Contacts of the strand formed by residues 260 - 266 (chain F) 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 260 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210F PHE* 3.6 20.5 - + - -
213F MSE 3.8 23.9 - - + +
214F ASP* 2.6 46.1 + - - +
217F VAL* 3.7 19.1 - - + -
249F VAL* 5.7 0.2 - - + -
252F ILE* 4.2 7.6 - - + -
253F LYS* 6.2 0.7 - - - -
257F PRO 3.7 13.6 + - - +
259F SER* 1.3 94.7 + - - +
261F ARG* 1.3 63.7 + - - +
262F PHE* 3.5 39.9 - + + -
284F ILE* 3.4 17.9 - - + -
285F GLU 3.3 3.1 - - - +
286F PRO* 3.8 11.0 - - + -
287F LEU* 3.5 8.3 - - - +
306F ARG* 3.3 14.4 - - - -
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Residues in contact with ARG 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F LYS* 4.8 11.7 - - - +
260F TYR* 1.3 77.1 + - - +
262F PHE* 1.3 112.9 + - - +
263F ARG* 3.9 29.5 + - - +
283F THR 3.6 2.4 - - - +
284F ILE* 3.7 2.1 - - - -
285F GLU* 2.8 45.4 + - - +
287F LEU* 3.1 20.1 - - + +
361F PRO* 4.9 6.9 - - - +
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Residues in contact with PHE 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F VAL* 3.8 24.5 - - + -
253F LYS* 4.0 28.3 - - + -
260F TYR* 3.5 40.2 - + + -
261F ARG* 1.3 108.9 + - - +
263F ARG* 1.3 72.7 + - - +
282F LEU* 3.7 13.9 - - + -
283F THR 3.4 2.2 - - - -
284F ILE* 3.7 32.5 - - + -
360F LEU* 3.7 23.6 - - + -
361F PRO* 3.6 23.0 - - + +
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Residues in contact with ARG 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F ARG* 3.9 20.3 + - + +
262F PHE* 1.3 85.0 - - - +
264F GLN* 1.3 64.3 + - - +
265F GLU* 3.0 27.6 + - + +
281F GLN 3.4 0.3 - - - +
282F LEU* 3.2 8.7 - - - +
283F THR* 2.7 48.0 + - - +
285F GLU* 2.4 34.9 + - - +
361F PRO* 4.4 6.1 - - - -
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Residues in contact with GLN 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F ARG* 1.3 73.5 - - - +
265F GLU* 1.3 62.3 + - - +
280F TYR* 3.2 27.7 - - + +
281F GLN* 3.0 29.8 - - - +
282F LEU* 3.0 22.5 + - - +
361F PRO* 3.3 32.2 - - + +
362F GLN* 3.5 6.7 + - - +
363F PRO* 3.2 42.1 - - + +
364F PRO* 4.8 3.7 - - + +
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Residues in contact with GLU 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F THR* 4.4 13.8 - - + +
263F ARG* 3.0 39.8 + - + -
264F GLN* 1.3 77.5 - - - +
266F CYS* 1.3 63.5 + - - +
280F TYR* 3.5 4.0 - - - -
281F GLN* 3.0 34.6 + - - +
283F THR* 3.4 29.9 + - + +
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Residues in contact with CYS 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F GLU* 1.3 78.5 - - - +
267F ASN* 1.3 65.9 + - - +
268F VAL* 3.6 29.4 - - - -
275F ILE* 3.7 21.8 - - + -
279F ASP* 4.0 17.5 - - - +
280F TYR* 3.7 27.4 - - + -
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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