Contacts of the strand formed by residues 276 - 284 (chain B) in PDB entry 1ZXC
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 GLY 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ASN 3.1 7.2 + - - +
224B THR* 3.5 2.1 - - - -
225B CYS* 2.9 25.0 + - - +
259B ASP* 3.4 13.2 - - - -
262B TYR* 3.7 13.5 - - - -
263B ARG 4.4 0.4 - - - -
274B GLY 3.7 2.6 + - - -
275B TYR* 1.3 75.5 - - - +
277B ILE* 1.3 67.2 + - - +
411B PHE* 4.3 5.4 - - - -
470B PHE* 5.3 0.3 - - - -
473B ARG* 3.7 9.3 - - - +
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Residues in contact with ILE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B THR* 4.1 0.9 - - - -
225B CYS* 3.6 13.5 - - + +
227B LEU* 4.1 13.9 - - + -
255B ILE* 3.6 30.6 - - + +
258B VAL* 3.7 22.0 - - + -
259B ASP* 3.1 34.2 + - + +
262B TYR* 4.8 7.9 - - + -
276B GLY* 1.3 81.3 - - - +
278B GLN* 1.3 66.7 + - - +
407B LEU* 3.6 30.3 - - + -
411B PHE* 4.1 23.1 - - + -
473B ARG* 3.8 0.2 - - - +
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Residues in contact with GLN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B THR* 3.7 10.8 - - + +
225B CYS 3.4 4.1 + - - +
226B LYS* 3.2 24.1 - - + +
227B LEU* 2.8 27.8 + - - +
255B ILE* 4.9 2.5 - - - -
259B ASP* 4.6 0.7 - - - +
277B ILE* 1.3 80.5 - - - +
279B ILE* 1.3 66.6 + - - +
473B ARG* 3.4 33.5 + - - +
474B SER* 2.7 53.9 - - - +
475B ASN* 4.2 5.1 + - - -
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B LYS* 5.1 3.7 + - - -
227B LEU* 3.8 7.6 - - + +
229B VAL* 3.8 20.6 - - + -
251B LEU 4.0 9.0 - - - +
252B ILE* 4.1 12.1 - - + +
255B ILE* 3.7 34.9 - - + +
278B GLN* 1.3 75.0 - - - +
280B GLU* 1.3 62.6 + - - +
281B GLN* 3.6 16.2 - - - +
282B ILE* 3.4 43.5 - - + +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B LYS* 3.6 42.4 + - + +
227B LEU 2.7 18.0 + - - +
278B GLN 3.3 3.4 + - - -
279B ILE* 1.3 75.5 - - - +
281B GLN* 1.3 81.9 + - + +
331B LYS 5.7 0.9 - - - +
332B VAL* 4.2 16.4 - - + -
471B GLN* 4.5 8.0 + - - +
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Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU 3.1 5.2 + - - +
228B LEU* 3.5 20.0 - - + +
229B VAL 2.9 26.3 + - - +
279B ILE* 3.7 6.0 - - - +
280B GLU* 1.3 106.0 - - + +
282B ILE* 1.3 65.5 + - - +
283B ARG* 4.4 24.6 - - - +
332B VAL* 6.1 1.1 - - + -
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B VAL* 3.3 17.3 - - + +
248B THR* 3.7 23.8 - - + +
251B LEU* 4.8 5.4 - - + -
252B ILE* 3.6 33.2 - - + +
279B ILE* 3.4 30.3 - - + -
281B GLN* 1.3 78.7 + - - +
283B ARG* 1.3 73.4 + - - +
284B ILE* 3.6 28.4 + - + -
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 3.9 24.3 - - + +
229B VAL 2.8 12.3 + - - +
230B VAL* 3.4 17.3 - - + +
231B ALA 2.9 26.5 + - - +
281B GLN* 4.4 23.2 - - - +
282B ILE* 1.3 80.3 + - - +
284B ILE* 1.3 65.7 + - - +
285B LEU* 4.9 8.3 - - + -
325B ILE* 5.5 2.6 - - - +
328B GLU* 3.8 33.9 + - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ALA* 3.7 14.8 - - + +
236B TYR* 3.3 40.2 - - + -
244B GLU* 4.1 20.4 - - + +
247B THR* 3.7 26.9 - - + -
248B THR* 3.7 20.2 - - - +
251B LEU* 4.4 3.4 - - + -
282B ILE* 3.6 26.0 + - + -
283B ARG* 1.3 73.6 - - - +
285B LEU* 1.3 69.4 + - - +
286B LYS* 3.7 9.9 + - + +
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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