Contacts of the strand formed by residues 279 - 288 (chain A) in PDB entry 4IO8
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 GLN 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A THR* 4.1 2.9 - - - +
274A LEU* 3.7 4.3 - - - -
277A SER* 3.3 19.6 + - - -
278A THR* 1.3 84.1 + - - +
280A ALA* 1.3 64.5 + - - +
281A SER* 6.1 0.2 - - - -
296A SER* 3.9 24.4 + - - +
297A ILE 3.5 11.1 + - - +
298A THR* 3.9 20.7 - - + +
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA* 3.8 30.5 - - + +
273A THR* 4.1 14.6 - - - -
274A LEU* 3.5 19.9 - - + +
279A GLN* 1.3 74.3 - - - +
281A SER* 1.3 60.5 + - - +
282A LEU* 5.2 0.4 - - - -
296A SER* 2.9 15.0 + - - -
297A ILE* 3.0 27.1 + - + +
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Residues in contact with SER 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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270A ALA* 5.4 2.3 - - - +
280A ALA* 1.3 76.3 - - - +
282A LEU* 1.4 63.3 + - - +
283A GLU* 4.1 22.4 + - - +
295A THR 3.5 6.5 - - - -
296A SER* 3.5 14.1 - - - -
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PHE* 3.6 46.4 - - + -
263A LEU* 4.5 9.2 - - + -
266A ALA* 3.7 38.8 - - + +
267A CYS* 4.2 5.4 - - - -
270A ALA* 3.8 22.9 - - + -
280A ALA 5.1 0.4 - - - +
281A SER* 1.4 73.7 - - - +
283A GLU* 1.3 63.5 + - - +
284A ILE* 4.6 5.2 - - + -
293A PHE* 3.2 7.1 - - + +
295A THR* 2.8 49.3 + - + +
296A SER* 5.4 0.2 - - - -
297A ILE* 4.6 8.3 - - + +
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Residues in contact with GLU 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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266A ALA* 5.8 0.6 - - - +
281A SER* 4.1 21.0 + - - +
282A LEU* 1.3 78.8 - - - +
284A ILE* 1.3 62.9 - - - +
285A ASP* 4.2 2.1 + - - +
293A PHE 3.5 2.7 - - - -
294A TYR* 3.6 45.1 + - + +
295A THR 5.0 1.5 - - - +
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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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262A ARG* 3.4 40.2 - - + +
263A LEU* 3.9 22.7 - - + -
266A ALA* 3.9 30.1 - - + -
282A LEU* 4.6 5.8 - - + -
283A GLU* 1.3 77.4 - - - +
285A ASP* 1.3 63.5 + - - +
287A LEU* 3.9 38.0 + - + -
292A ASP* 3.4 2.3 - - - +
293A PHE* 2.8 45.4 + - + +
294A TYR* 4.2 1.3 - - - -
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Residues in contact with ASP 285 (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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262A ARG* 2.7 33.3 + - - +
283A GLU 4.2 2.1 + - - -
284A ILE* 1.3 71.1 - - - +
286A SER* 1.4 67.9 + - - +
287A LEU 3.3 0.3 + - - -
292A ASP* 3.3 11.6 - - - +
294A TYR* 2.9 31.7 + - - -
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Residues in contact with SER 286 (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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262A ARG* 3.1 15.3 + - - -
285A ASP* 1.4 71.1 - - - +
287A LEU* 1.3 64.8 + - - +
288A PHE* 3.5 3.3 - - - -
290A GLY* 3.7 24.4 + - - -
291A ILE 3.4 13.0 + - - -
292A ASP* 3.0 13.6 + - - -
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Residues in contact with LEU 287 (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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245A PHE* 3.7 27.8 - - + -
253A ILE* 4.1 18.8 - - + -
259A ALA* 3.4 42.6 - - + +
262A ARG* 4.2 12.2 + - + +
263A LEU* 4.3 11.0 - - + +
284A ILE* 3.9 33.6 + - + +
285A ASP 3.3 2.5 + - - -
286A SER* 1.3 76.6 - - - +
288A PHE* 1.3 59.4 + - + +
291A ILE 2.8 14.7 + - - +
293A PHE* 3.8 28.0 - - + -
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Residues in contact with PHE 288 (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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245A PHE* 3.6 8.0 - + + -
251A LYS* 4.0 21.1 - - + -
252A ASP 3.7 21.8 - - - -
253A ILE* 3.6 32.5 - - + -
255A GLN 5.8 0.2 - - - -
256A ASN* 3.8 37.2 - - + -
259A ALA* 4.2 6.5 - - + -
286A SER 3.5 0.6 - - - -
287A LEU* 1.3 80.3 - - - +
289A GLU* 1.4 92.5 + - + +
290A GLY 3.1 4.3 - - - -
291A ILE* 2.9 28.3 + - - +
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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