Contacts of the helix formed by residues 301 - 306 (chain B) in PDB entry 2WZJ
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 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ASP 4.9 1.6 - - - +
279B ASN* 4.8 2.4 - - - +
280B LEU* 3.1 35.6 + - + +
283B LYS* 2.8 38.6 + - + +
297B GLN 4.2 0.8 + - - -
298B ILE 2.9 18.4 + - - +
299B MET 3.2 0.8 - - - -
300B LYS* 1.3 78.5 - - - +
302B ARG* 1.3 67.0 + - - +
303B TRP* 2.7 24.4 + - - +
304B MET* 3.0 19.4 + - + +
305B ASN* 2.9 21.5 + - - -
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Residues in contact with ARG 302 (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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276B ASP* 3.8 30.3 + - - +
283B LYS* 4.6 1.0 - - - +
300B LYS 3.8 1.2 + - - -
301B ASP* 1.3 77.6 + - - +
303B TRP* 1.3 66.8 + - - +
305B ASN* 3.0 6.1 + - - +
306B VAL* 3.0 27.4 + - + +
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Residues in contact with TRP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLU* 2.9 58.4 + - + +
152B ALA* 4.0 8.5 - - + -
153B ARG* 2.6 83.1 + - + +
156B PHE* 3.9 23.8 - + + -
240B LEU* 3.7 19.5 - - + -
244B VAL* 4.8 2.0 - - + -
274B SER* 3.9 2.2 - - - -
276B ASP* 3.8 24.6 + - + +
277B CYS* 3.4 22.8 - - + +
280B LEU* 3.5 21.1 - - + -
301B ASP* 2.7 15.0 + - - +
302B ARG* 1.3 76.5 - - - +
304B MET* 1.3 61.2 + - - +
305B ASN 3.1 1.0 + - - -
306B VAL* 3.3 8.1 + - - -
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Residues in contact with MET 304 (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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153B ARG* 3.8 5.1 - - - -
156B PHE* 3.7 27.8 - - - -
157B ARG* 3.1 62.9 + - + +
160B VAL* 4.1 14.6 - - + -
280B LEU* 4.0 11.0 - - + -
298B ILE* 3.6 26.5 - - + +
299B MET 4.0 4.5 - - - +
301B ASP* 3.0 23.7 + - + +
302B ARG 3.1 0.4 - - - -
303B TRP* 1.3 83.2 - - - +
305B ASN* 1.3 65.7 + - - +
313B LEU* 3.4 28.0 - - + -
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Residues in contact with ASN 305 (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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157B ARG* 3.1 14.1 + - - +
299B MET 2.8 25.0 + - - -
300B LYS 3.8 5.3 + - - -
301B ASP 2.9 18.9 + - - +
302B ARG* 3.0 6.0 + - - +
304B MET* 1.3 79.7 - - - +
306B VAL* 1.3 65.9 + - - +
307B GLY 3.2 0.5 + - - -
308B HIS* 2.9 22.7 + - - +
309B GLU* 3.5 16.3 + - + +
312B GLU* 3.5 24.4 + - + +
313B LEU* 3.0 28.1 + - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG* 3.3 49.1 + - - +
276B ASP* 4.1 16.6 - - + +
302B ARG* 3.0 29.3 + - + +
303B TRP* 3.3 7.8 + - - +
305B ASN* 1.3 76.8 - - - +
307B GLY* 1.3 62.9 + - - +
308B HIS* 3.5 3.5 + - - -
309B GLU* 3.5 9.0 - - - +
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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