Contacts of the strand formed by residues 275 - 281 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ALA* 3.5 26.2 - - + +
171A ARG* 3.6 33.7 + - - +
172A PRO* 3.5 17.7 - - + +
174A MSE 3.7 5.8 - - + +
247A GLY 4.2 7.7 - - - +
248A PHE* 3.5 34.7 - - + -
249A ASN* 3.0 23.2 + - - +
274A GLY* 1.3 80.6 - - - +
276A GLN* 1.3 64.6 + - - +
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A MSE 2.8 14.8 + - - +
175A LEU* 3.5 20.1 - - + -
176A VAL 2.8 24.6 + - - -
248A PHE* 3.4 7.8 - - - -
249A ASN* 2.8 40.7 + - - +
269A MSE 3.6 30.6 - - + +
272A LEU* 3.7 22.4 - - + +
273A LYS 2.8 25.3 + - - -
274A GLY 3.5 10.0 + - - +
275A PRO* 1.3 75.0 + - - +
277A PHE* 1.3 61.5 + - - +
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE* 4.0 9.4 - - + -
164A MSE 4.1 6.7 - - - -
176A VAL* 3.3 29.8 - - + -
178A LEU* 3.6 35.2 - - + -
243A PHE* 3.5 56.1 - + + -
248A PHE* 3.7 23.8 - + + -
249A ASN 2.9 15.7 + - - +
250A TYR* 3.8 20.0 - + + -
251A ILE 2.9 27.5 + - - +
269A MSE 3.8 4.8 - - - +
276A GLN* 1.3 74.0 - - - +
278A LEU* 1.3 63.5 + - - +
279A HIS* 4.3 0.9 - - + -
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 6.2 0.4 - - + -
175A LEU* 3.9 9.5 - - + +
176A VAL 2.9 8.6 + - - +
177A ILE* 3.3 11.1 - - + +
178A LEU 2.8 26.2 + - - -
251A ILE* 3.5 29.6 - - + +
254A VAL* 4.2 15.5 - - + -
262A LEU* 4.6 8.3 - - + -
265A THR* 4.0 20.6 - - + -
266A LEU* 3.9 28.0 - - + -
269A MSE 4.0 12.3 - - + -
277A PHE* 1.3 73.9 - - - +
279A HIS* 1.3 64.7 + - - +
280A ILE* 3.7 21.2 + - + -
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Residues in contact with HIS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 3.5 29.0 - - + +
180A ASP* 2.6 32.1 + - + +
239A PRO* 4.6 15.8 - - + +
243A PHE* 5.1 2.1 - + - -
250A TYR* 2.7 44.3 + - + +
251A ILE 2.9 8.5 + - - +
252A GLY* 3.7 2.3 - - - -
253A PRO* 3.2 19.5 - - + +
254A VAL* 2.8 31.7 + - - +
277A PHE* 4.0 3.1 + - + -
278A LEU* 1.3 73.3 - - - +
280A ILE* 1.3 68.3 + - - +
281A MSE 4.6 1.6 - - - +
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 3.7 35.7 - - + -
177A ILE* 4.2 11.4 - - + -
178A LEU 3.0 16.5 + - - +
179A ASN* 3.9 17.7 - - - +
180A ASP* 3.1 30.5 + - - +
254A VAL* 3.3 10.8 - - + +
256A GLY* 4.1 11.4 - - - -
262A LEU* 4.1 14.4 - - + -
278A LEU* 3.7 29.2 - - + -
279A HIS* 1.3 78.5 - - - +
281A MSE 1.3 64.5 + - - +
282A THR* 4.0 12.1 - - + -
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Residues in contact with MSE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP* 3.0 16.8 - - + +
253A PRO* 3.6 42.6 - - + +
254A VAL 2.8 21.8 + - - +
255A ASP* 4.3 7.7 - - - +
256A GLY* 2.8 26.9 + - - -
257A HIS* 4.3 1.9 + - - -
279A HIS* 4.6 1.8 - - - +
280A ILE* 1.3 80.3 - - - +
282A THR* 1.3 62.9 + - - +
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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