Contacts of the helix formed by residues 277 - 285 (chain A) in PDB entry 4PTE
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 THR 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A THR 4.7 3.6 - - - +
276A PRO* 1.3 76.8 - - - +
278A ARG* 1.3 59.7 + - - +
279A GLU* 3.5 8.6 + - - +
280A GLN* 2.9 40.8 + - - +
281A ILE* 2.8 29.6 + - - +
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Residues in contact with ARG 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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277A THR* 1.3 72.9 - - - +
279A GLU* 1.3 52.8 + - - +
281A ILE* 3.2 12.2 + - - +
282A ARG* 2.8 35.3 + - - +
289A THR* 4.1 15.0 - - + +
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Residues in contact with GLU 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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277A THR* 3.3 8.1 + - - +
278A ARG* 1.3 79.8 - - - +
280A GLN* 1.3 57.1 + - + +
282A ARG* 3.1 9.2 + - - +
283A GLU* 2.9 32.6 + - - +
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Residues in contact with GLN 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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275A THR 4.3 1.4 - - - +
276A PRO* 3.4 11.7 - - + +
277A THR* 2.9 46.0 + - - +
279A GLU* 1.3 76.7 - - + +
281A ILE* 1.3 62.6 + - - +
283A GLU* 3.4 4.1 + - - +
284A MET* 3.1 28.5 + - - +
322A GLU* 5.5 4.2 + - - -
323A TYR* 3.7 34.1 - - + +
324A THR* 3.6 25.4 + - - +
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Residues in contact with ILE 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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229A PHE* 4.7 7.4 - - + -
276A PRO* 4.0 26.0 - - + +
277A THR 2.8 20.0 + - - +
278A ARG* 3.4 10.8 - - - +
280A GLN* 1.3 74.7 - - - +
282A ARG* 1.3 57.4 + - - +
284A MET* 2.8 12.7 + - + +
285A ASN 2.6 50.7 + - - +
288A TYR* 3.8 9.2 - - + +
289A THR* 3.6 28.3 - - + +
293A PHE* 3.5 32.8 - - + -
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Residues in contact with ARG 282 (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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278A ARG 2.8 17.6 + - - +
279A GLU* 3.1 12.8 + - - +
281A ILE* 1.3 75.2 - - - +
283A GLU* 1.3 60.0 + - + +
285A ASN 4.4 0.2 - - - -
286A PRO* 3.3 37.8 - - + +
289A THR* 4.5 6.5 - - + +
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Residues in contact with GLU 283 (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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226A GLU* 5.2 0.3 - - - +
279A GLU* 2.9 17.6 + - + +
280A GLN 3.8 5.6 - - - +
281A ILE 3.2 0.2 - - - -
282A ARG* 1.3 77.9 - - + +
284A MET* 1.3 61.6 + - - +
324A THR* 4.0 31.4 - - + +
325A PRO* 3.9 17.8 - - + +
326A THR* 5.5 1.6 - - - +
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Residues in contact with MET 284 (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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225A PRO* 3.5 36.1 - - - -
226A GLU* 3.6 30.8 - - + +
229A PHE* 3.7 25.4 - - + -
231A ALA* 3.6 10.6 - - - +
233A ASP* 4.7 3.8 - - - +
276A PRO* 3.8 22.4 - - + -
280A GLN 3.1 27.5 + - - +
281A ILE* 2.8 12.4 + - - +
282A ARG 4.3 0.2 - - - -
283A GLU* 1.3 81.5 - - - +
285A ASN* 1.3 63.2 + - - +
286A PRO* 4.5 0.8 - - - +
323A TYR* 3.5 32.1 - - + +
325A PRO* 4.6 1.3 - - + -
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Residues in contact with ASN 285 (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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229A PHE* 2.6 46.0 + - + -
230A GLY 4.2 2.6 + - - -
231A ALA* 4.2 13.9 - - + +
281A ILE* 2.6 22.6 + - - +
284A MET* 1.3 77.5 - - - +
286A PRO* 1.3 95.1 - - - +
288A TYR* 3.3 31.4 + - + +
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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