Contacts of the strand formed by residues 276 - 284 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ASN 3.1 8.1 + - - +
224A THR* 3.5 6.3 - - - -
225A CYS* 2.9 25.7 + - - +
259A ASP* 3.2 13.9 - - - -
262A TYR* 4.1 9.4 - - - -
263A ARG 4.5 0.9 - - - -
274A GLY 3.6 2.4 + - - -
275A TYR* 1.3 76.2 - - - +
277A ILE* 1.3 66.5 + - - +
411A PHE* 4.4 4.7 - - - -
470A PHE* 5.2 0.3 - - - -
473A ARG* 3.7 6.4 - - - +
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A THR* 4.1 0.2 - - - -
225A CYS* 3.2 13.9 - - + +
227A LEU* 4.4 11.9 - - + -
255A ILE* 3.5 33.4 - - + +
258A VAL* 3.6 19.5 - - + -
259A ASP* 2.9 34.2 + - - +
262A TYR* 4.9 7.4 - - + -
276A GLY* 1.3 80.2 - - - +
278A GLN* 1.3 65.9 + - - +
407A LEU* 3.6 32.8 - - + -
411A PHE* 4.0 26.0 - - + -
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Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A THR* 3.7 13.0 - - + +
225A CYS 3.1 6.5 + - - -
226A LYS* 2.8 42.9 + - + +
227A LEU* 2.6 33.6 + - - -
255A ILE* 4.7 2.9 - - - -
259A ASP* 5.1 0.4 - - - +
277A ILE* 1.3 79.0 - - - +
279A ILE* 1.3 58.5 + - - +
473A ARG* 3.6 28.7 - - - +
474A SER* 2.8 43.7 + - - +
475A ASN 4.7 4.0 + - - -
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LYS* 5.3 1.4 + - - +
227A LEU* 3.7 6.5 - - + +
229A VAL* 3.8 22.4 - - + -
251A LEU 3.9 21.8 - - - +
252A ILE* 3.9 26.7 - - + +
255A ILE* 3.9 19.0 - - + +
278A GLN* 1.3 75.4 - - - +
280A GLU* 1.3 61.8 + - - +
281A GLN 3.6 29.8 - - - +
282A ILE* 3.8 21.5 - - + -
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LYS* 3.8 23.9 - - + +
227A LEU 2.7 14.5 + - - +
278A GLN 3.4 2.8 + - - -
279A ILE* 1.3 74.9 - - - +
281A GLN* 1.3 77.4 + - + +
331A LYS 5.7 0.7 - - - +
332A VAL* 4.1 11.2 - - + +
471A GLN* 4.1 23.6 + - - +
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU 3.2 2.7 + - - +
228A LEU* 3.4 29.0 - - + +
229A VAL 3.0 24.3 + - - -
279A ILE* 3.6 6.9 - - - +
280A GLU* 1.3 98.3 - - + +
282A ILE* 1.3 62.6 + - - +
283A ARG* 4.5 5.9 - - - +
328A GLU* 3.1 33.9 + - - +
331A LYS* 5.0 7.2 - - - +
332A VAL* 3.6 14.5 - - - +
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A VAL* 3.5 25.8 - - + +
248A THR* 3.6 32.5 - - + +
251A LEU* 4.9 8.3 - - + -
252A ILE* 3.9 22.4 - - + -
279A ILE* 3.8 19.1 - - + -
281A GLN* 1.3 80.4 - - - +
283A ARG* 1.3 64.2 + - - +
284A ILE* 4.3 18.4 - - + -
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 4.1 13.4 - - + +
229A VAL 3.1 9.6 + - - +
230A VAL* 3.6 19.1 - - + +
231A ALA 3.1 24.6 + - - +
281A GLN* 4.5 7.1 - - - +
282A ILE* 1.3 77.8 + - - +
284A ILE* 1.3 65.0 + - - +
285A LEU* 3.8 26.9 - - + +
298A TYR* 5.0 4.7 - - - -
325A ILE* 5.1 6.7 - - - -
328A GLU* 2.8 37.0 + - - -
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ALA* 3.6 20.9 - - + +
236A TYR* 3.6 35.0 - - + -
244A GLU* 3.9 28.7 + - + +
247A THR* 3.9 17.7 - - + -
248A THR* 3.7 25.4 - - - +
251A LEU* 4.6 2.9 - - + -
282A ILE* 4.3 17.0 - - + -
283A ARG* 1.3 85.5 - - - +
285A LEU* 1.3 67.0 + - - +
286A LYS* 3.4 13.2 + - + +
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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