Contacts of the helix formed by residues 271 - 276 (chain H) in PDB entry 5U0A
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 LYS 271 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16H ASN* 4.1 23.8 - - - +
19H ARG* 4.1 25.9 - - - +
224H GLY* 6.6 0.2 - - - -
226H PHE* 3.6 29.6 - - + -
270H GLY* 1.3 72.7 - - - +
272H GLN* 1.3 63.8 + - - +
273H ASN 3.1 3.4 - - - +
274H ALA* 3.1 24.6 + - + +
275H THR* 2.9 19.3 + - + +
17K A 2.8 40.5 + - - +
18K A 4.7 23.6 + - - +
19K G 5.3 6.5 + - - -
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Residues in contact with GLN 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G GLN* 3.3 28.9 - - - +
17H ILE* 3.2 33.5 - - - +
267H VAL* 3.8 9.9 - - - +
269H SER* 3.2 30.0 - - - -
270H GLY 3.8 5.3 + - - +
271H LYS* 1.3 77.7 - - - +
273H ASN* 1.3 60.2 + - - +
274H ALA 3.1 0.2 - - - -
275H THR* 3.8 3.3 + - - -
276H ALA* 2.9 23.7 + - - -
277H ALA* 2.8 37.2 + - - +
278H MET* 3.6 21.8 + - + +
17K A 4.7 0.4 + - - -
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Residues in contact with ASN 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LYS* 3.0 22.3 + - - +
170G PHE 5.9 1.1 - - - +
184G GLY* 4.0 25.0 + - - +
185G ALA 5.2 0.4 - - - -
186G VAL 3.6 21.3 + - - +
187G GLN* 3.6 24.0 - - - +
188G PHE 3.7 4.9 + - - -
241G ARG* 4.5 12.4 + - - +
271H LYS 3.1 1.2 - - - -
272H GLN* 1.3 77.9 - - - +
274H ALA* 1.3 57.3 + - - +
275H THR 3.7 0.2 - - - -
17K A 4.7 5.4 - - - +
18K A 3.1 33.6 + - - +
19K G 5.8 0.9 - - - -
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Residues in contact with ALA 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G SER* 3.0 25.3 + - - +
41G GLN* 5.8 2.2 - - - +
44G LYS* 4.4 3.6 - - - +
188G PHE 3.1 10.1 - - - +
190G HIS* 3.6 8.0 + - - +
226H PHE* 5.5 2.5 - - + -
271H LYS* 3.1 25.8 + - + +
272H GLN 3.1 0.6 - - - -
273H ASN* 1.3 80.2 - - - +
275H THR* 1.3 65.5 + - + +
18K A 5.5 2.7 + - - +
19K G 4.6 13.9 - - - +
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Residues in contact with THR 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G PHE 4.0 1.3 - - - -
189G ALA* 3.3 18.6 - - - +
190G HIS* 4.3 10.2 + - + +
13H PRO* 4.7 6.1 - - - +
14H TYR 3.5 21.3 - - - +
15H SER* 3.3 28.4 + - - +
226H PHE* 3.7 22.2 - - + -
270H GLY 4.3 1.2 + - - -
271H LYS 2.9 18.3 + - - +
272H GLN* 3.4 3.0 + - - -
274H ALA* 1.3 87.0 - - + +
276H ALA* 1.3 73.8 + - - +
277H ALA* 3.4 7.9 + - - +
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Residues in contact with ALA 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G GLN* 3.8 24.2 - - + +
189G ALA* 3.7 24.6 - - + +
234G TYR* 3.7 29.6 - - + -
295G SER* 4.2 6.4 + - - -
13H PRO* 5.0 3.3 - - - +
272H GLN* 2.9 19.7 + - - -
275H THR* 1.3 80.1 + - - +
277H ALA* 1.3 58.1 + - - +
278H MET* 3.2 10.4 + - - -
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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