Contacts of the helix formed by residues 241 - 249 (chain B) in PDB entry 5U2H
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 SER 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B PHE* 4.5 0.2 - - - -
239B GLY 4.2 1.8 + - - -
240B ASP* 1.3 72.3 - - - +
242B PHE* 1.3 65.5 + - - +
243B SER* 3.6 12.5 + - - -
244B ASP* 3.8 26.1 + - - +
245B VAL* 3.4 22.0 + - - +
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Residues in contact with PHE 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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106B THR* 4.5 0.2 - - + -
182B LEU 3.3 6.3 - - - -
183B ASN* 2.9 30.7 - - - -
185B ALA* 3.1 25.1 - - + -
186B GLU* 3.1 57.0 - - + +
231B LEU* 5.0 0.4 - - + -
232B GLY* 5.5 0.2 - - - -
235B PHE* 3.3 42.5 - + + +
240B ASP 3.4 3.4 + - - -
241B SER* 1.3 71.0 + - - +
243B SER* 1.3 77.6 + - - +
245B VAL* 3.2 4.0 + - - +
246B ALA* 2.9 34.1 + - + +
315B ILE* 3.9 16.6 - - + -
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Residues in contact with SER 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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180B ALA* 4.9 4.9 - - - -
183B ASN* 5.3 7.8 + - - +
186B GLU* 5.3 2.4 + - - -
241B SER* 3.4 6.7 + - - -
242B PHE* 1.3 90.2 - - - +
244B ASP* 1.3 66.8 + - - +
246B ALA* 3.1 3.8 + - - +
247B ILE* 2.9 39.6 + - - +
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Residues in contact with ASP 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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241B SER* 3.6 26.4 + - - +
242B PHE 3.3 0.6 - - - -
243B SER* 1.3 81.5 - - - +
245B VAL* 1.3 64.1 + - + +
247B ILE* 3.5 20.5 + - - +
248B GLN* 3.7 11.6 + - - +
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Residues in contact with VAL 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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235B PHE* 4.2 15.3 - - + -
240B ASP* 4.4 14.1 - - + -
241B SER 3.5 13.5 - - - +
242B PHE 3.2 7.0 + - - +
244B ASP* 1.3 78.7 - - + +
246B ALA* 1.3 53.2 + - - +
249B GLY* 2.5 43.0 + - - +
250B GLY* 3.4 31.1 + - - +
251B ILE 4.8 0.2 - - - +
315B ILE* 3.8 18.6 - - + -
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Residues in contact with ALA 246 (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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106B THR* 2.7 47.2 + - + -
107B ASN* 3.6 9.9 - - - +
180B ALA* 3.6 19.1 - - + -
242B PHE* 2.9 32.5 + - + +
243B SER 3.1 1.3 + - - +
245B VAL* 1.3 75.8 - - - +
247B ILE* 1.3 66.1 + - - +
248B GLN 3.5 0.3 + - - -
249B GLY 3.7 3.1 + - - -
313B PHE* 4.6 0.3 - - - +
315B ILE* 4.4 2.2 - - + +
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Residues in contact with ILE 247 (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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107B ASN* 3.7 15.6 + - - +
176B ALA* 2.9 28.8 - - + +
177B PRO 3.0 25.1 - - - +
178B ARG* 2.9 26.0 - - - +
179B PRO* 4.9 0.9 - - + -
180B ALA* 3.8 11.9 - - + +
243B SER* 2.9 37.8 + - - +
244B ASP* 3.8 16.4 - - - +
245B VAL 3.3 0.4 - - - -
246B ALA* 1.3 78.6 - - - +
248B GLN* 1.3 60.0 + - + +
313B PHE* 4.4 1.6 - - - +
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Residues in contact with GLN 248 (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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176B ALA* 4.3 9.6 - - + -
244B ASP 3.7 7.6 + - - +
245B VAL 3.7 1.2 + - - -
247B ILE* 1.3 80.6 - - + +
249B GLY* 1.3 62.1 + - - +
289B PRO* 4.4 13.4 - - + +
290B GLY* 3.4 18.1 - - - -
291B TYR 3.9 2.1 + - - -
292B ASN* 5.3 0.5 - - - +
313B PHE* 4.1 16.7 - - - -
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Residues in contact with GLY 249 (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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245B VAL* 2.5 27.5 + - - +
246B ALA 3.7 4.2 + - - -
247B ILE 3.6 1.8 - - - -
248B GLN* 1.3 76.1 - - - +
250B GLY* 1.3 58.3 + - - -
290B GLY* 3.0 16.3 + - - -
291B TYR 3.5 13.0 - - - -
314B GLY 3.3 20.6 - - - -
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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