Contacts of the strand formed by residues 174 - 180 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D ILE* 4.3 5.2 - - + +
130D GLY* 3.7 18.4 - - - +
131D ILE* 3.5 32.5 - - + +
134D ALA* 4.1 9.0 - - + -
146D THR* 3.4 14.4 - - + +
148D CYS* 3.6 31.9 - - - -
167D ALA* 4.5 12.8 - - - -
172D PRO* 3.2 15.8 + - - +
173D ASP* 1.3 75.9 - - - +
175D LEU* 1.3 61.3 + - - +
176D VAL* 4.3 18.8 - - + -
248D PHE* 5.1 0.7 - - + -
274D GLY 3.5 4.1 + - - +
275D PRO* 4.5 7.6 - - + -
276D GLN* 2.9 29.3 + - - +
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D TYR* 3.5 29.2 - - + +
146D THR 3.0 8.5 + - - +
147D VAL* 3.0 7.9 - - + +
148D CYS* 2.7 24.9 + - - +
174D MSE 1.3 76.5 - - - +
176D VAL* 1.3 71.0 + - - +
177D ILE* 3.9 24.2 - - + -
266D LEU* 5.0 9.2 - - + -
269D MSE 4.0 24.0 - - + +
270D ARG* 5.2 0.7 - - - +
276D GLN* 3.4 30.7 - - + +
277D PHE 4.0 0.2 - - - +
278D LEU* 3.7 20.9 - - + +
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ILE* 4.1 19.5 - - + -
148D CYS* 3.1 16.2 - - + +
150D ILE* 4.1 18.4 - - + -
174D MSE 4.3 17.0 - - + -
175D LEU* 1.3 78.6 - - - +
177D ILE* 1.3 62.6 + - - +
178D LEU 4.1 0.2 + - - -
248D PHE* 3.5 32.3 - - + -
276D GLN 3.1 3.6 + - - +
277D PHE* 3.4 31.4 - - + -
278D LEU 3.1 22.0 + - - +
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Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 4.2 24.2 - - + -
63D LEU* 3.9 17.5 - - + -
147D VAL* 3.7 22.2 - - + -
148D CYS 2.4 19.4 + - - +
149D VAL* 3.4 10.5 - - + +
150D ILE* 2.9 31.0 + - - -
175D LEU* 3.9 20.9 - - + -
176D VAL* 1.3 78.3 - - - +
178D LEU* 1.3 64.5 + - - +
179D ASN 3.3 1.8 + - - +
266D LEU* 4.9 2.7 - - + -
278D LEU* 3.3 17.5 - - + +
280D ILE* 3.6 31.9 - - + -
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ILE* 3.4 25.7 - - + +
151D GLY 3.9 6.3 - - - +
152D ASP* 4.0 13.5 - - + -
155D ILE* 3.5 21.5 - - + -
176D VAL 4.1 1.4 + - - -
177D ILE* 1.3 70.5 - - - +
179D ASN* 1.3 57.8 + - - +
180D ASP* 3.1 8.6 + - + +
243D PHE* 4.3 12.1 - - + -
277D PHE* 3.5 29.0 - - + -
278D LEU 2.8 10.7 + - - +
279D HIS* 3.3 37.7 - - + +
280D ILE* 2.8 33.3 + - - +
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Residues in contact with ASN 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLY 5.3 0.4 - - - -
56D THR* 3.5 28.1 - - - +
59D LEU* 5.0 5.0 - - + +
81D GLN* 4.4 14.7 - - - +
149D VAL* 4.0 17.5 - - + -
150D ILE 2.8 17.5 + - - +
151D GLY* 3.8 12.9 - - - -
152D ASP* 3.5 7.4 - - - +
177D ILE* 3.3 2.4 + - - -
178D LEU* 1.3 68.2 - - - +
180D ASP* 1.3 60.7 + - - +
181D ASN* 3.6 6.7 + - - +
280D ILE* 3.9 6.9 - - - +
282D THR* 3.0 39.5 + - - +
1004D MG 4.1 2.6 - - - -
4002D DPO 5.5 4.2 + - - -
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Residues in contact with ASP 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ASP* 3.2 20.2 - - + +
178D LEU* 3.1 6.5 + - + +
179D ASN* 1.3 71.4 - - - +
181D ASN* 1.3 89.3 + - - +
279D HIS* 3.1 35.7 + - + +
280D ILE 2.8 14.6 + - - +
281D MSE 3.5 21.6 - - - +
282D THR* 2.9 31.0 + - - +
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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