Contacts of the strand formed by residues 275 - 281 (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 PRO 275 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C ALA* 3.7 15.3 - - + +
171C ARG* 3.7 46.7 + - - +
172C PRO* 3.1 15.2 - - + +
174C MSE 4.1 4.9 - - + +
247C GLY 3.9 11.6 - - - +
248C PHE* 3.4 32.5 - - + -
249C ASN* 2.9 27.9 + - - +
274C GLY* 1.3 80.5 - - - +
276C GLN* 1.3 61.2 + - - +
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Residues in contact with GLN 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C MSE 2.9 16.5 + - - +
175C LEU* 3.6 18.3 - - + -
176C VAL 2.9 22.7 + - - -
248C PHE* 3.4 8.7 - - - -
249C ASN* 2.8 44.3 + - - +
251C ILE* 4.2 5.3 - - - +
269C MSE 4.0 15.1 - - + +
272C LEU* 3.2 36.4 - - + +
273C LYS 3.1 19.1 - - - +
274C GLY 3.4 10.1 - - - +
275C PRO* 1.3 73.5 - - - +
277C PHE* 1.3 61.1 + - - +
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Residues in contact with PHE 277 (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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155C ILE* 4.0 8.7 - - + -
164C MSE 4.3 5.6 - - - -
175C LEU* 4.4 1.3 - - - -
176C VAL* 3.3 26.9 - - + -
178C LEU* 3.6 37.2 - - + -
243C PHE* 3.5 53.4 - + + -
248C PHE* 3.7 31.0 - + + -
249C ASN 3.0 13.0 + - - +
250C TYR* 3.7 19.7 - + + -
251C ILE* 3.1 27.2 + - - +
269C MSE 5.1 1.6 - - - -
276C GLN* 1.3 75.8 - - - +
278C LEU* 1.3 64.3 + - - +
279C HIS* 4.4 0.4 - - + -
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Residues in contact with LEU 278 (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* 6.1 0.4 - - + -
175C LEU* 4.0 7.7 - - + +
176C VAL 2.9 7.5 + - - -
177C ILE* 3.3 13.0 - - + +
178C LEU* 2.7 32.6 + - - +
251C ILE* 3.5 31.0 - - + +
254C VAL* 4.1 17.3 - - + -
262C LEU* 4.5 10.1 - - + -
265C THR* 4.1 8.7 - - + -
266C LEU* 3.9 17.0 - - + -
269C MSE 3.1 34.3 - - + -
277C PHE* 1.3 74.4 - - - +
279C HIS* 1.3 59.9 - - - +
280C ILE* 3.8 20.6 - - + -
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Residues in contact with HIS 279 (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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178C LEU* 3.8 23.8 - - + +
180C ASP* 3.1 41.4 + - + +
240C GLY 5.4 2.2 - - - -
243C PHE* 4.9 4.0 - + - -
250C TYR* 2.8 46.9 - + + +
251C ILE 3.5 5.8 + - - +
252C GLY 3.5 2.1 - - - +
253C PRO* 3.0 13.1 - - + +
254C VAL* 2.9 25.1 + - - +
277C PHE* 4.1 2.8 + - + -
278C LEU* 1.3 74.3 - - - +
280C ILE* 1.3 66.9 + - - +
281C MSE 3.5 16.3 - - - -
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Residues in contact with ILE 280 (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* 3.7 36.6 - - + -
177C ILE* 4.1 8.7 - - + -
178C LEU 3.0 17.8 + - - +
179C ASN* 3.8 19.7 - - - +
180C ASP* 3.1 25.8 + - - +
254C VAL* 3.5 20.6 - - + +
256C GLY* 3.9 14.1 - - - -
262C LEU* 4.2 7.9 - - + -
278C LEU* 3.8 20.4 - - + -
279C HIS* 1.3 78.0 + - - +
281C MSE 1.3 64.0 + - - +
282C THR* 3.8 13.0 - - + -
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Residues in contact with MSE 281 (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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180C ASP* 3.3 16.6 - - - +
182C GLU* 3.3 38.1 - - + +
253C PRO* 4.2 17.3 - - + -
254C VAL 3.0 18.6 + - - +
255C ASP* 4.3 4.0 - - - +
256C GLY* 2.8 24.8 + - - -
257C HIS* 4.2 2.4 + - - -
279C HIS* 3.5 30.7 - - - -
280C ILE* 1.3 75.4 - - - +
282C THR* 1.3 61.6 + - - +
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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