Contacts of the helix formed by residues 248 - 256 (chain A) in PDB entry 1U1H
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 PRO 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A LEU 3.6 18.6 - - - +
211A VAL 4.1 2.5 - - - +
212A MSE 3.6 11.4 - - - +
213A ASP* 4.7 6.5 - - - +
214A LEU 5.9 1.1 - - - +
246A ASP* 3.6 12.1 - - - +
247A ILE* 1.3 85.5 - - + +
249A ALA* 1.3 67.4 + - - +
250A GLU* 3.3 2.5 - - + +
251A ALA* 2.8 14.1 + - + +
252A TYR* 2.8 20.1 + - - +
616A ARG* 3.6 26.7 - - - +
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Residues in contact with ALA 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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247A ILE 3.5 1.6 + - - -
248A PRO* 1.3 69.9 - - - +
250A GLU* 1.3 68.9 + - + +
252A TYR* 3.1 17.3 + - - +
253A LYS* 3.3 12.3 + - - +
277A LEU* 3.8 27.7 - - + +
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Residues in contact with GLU 250 (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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214A LEU 5.9 0.4 - - - +
219A LEU* 3.9 16.6 - - + +
248A PRO* 3.3 3.2 - - + +
249A ALA* 1.3 82.8 - - + +
251A ALA* 1.3 63.8 + - - +
253A LYS* 2.9 49.3 + - - +
254A THR* 3.2 12.6 + - - -
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Residues in contact with ALA 251 (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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210A LEU* 3.7 20.9 - - + +
212A MSE 5.3 1.6 - - - +
214A LEU* 6.0 0.9 - - + -
219A LEU* 3.7 28.2 - - + +
247A ILE* 3.5 15.0 - - + -
248A PRO* 2.8 23.3 + - + +
250A GLU* 1.3 78.7 - - - +
252A TYR* 1.3 55.6 + - - +
254A THR* 3.4 2.6 + - - -
255A LEU* 3.0 30.7 + - - +
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Residues in contact with TYR 252 (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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247A ILE* 3.4 10.0 - - + +
248A PRO 2.8 6.8 + - - +
249A ALA 3.2 12.8 - - - +
250A GLU 3.0 0.2 - - - -
251A ALA* 1.3 75.0 - - - +
253A LYS* 1.3 61.9 + - + +
255A LEU* 4.3 3.1 - - + -
256A THR* 2.7 50.8 + - + +
266A PHE* 3.6 34.8 - + - -
274A THR* 4.5 4.7 - - + -
277A LEU* 3.6 49.6 - - + -
278A VAL* 3.4 20.7 - - + -
281A GLY 3.1 27.4 + - - -
282A PHE* 3.4 15.4 - - - -
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Residues in contact with LYS 253 (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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249A ALA 3.3 8.0 + - - +
250A GLU* 2.9 39.9 + - - +
252A TYR* 1.3 81.6 - - + +
254A THR* 1.3 65.2 + - - +
256A THR* 3.5 6.4 + - - -
257A SER* 2.8 27.6 + - - -
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Residues in contact with THR 254 (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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210A LEU* 5.3 2.0 - - + -
219A LEU* 3.5 44.2 - - + +
222A PHE* 4.0 7.9 - - + -
223A THR* 3.4 25.2 + - - +
250A GLU 3.2 8.5 + - - -
251A ALA 3.6 7.0 - - - -
253A LYS* 1.3 82.2 - - - +
255A LEU* 1.3 63.4 + - - +
257A SER* 3.4 12.1 + - - -
258A LEU* 3.0 30.8 - - + +
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Residues in contact with LEU 255 (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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210A LEU* 3.8 22.2 - - + -
240A VAL* 3.7 31.6 - - + +
242A THR* 5.1 6.3 - - - +
247A ILE* 5.3 6.1 - - + -
251A ALA 3.0 18.1 + - - +
252A TYR* 3.9 7.4 - - + +
253A LYS 3.3 0.2 - - - -
254A THR* 1.3 74.3 - - - +
256A THR* 1.3 64.6 + - + +
257A SER 3.1 9.3 + - - -
258A LEU* 3.3 24.8 + - + +
264A PHE* 3.0 52.5 - - + -
266A PHE* 4.1 22.0 - - + -
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Residues in contact with THR 256 (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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252A TYR* 2.7 60.3 + - + +
253A LYS* 3.5 8.0 + - - -
255A LEU* 1.3 80.8 - - + +
257A SER* 1.3 57.1 + - - +
258A LEU 3.7 0.7 - - - -
264A PHE* 3.5 18.9 - - + -
282A PHE* 4.9 1.6 - - + -
283A PRO* 3.4 40.1 - - + +
286A LYS* 4.5 5.4 + - - -
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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