Contacts of the helix formed by residues 270 - 277 (chain B) in PDB entry 1WB9
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 ASP 270 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B GLU* 5.6 3.1 - - + +
168B ALA* 3.9 13.0 - - + -
268B ILE* 4.4 2.9 - - + +
269B MET* 1.3 76.3 - - - +
271B ALA* 1.3 64.0 + - - +
272B ALA* 3.4 9.9 + - - +
273B THR* 2.9 42.4 + - - -
274B ARG* 2.9 20.2 + - - +
653B ILE 4.8 1.3 + - - +
654B PHE* 3.8 16.6 - - - -
679B ASN* 3.2 27.5 + - - +
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Residues in contact with ALA 271 (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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167B ALA* 5.1 6.5 - - + +
168B ALA* 4.6 5.7 - - - +
171B GLN* 3.4 43.2 + - + +
270B ASP* 1.3 73.8 - - - +
272B ALA* 1.3 64.1 + - - +
274B ARG* 3.2 1.3 + - - +
275B ARG* 2.9 41.4 + - - +
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Residues in contact with ALA 272 (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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270B ASP* 3.3 8.8 + - - +
271B ALA* 1.3 78.2 - - - +
273B THR* 1.3 58.1 + - - +
275B ARG* 3.6 22.6 - - - +
276B ASN* 2.9 40.3 + - - +
655B THR 5.4 0.9 - - - +
676B GLU* 3.4 34.5 - - + +
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Residues in contact with THR 273 (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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269B MET* 4.1 15.0 - - + -
270B ASP* 2.9 25.8 + - - -
272B ALA* 1.3 73.6 - - - +
274B ARG* 1.3 66.4 + - - +
276B ASN* 3.2 1.2 + - - +
277B LEU* 3.0 33.9 + - + +
653B ILE* 3.3 22.5 + - + +
654B PHE* 3.5 6.9 - - - -
655B THR* 3.0 45.2 + - - +
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ALA* 4.3 4.6 + - - +
171B GLN* 3.9 24.3 - - + +
172B ARG* 3.7 33.6 - - - +
267B ILE 5.1 1.8 + - - -
269B MET* 3.1 51.4 + - + +
270B ASP 2.9 9.2 + - - +
271B ALA* 3.5 9.4 - - - +
273B THR* 1.3 78.2 - - - +
275B ARG* 1.3 62.2 - - - +
277B LEU* 3.4 1.4 + - - -
278B GLU* 3.4 13.7 + - - -
279B ILE* 4.0 19.9 + - + +
281B GLN 5.5 0.2 - - - +
312B HIS* 2.9 71.9 + - + +
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Residues in contact with ARG 275 (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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171B GLN* 3.4 18.0 + - - +
271B ALA* 2.9 40.1 + - - +
272B ALA* 3.6 27.5 - - - +
274B ARG* 1.3 76.9 - - - +
276B ASN* 1.3 64.8 + - - +
278B GLU* 3.1 16.9 + - - +
281B GLN* 4.5 8.1 - - + +
282B ASN 5.3 0.2 - - - -
283B LEU* 3.5 24.5 + - + +
676B GLU* 4.8 4.4 + - - -
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Residues in contact with ASN 276 (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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272B ALA* 2.9 26.4 + - - +
273B THR 3.9 3.6 - - - +
275B ARG* 1.3 79.3 + - - +
277B LEU* 1.3 61.2 + - - +
278B GLU* 3.7 7.7 + - - +
283B LEU* 4.1 18.4 - - - +
625B ARG* 3.7 24.4 + - - +
655B THR* 2.9 34.5 + - + +
656B ARG* 4.3 7.9 + - - +
657B VAL 2.9 31.2 + - - +
658B GLY* 5.0 2.3 - - - -
676B GLU* 4.5 5.5 + - - -
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Residues in contact with LEU 277 (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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269B MET* 4.3 16.4 - - - -
273B THR* 3.0 33.4 + - + +
276B ASN* 1.3 76.7 - - - +
278B GLU* 1.3 73.2 + - - +
279B ILE* 3.3 15.8 + - + -
291B LEU* 4.9 0.7 + - - +
587B VAL* 6.0 0.9 - - - +
625B ARG* 4.3 19.3 - - + +
628B ALA* 3.8 34.3 - - + +
629B LEU* 4.1 27.8 - - + +
632B LEU* 4.6 11.0 - - + -
653B ILE* 4.6 2.9 - - + -
655B THR* 3.9 19.7 - - + +
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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