Contacts of the helix formed by residues 241 - 249 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A PHE* 4.9 0.2 - - - -
239A GLY 4.2 1.4 + - - -
240A ASP* 1.3 70.7 - - - +
242A PHE* 1.3 60.5 + - - +
243A SER* 3.7 6.9 + - - -
244A ASP* 3.3 30.2 + - - +
245A VAL* 3.1 28.7 + - - +
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Residues in contact with PHE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A THR* 4.9 2.7 - - + -
180A ALA* 6.2 0.2 - - + -
182A LEU 4.2 4.9 - - - -
183A ASN* 3.9 14.4 - - - -
185A ALA* 3.2 20.6 - - + -
186A GLU* 3.1 60.8 - - + +
231A LEU* 4.6 10.5 - - + -
232A GLY* 5.1 2.5 - - - -
235A PHE* 3.2 42.8 - + + +
240A ASP 3.2 4.0 + - - -
241A SER* 1.3 71.2 + - - +
243A SER* 1.3 67.8 + - - +
245A VAL* 4.0 0.3 - - - +
246A ALA* 2.9 42.1 + - + +
315A ILE* 4.0 17.0 - - + -
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Residues in contact with SER 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ALA* 4.4 5.7 + - - +
186A GLU* 5.0 6.1 + - - -
241A SER* 3.4 5.5 + - - -
242A PHE* 1.3 87.4 - - - +
244A ASP* 1.3 62.1 + - - +
246A ALA* 3.8 6.9 + - - +
247A ILE* 3.4 20.8 + - - +
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Residues in contact with ASP 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A SER* 3.3 25.3 + - - +
242A PHE 3.2 0.8 - - - -
243A SER* 1.3 79.2 - - - +
245A VAL* 1.3 64.0 + - + +
246A ALA 3.6 0.2 + - - -
247A ILE* 3.6 24.0 + - - +
248A GLN* 4.3 3.6 + - - +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A PHE* 4.7 8.5 - - + -
240A ASP* 4.6 16.6 - - + +
241A SER 3.1 21.0 + - - +
242A PHE* 4.0 4.5 - - - +
244A ASP* 1.3 75.2 - - + +
246A ALA* 1.3 56.7 + - - +
247A ILE 3.1 3.4 + - - -
248A GLN* 3.3 2.7 + - - +
249A GLY* 2.7 53.6 + - - +
250A GLY* 4.0 10.3 - - - +
279A ASP* 4.8 12.3 - - - +
315A ILE* 4.2 14.4 - - + -
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A THR* 2.5 44.2 + - + -
107A ASN* 3.4 9.7 - - - +
180A ALA* 3.5 22.2 - - + -
182A LEU 5.1 0.7 - - - +
242A PHE* 2.9 34.5 + - + +
243A SER* 4.1 2.5 - - - +
244A ASP 3.4 0.4 - - - -
245A VAL* 1.3 77.1 - - - +
247A ILE* 1.3 63.7 + - - +
249A GLY 3.9 1.4 + - - -
313A PHE* 4.8 0.2 - - - +
315A ILE* 4.9 2.6 - - - +
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Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN* 3.4 15.6 + - - +
176A ALA* 3.1 36.4 - - + +
177A PRO 3.0 24.9 - - - +
178A ARG* 2.9 30.1 - - - +
180A ALA 4.2 8.3 - - - +
243A SER 3.4 20.0 - - - +
244A ASP* 3.8 18.4 - - - +
245A VAL 3.1 0.8 + - - -
246A ALA* 1.3 81.3 - - - +
248A GLN* 1.3 60.9 + - + +
313A PHE* 4.0 4.2 - - - +
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Residues in contact with GLN 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ALA* 4.6 5.2 - - + -
244A ASP 4.3 2.9 + - - +
245A VAL* 3.3 3.7 + - - +
247A ILE* 1.3 81.3 - - + +
249A GLY* 1.3 64.0 + - - +
289A PRO* 4.1 14.6 - - + +
290A GLY* 3.8 13.2 - - - +
291A TYR 3.9 3.1 + - - +
292A ASN* 4.9 0.3 - - - +
313A PHE* 3.7 22.5 - - - +
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Residues in contact with GLY 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A THR* 4.5 1.1 - - - -
245A VAL* 2.7 29.4 + - - +
246A ALA 3.9 4.3 + - - -
247A ILE 3.5 1.4 - - - -
248A GLN* 1.3 75.9 - - - +
250A GLY* 1.3 58.7 + - - -
279A ASP* 5.2 1.0 - - - +
290A GLY* 2.9 20.2 - - - -
291A TYR 3.7 6.1 - - - -
314A GLY* 3.4 20.4 - - - -
315A ILE* 4.8 0.4 - - - -
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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