9 - - - +
179C ASN* 1.3 59.0 + - - +
180C ASP* 3.1 14.5 + - + +
243C PHE* 4.0 14.4 - - + -
277C PHE* 3.6 30.0 - - + -
278C LEU 2.7 10.3 + - - +
279C HIS* 3.8 32.1 - - + +
280C ILE* 3.0 27.1 + - - +
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Residues in contact with ASN 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLY 4.5 0.5 - - - +
56C THR* 3.7 25.6 - - - +
59C LEU* 4.8 1.1 - - + -
81C GLN* 4.6 12.1 - - - +
149C VAL* 4.0 19.2 - - + +
150C ILE 2.8 15.5 + - - +
151C GLY* 3.4 6.1 - - - -
152C ASP* 3.4 20.9 + - - +
177C ILE 3.4 1.8 + - - -
178C LEU* 1.3 67.6 - - - +
180C ASP* 1.3 59.2 + - - +
181C ASN* 3.7 10.5 + - - +
280C ILE* 3.8 13.2 - - + +
282C THR* 2.8 38.3 + - - +
3002C TPP 4.8 0.3 + - - -
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Residues in contact with ASP 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ASP* 3.6 22.0 - - + +
178C LEU* 4.1 6.7 - - + +
179C ASN* 1.3 71.7 + - - +
181C ASN* 1.3 57.8 + - - +
182C GLU* 2.7 36.6 + - - +
279C HIS* 3.1 39.2 + - + +
280C ILE 3.1 7.4 + - - +
281C MSE 3.3 23.1 - - - +
282C THR* 3.2 19.7 + - - -
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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