Contacts of the helix formed by residues 279 - 285 (chain B) in PDB entry 1SIW
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 ALA 279 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ASP* 3.0 26.3 + - + +
278B ASP* 1.3 78.0 - - - +
280B ILE* 1.3 63.9 + - - +
281B GLU 3.4 2.0 - - - -
282B ARG* 3.4 30.3 + - + +
283B ALA* 3.0 24.4 + - - +
298B ASP 6.0 0.2 - - - +
299B VAL* 3.9 18.6 - - + -
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Residues in contact with ILE 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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17A PHE* 4.9 7.6 - - + -
18A ALA* 4.7 4.3 - - + -
21A HIS* 4.9 4.9 - - + -
188B LEU* 3.6 51.6 - - + +
189B ASN* 3.6 16.4 - - + +
275B TYR* 4.0 7.6 - - + -
276B ASP 3.8 12.3 - - - +
277B ALA* 3.0 27.9 + - + +
278B ASP 3.5 0.6 - - - -
279B ALA* 1.3 77.1 - - - +
281B GLU* 1.3 63.7 + - - +
283B ALA* 4.9 0.2 - - - -
284B ALA* 3.0 23.2 + - - +
299B VAL* 4.1 5.4 - - + -
350B LEU* 3.5 21.3 - - + +
219C GLN* 5.7 1.6 - - + -
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Residues in contact with GLU 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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18A ALA* 4.0 15.3 - - + +
19A ASP* 5.5 4.5 - - - +
21A HIS* 3.7 48.0 - - + +
72B GLY 4.7 3.8 - - - +
73B LYS* 5.2 11.9 + - - -
74B LEU* 4.4 11.5 + - + +
278B ASP 5.7 0.4 - - - +
279B ALA 3.4 0.4 - - - -
280B ILE* 1.3 76.3 - - - +
282B ARG* 1.3 71.3 + - - +
284B ALA* 3.4 3.8 + - - +
285B SER* 2.8 52.7 + - - -
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Residues in contact with ARG 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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19A ASP* 4.7 10.9 + - - -
276B ASP* 5.4 1.6 + - - -
278B ASP* 3.5 23.8 + - - +
279B ALA* 3.4 28.5 + - + +
280B ILE 3.4 0.2 - - - -
281B GLU* 1.3 89.6 + - - +
283B ALA* 1.3 62.9 + - - +
285B SER* 3.2 13.2 + - - -
286B THR* 3.6 6.1 + - - -
295B ARG* 3.2 32.0 + - - +
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Residues in contact with ALA 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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279B ALA 3.0 17.0 + - - +
280B ILE 4.0 2.7 - - - +
282B ARG* 1.3 78.1 - - - +
284B ALA* 1.3 63.2 + - - +
285B SER 3.2 1.0 + - - -
286B THR* 3.3 11.6 + - - +
292B LEU* 3.3 15.9 - - - +
295B ARG* 3.7 43.7 - - + +
299B VAL* 3.8 12.6 - - + -
350B LEU* 4.5 10.1 - - + -
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Residues in contact with ALA 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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74B LEU* 3.7 11.4 - - + +
189B ASN* 3.6 16.6 - - - +
280B ILE 3.0 18.6 + - - +
283B ALA* 1.3 76.2 - - - +
285B SER* 1.3 52.4 + - - +
286B THR 3.4 0.2 - - - -
292B LEU* 3.6 8.2 - - - +
348B ARG* 2.7 58.6 + - - +
350B LEU* 4.2 12.0 - - + +
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Residues in contact with SER 285 (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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68B ARG* 2.8 27.5 + - - +
72B GLY 3.8 12.9 + - - +
74B LEU* 3.6 21.3 - - - -
281B GLU* 2.8 39.3 + - - -
282B ARG* 3.2 8.8 + - - -
283B ALA 3.1 0.4 - - - -
284B ALA* 1.3 77.6 - - - +
286B THR* 1.3 60.0 + - - +
348B ARG* 3.7 1.1 - - - +
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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