Contacts of the strand formed by residues 280 - 286 (chain C) in PDB entry 2ZXX
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 TYR 280 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264C GLN* 3.4 42.7 + - + +
265C GLU* 3.5 7.6 - - - -
266C CYS* 4.2 15.4 - - + +
275C ILE* 3.6 35.1 - - + +
276C LYS 3.6 15.5 - - - -
277C ARG* 3.1 16.3 + - - +
278C SER 3.9 6.9 - - - +
279C ASP* 1.3 81.5 - - - +
281C GLN* 1.3 63.8 + - - +
363C PRO* 3.8 11.3 - - + +
364C PRO* 3.9 31.5 + - + +
365C VAL* 6.1 2.9 - - + -
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Residues in contact with GLN 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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228C THR* 3.8 27.3 + - + +
229C PHE* 5.5 2.4 - - + -
230C ALA* 3.2 38.6 + - - +
264C GLN* 3.1 10.0 - - - +
265C GLU 3.0 33.1 + - - +
267C ASN* 4.8 6.7 + - - +
279C ASP 4.6 5.3 + - - +
280C TYR* 1.3 77.3 - - - +
282C LEU* 1.3 67.1 + - - +
283C THR* 3.3 3.8 + - - +
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Residues in contact with LEU 282 (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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228C THR* 3.8 0.9 - - - -
229C PHE* 2.7 59.2 + - + +
246C GLU* 4.4 24.9 + - + +
249C VAL* 4.8 5.4 - - + -
262C PHE* 3.9 30.7 - - + -
263C ARG 3.4 7.6 - - - +
264C GLN* 3.4 11.5 - - - +
281C GLN* 1.3 73.3 - - - +
283C THR* 1.3 55.9 + - - +
284C ILE* 4.5 3.3 - - + +
360C LEU* 4.1 15.5 - - + -
361C PRO* 3.8 42.6 - - + +
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Residues in contact with THR 283 (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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226C THR* 5.3 1.6 - - + -
227C VAL 3.4 11.0 - - - +
228C THR* 4.1 21.5 - - + -
261C ARG 3.8 0.3 - - - +
262C PHE* 3.5 7.1 - - - -
263C ARG* 2.8 44.4 + - - +
265C GLU* 3.4 35.9 + - + +
267C ASN* 4.4 6.3 - - - +
281C GLN 3.6 13.9 - - - +
282C LEU* 1.3 74.3 - - - +
284C ILE* 1.3 67.5 + - - +
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Residues in contact with ILE 284 (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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213C MSE 3.6 23.8 - - + -
217C VAL* 5.5 0.9 - - + -
227C VAL* 2.9 42.3 + - + +
229C PHE* 4.3 21.3 - - + +
232C VAL* 3.8 27.6 - - + -
249C VAL* 5.2 0.7 - - + -
260C TYR* 3.6 26.7 - - + -
261C ARG 3.5 0.9 - - - -
262C PHE* 3.3 32.3 - - + -
263C ARG* 5.6 0.2 - - - -
282C LEU* 4.5 6.5 - - + +
283C THR* 1.3 82.9 - - - +
285C GLU* 1.3 64.2 + - - +
286C PRO* 4.1 1.1 - - - +
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Residues in contact with GLU 285 (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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221C HIS* 4.7 10.6 + - + +
227C VAL* 5.0 1.6 - - + -
260C TYR* 3.0 8.1 - - - -
261C ARG* 2.5 50.8 + - + +
263C ARG* 2.5 48.6 + - - +
284C ILE* 1.3 77.1 - - - +
286C PRO* 1.3 73.9 - - + +
287C LEU* 3.4 9.9 - - - +
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Residues in contact with PRO 286 (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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217C VAL* 4.1 24.0 - - + -
221C HIS* 3.4 38.9 + - + +
227C VAL* 5.1 1.1 - - + -
260C TYR* 3.9 11.2 - - + -
284C ILE 4.1 2.7 - - - +
285C GLU* 1.3 94.1 - - + +
287C LEU* 1.3 63.1 + - - +
288C LEU* 3.4 17.0 + - + +
298C LEU* 4.0 22.4 - - + -
306C ARG* 3.9 8.3 - - - +
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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