Contacts of the helix formed by residues 276 - 281 (chain A) in PDB entry 5T0H
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 GLU 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A GLY* 3.6 12.3 - - - -
243A SER* 3.7 3.6 + - - -
275A ASP* 1.3 85.6 + - - +
277A ILE* 1.3 64.4 + - - +
278A ASP* 3.1 14.6 - - - +
279A ALA* 3.1 19.5 + - + +
280A ILE* 3.2 14.2 + - - +
320A ALA 4.4 4.0 + - - -
321A THR* 5.9 0.9 - - - +
307B ARG* 4.6 3.5 - - - +
310B LEU* 3.1 52.5 - - + +
311B GLU* 2.8 28.4 + - - +
314B ASN* 3.2 26.8 - - - +
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Residues in contact with ILE 277 (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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213A LEU* 6.4 0.4 - - + -
274A PHE* 4.4 16.4 - - + +
275A ASP 3.2 1.5 - - - -
276A GLU* 1.3 76.1 - - - +
278A ASP* 1.3 59.8 + - - +
280A ILE* 3.7 20.4 - - + -
281A GLY* 3.0 26.3 + - - -
302A LEU* 4.9 10.5 - - + -
319A MET* 3.6 43.7 - - + -
320A ALA 3.5 22.1 + - - +
321A THR* 3.6 14.8 - - + -
326A THR* 4.4 3.3 + - - -
329A PRO* 5.8 9.6 - - + -
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Residues in contact with ASP 278 (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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276A GLU* 3.3 16.8 - - - +
277A ILE* 1.3 75.7 + - - +
279A ALA* 1.3 74.1 + - - +
281A GLY 3.7 0.3 + - - -
282A GLY* 3.9 1.4 + - - -
321A THR* 3.1 21.9 + - - +
322A ASN* 3.7 24.5 + - - +
323A ARG* 4.4 10.3 + - + +
325A ASP 4.0 17.0 - - - +
326A THR* 3.1 31.1 - - + +
310B LEU* 4.9 7.9 - - - +
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Residues in contact with ALA 279 (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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242A GLY 6.2 0.2 - - - -
276A GLU* 3.1 14.0 + - + +
278A ASP* 1.3 90.8 + - - +
280A ILE* 1.3 62.3 + - + +
282A GLY* 3.6 8.3 + - - -
303B ARG* 4.3 1.4 + - - -
306B GLN* 6.5 0.7 - - - -
307B ARG* 2.4 56.8 + - + +
310B LEU* 4.2 14.6 - - + -
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Residues in contact with ILE 280 (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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240A VAL* 6.3 0.9 - - + -
242A GLY* 3.1 39.0 - - - +
245A LEU* 3.7 36.1 - - + -
246A VAL* 4.7 4.3 - - + +
274A PHE* 4.7 10.1 - - + -
275A ASP 4.7 3.1 - - - +
276A GLU 3.2 15.5 - - - +
277A ILE* 3.7 24.7 - - + +
279A ALA* 1.3 75.5 - - + +
281A GLY* 1.3 61.1 + - - +
282A GLY 3.2 4.8 + - - -
295A VAL* 3.9 6.1 - - - +
298A THR* 3.5 22.0 + - - -
299A MET 4.8 0.5 + - - -
302A LEU* 5.1 7.9 - - + -
307B ARG* 3.4 15.0 - - - +
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Residues in contact with GLY 281 (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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277A ILE* 3.0 20.8 + - - -
279A ALA 3.3 1.0 - - - -
280A ILE* 1.3 81.8 - - - +
282A GLY* 1.3 64.6 + - - +
283A ALA* 4.0 2.3 - - - +
299A MET* 4.0 21.0 - - - +
302A LEU* 6.4 1.1 - - - -
326A THR* 3.1 23.3 + - - -
329A PRO* 4.1 10.1 - - - +
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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