Contacts of the strand formed by residues 270 - 275 (chain C) in PDB entry 2F8X
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 HIS 270 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C PRO* 5.3 1.3 - - + -
154C SER 2.7 32.9 + - - -
155C LYS* 3.9 11.8 - - + +
156C LYS 4.8 6.7 - - - -
158C GLN* 5.1 3.1 - - + -
230C TYR* 2.8 30.1 + + - +
252C LYS* 4.9 11.8 - - - -
265C PRO 4.7 5.2 - - - -
266C VAL* 4.6 0.4 - - + -
267C SER* 3.2 42.6 + - - +
268C GLN 4.1 7.0 - - - -
269C LEU* 1.3 81.7 - - - +
271C LYS* 1.3 65.3 + - - +
272C CYS* 3.3 9.5 + - - -
315C THR* 4.6 0.9 - - - -
316C ILE* 3.4 24.0 + - + +
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Residues in contact with LYS 271 (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 LYS* 6.5 1.1 - - - -
230C TYR* 4.3 4.9 + - - -
252C LYS* 4.9 1.0 - - - +
253C VAL* 3.5 35.9 + - + +
254C ASP* 5.8 4.0 - - - +
255C LYS 5.8 3.8 - - - +
269C LEU 4.1 2.2 + - - +
270C HIS* 1.3 72.6 - - - +
272C CYS* 1.3 62.5 + - - +
313C SER* 4.2 21.5 - - - +
314C TRP 3.2 10.3 - - - +
315C THR* 4.0 17.3 - - - +
8X G 5.0 3.6 - - - -
9X G 3.1 31.0 + - - -
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Residues in contact with CYS 272 (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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175C LEU* 5.5 0.4 - - - -
230C TYR* 3.6 22.9 - - + -
250C ILE* 4.8 4.5 - - + -
251C ARG 3.3 15.3 - - - +
253C VAL* 3.6 7.5 - - - +
266C VAL* 4.9 3.4 - - - -
270C HIS 3.7 11.4 - - - +
271C LYS* 1.3 75.1 - - - +
273C ALA* 1.3 61.7 + - - +
274C PHE* 3.4 29.4 - - - -
312C ALA 3.8 0.7 - - - +
313C SER* 4.7 0.4 - - - -
314C TRP* 3.0 31.3 + - - +
316C ILE* 4.2 17.5 - - - -
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Residues in contact with ALA 273 (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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249C ILE 3.7 0.5 - - - +
250C ILE* 3.4 0.3 - - - -
251C ARG* 2.8 36.6 + - + +
253C VAL* 3.1 16.0 - - + +
258C ALA* 4.2 5.6 - - + -
272C CYS* 1.3 71.0 - - - +
274C PHE* 1.3 68.5 + - - +
275C TYR 4.0 0.4 - - - -
283C TYR* 4.1 29.8 - - + -
308C ILE* 5.3 4.0 - - + -
312C ALA* 3.6 17.0 - - + +
313C SER* 5.3 0.4 - - - -
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Residues in contact with PHE 274 (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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175C LEU* 4.4 20.9 - - + -
208C ILE* 5.4 3.4 - - + -
234C VAL* 4.8 1.8 - - + -
236C LEU* 3.2 34.5 - - + -
248C LEU* 3.4 30.5 - - + -
249C ILE 3.9 2.7 - - - -
250C ILE* 3.2 27.8 - - + -
272C CYS* 3.4 35.0 - - - -
273C ALA* 1.3 80.2 - - - +
275C TYR* 1.3 63.1 + - - +
276C LEU* 3.6 4.0 - - - +
283C TYR* 3.6 4.7 - - - -
284C LEU* 3.2 38.1 + - + -
312C ALA 4.6 2.8 + - - -
314C TRP* 4.4 13.0 - + + -
316C ILE* 4.6 7.0 - - + -
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Residues in contact with TYR 275 (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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248C LEU* 2.8 10.0 - - - +
249C ILE* 2.7 54.7 + - + +
251C ARG* 3.4 31.8 - - - +
273C ALA 4.0 0.8 + - - -
274C PHE* 1.3 73.0 - - - +
276C LEU* 1.3 90.1 + - + +
278C ASP* 3.1 38.6 + - - +
280C GLU 2.7 23.6 + - - -
281C ARG* 3.5 22.0 - - - -
282C MET 3.1 13.7 - - - -
283C TYR* 3.4 27.0 - + + -
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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
------------------------------------------------------------
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