Contacts of the helix formed by residues 280 - 285 (chain A) in PDB entry 5I73
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 VAL 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A VAL* 6.5 0.7 - - + -
268A PHE 4.6 3.4 - - - +
269A SER* 3.4 37.7 - - - +
276A THR* 2.6 29.1 + - + +
277A SER* 5.1 0.4 - - - -
279A LYS* 1.3 71.4 - - + +
281A VAL* 1.3 65.5 + - - +
283A VAL* 2.9 21.2 + - + +
284A THR* 3.3 14.6 + - + +
440A PHE* 3.7 20.2 - - + -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 4.5 0.4 - - - +
90A LEU* 4.0 6.3 - - + +
91A SER* 3.5 41.7 - - - +
94A GLY* 4.8 3.6 - - - -
277A SER* 2.3 35.0 - - - +
278A GLY* 4.4 7.0 - - - +
280A VAL* 1.3 77.0 - - - +
282A TRP* 1.3 63.5 + - + +
284A THR* 2.9 11.1 + - - +
285A ALA* 2.8 42.9 + - + +
437A ASP* 5.0 4.0 - - + +
440A PHE* 4.5 16.4 - - + -
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Residues in contact with TRP 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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84A LYS* 5.5 7.0 - - + -
86A VAL* 4.0 26.0 - - + -
87A ASP* 2.6 29.5 + - - +
90A LEU* 4.6 18.6 - - + -
278A GLY 3.0 23.1 - - - -
279A LYS* 3.2 23.6 + - + +
281A VAL* 1.3 78.4 - - + +
283A VAL* 1.3 54.3 + - + +
286A THR* 2.6 39.8 + - + +
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Residues in contact with VAL 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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279A LYS 4.8 3.1 - - - +
280A VAL* 2.9 13.5 + - + +
282A TRP* 1.3 82.7 - - + +
284A THR* 1.3 67.4 + - + +
285A ALA 3.3 0.9 - - - -
286A THR* 3.7 2.1 + - - -
287A PHE* 3.4 29.4 + - + +
433A THR* 4.9 5.5 - - + +
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Residues in contact with THR 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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280A VAL* 3.3 16.5 + - + +
281A VAL* 3.2 20.3 + - - -
283A VAL* 1.3 81.4 - - + +
285A ALA* 1.3 57.8 + - - +
286A THR 3.6 0.2 - - - -
288A PRO* 3.4 14.8 - - - +
433A THR* 2.8 31.0 - - + +
436A LEU* 4.3 19.1 - - + -
437A ASP* 2.8 32.8 + - - +
440A PHE* 4.0 19.1 - - + -
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Residues in contact with ALA 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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90A LEU* 4.8 11.0 - - + +
93A ILE* 5.3 4.7 - - + +
94A GLY* 4.1 14.4 - - - +
281A VAL* 2.8 28.8 + - + +
284A THR* 1.3 77.8 - - - +
286A THR* 1.3 65.2 + - + +
287A PHE 3.7 0.2 - - - -
288A PRO* 3.9 4.1 - - - +
289A TYR* 3.4 27.4 - - - -
437A ASP* 3.5 10.5 - - - +
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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