Contacts of the helix formed by residues 238 - 245 (chain B) in PDB entry 1WVV
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 THR 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B TRP 3.7 11.7 - - - -
229B ASN 3.8 11.5 + - - +
230B SER 3.6 30.7 - - - +
231B GLN 3.5 3.1 - - - +
232B ASN* 3.7 10.1 - - - +
237B MET* 1.3 75.9 - - - +
239B PRO* 1.4 72.0 - - - +
240B HIS* 3.7 4.9 + - - +
241B ASN* 3.0 36.3 + - - +
242B ALA* 2.9 21.1 + - - +
255B SER* 4.8 0.2 - - - -
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Residues in contact with PRO 239 (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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227B TYR* 4.1 5.8 - - + +
228B TRP* 3.2 60.1 - - + +
231B GLN 3.3 16.4 - - - +
238B THR* 1.4 81.4 - - - +
240B HIS* 1.3 62.8 + - - +
242B ALA* 3.3 12.9 + - + +
243B ILE* 3.3 18.5 + - - +
252B THR* 3.8 13.8 - - + +
255B SER* 4.0 19.1 - - - -
256B ILE* 4.4 12.8 - - + -
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Residues in contact with HIS 240 (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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123B ALA* 3.4 43.3 - - + +
124B PHE* 4.2 0.2 - - - -
127B THR* 4.0 4.8 + - - +
136B GLU* 2.5 41.6 + - - +
228B TRP* 3.0 16.8 + - + +
229B ASN* 3.3 27.2 + - + +
238B THR* 3.1 4.9 - - - +
239B PRO* 1.3 76.0 - - - +
241B ASN* 1.3 87.0 + - - +
243B ILE* 3.3 2.4 + - - +
244B VAL* 3.0 45.1 + - + +
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Residues in contact with ASN 241 (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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237B MET* 4.5 9.0 - - + -
238B THR* 3.0 31.7 + - - +
240B HIS* 1.3 93.7 + - - +
242B ALA* 1.3 60.5 + - - +
244B VAL* 4.4 7.2 - - - +
245B ASN* 2.7 57.0 + - - +
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Residues in contact with ALA 242 (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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237B MET* 3.6 15.8 - - + -
238B THR 2.9 12.7 + - - +
239B PRO* 3.3 10.9 + - + +
241B ASN* 1.3 76.9 - - - +
243B ILE* 1.3 61.2 + - - +
246B ASN 3.3 0.3 + - - -
247B ALA* 2.8 30.0 + - - -
248B GLY 3.3 13.8 + - - +
251B GLU* 3.7 30.1 - - + -
252B THR* 4.0 11.0 - - + +
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Residues in contact with ILE 243 (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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132B VAL* 4.0 17.0 - - + +
135B ARG* 4.1 25.8 + - + -
136B GLU* 3.7 35.0 - - + +
139B ALA* 4.0 22.4 - - + -
228B TRP* 4.3 5.6 - - + -
239B PRO 3.3 13.4 + - - +
240B HIS 3.9 4.0 - - - +
241B ASN 3.2 0.2 - - - -
242B ALA* 1.3 75.5 - - - +
244B VAL* 1.3 68.3 + - - +
245B ASN 3.2 0.2 - - - -
246B ASN* 3.1 16.7 + - - +
248B GLY* 4.4 1.6 - - - +
249B PHE* 4.1 21.1 - - + +
252B THR* 3.9 21.3 - - + -
277B PHE* 5.2 0.2 - - + -
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Residues in contact with VAL 244 (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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127B THR* 3.4 42.4 - - + +
128B GLY* 5.6 2.0 - - - -
132B VAL* 4.2 13.5 - - + +
136B GLU* 4.0 10.5 - - - +
240B HIS* 3.0 47.5 + - + +
241B ASN* 4.4 6.7 - - - +
243B ILE* 1.3 76.0 - - + +
245B ASN* 1.3 67.8 + - - +
246B ASN* 3.3 1.6 + - - +
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Residues in contact with ASN 245 (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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237B MET* 6.1 1.9 - - - -
241B ASN* 2.7 45.6 + - - +
244B VAL* 1.3 80.7 - - - +
246B ASN* 1.3 69.1 - - - +
247B ALA* 3.3 7.8 + - + +
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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