Contacts of the helix formed by residues 273 - 278 (chain A) in PDB entry 4B92
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 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A THR* 1.3 73.0 - - - +
274A ALA* 1.3 57.7 + - - +
276A ALA* 3.2 3.4 + - - -
277A THR* 2.6 34.8 + - - +
322A VAL* 3.7 7.7 - - - +
323A ALA 2.9 16.3 + - - -
324A SER* 4.1 5.8 + - - +
350A GLY* 5.1 3.5 + - - -
354A ARG* 3.3 30.6 - - - +
357A VAL* 3.6 30.7 - - + -
358A ILE* 4.2 13.2 - - + -
427A TYR* 3.2 17.9 - - + +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A THR* 3.3 7.5 + - - +
273A THR* 1.3 78.5 - - - +
275A HIS* 1.3 60.1 + - + +
277A THR* 3.9 2.7 - - - -
278A LEU* 2.9 38.1 + - + +
296A THR* 5.9 2.9 - - + -
300A LEU* 3.4 16.8 - - + +
324A SER 5.8 0.6 + - - +
348A VAL* 5.1 9.6 - - + -
426A LEU* 3.9 24.0 - - + -
427A TYR* 3.1 13.7 + - - +
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Residues in contact with HIS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 4.0 20.9 + - + -
248A VAL 3.9 4.5 - - - +
249A SER* 3.4 29.5 - - - -
271A THR* 3.4 17.9 - - - +
272A THR* 2.5 37.7 + - + +
274A ALA* 1.3 79.9 - - + +
276A ALA* 1.3 60.6 + - - +
277A THR 3.4 0.5 + - - -
278A LEU 4.3 2.4 - - - +
296A THR* 4.2 16.7 - - + +
298A PRO 2.6 29.2 + - - -
299A PRO 4.0 6.5 + - - -
300A LEU* 3.8 18.5 + - + -
306A THR* 5.3 0.9 - - - +
307A SER* 3.7 12.0 - - - -
310A LEU* 3.5 17.1 - - + +
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Residues in contact with ALA 276 (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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271A THR* 4.2 14.1 + - + -
272A THR 3.0 18.1 + - - +
273A THR 3.2 4.5 + - - +
275A HIS* 1.3 77.1 - - - +
277A THR* 1.3 62.4 + - + +
307A SER* 3.2 25.5 - - - +
310A LEU* 4.4 5.6 - - - -
311A MET* 3.5 30.4 - - + +
314A LEU* 4.3 10.5 - - + -
358A ILE* 4.4 5.8 - - + -
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Residues in contact with THR 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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273A THR 2.6 21.2 + - - +
274A ALA 3.7 1.0 + - - -
276A ALA* 1.3 86.6 - - + +
278A LEU* 1.3 66.5 + - - +
279A THR* 5.7 0.3 - - - +
307A SER* 3.7 11.2 + - - -
311A MET* 3.8 12.8 - - + -
357A VAL* 3.8 17.7 - - + -
358A ILE* 4.7 4.0 - - + -
361A ARG* 3.8 44.8 + - + +
427A TYR* 3.5 20.6 - - - -
430A MET* 5.2 2.2 - - - -
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Residues in contact with LEU 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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274A ALA* 2.9 25.0 + - + +
275A HIS 4.3 2.4 - - - +
277A THR* 1.3 91.1 - - - +
279A THR* 1.3 65.1 + - - +
282A HIS* 4.3 15.0 - - + +
294A TYR* 3.6 26.9 - - + -
300A LEU* 3.8 20.5 - - + +
301A ARG 5.1 0.9 + - - +
306A THR* 6.1 0.2 - - - -
307A SER* 3.7 10.3 + - - -
361A ARG* 5.9 3.4 - - - +
426A LEU* 3.6 35.7 - - + +
427A TYR* 3.8 19.3 - - + -
430A MET* 6.2 1.6 - - + -
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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