Contacts of the helix formed by residues 273 - 278 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B THR* 1.3 73.6 - - - +
274B ALA* 1.3 57.4 + - - +
276B ALA* 3.2 4.1 + - - -
277B THR* 2.6 34.1 + - - +
322B VAL* 3.8 7.9 - - - +
323B ALA 2.9 15.4 + - - -
324B SER* 4.2 6.0 - - - +
350B GLY* 5.1 3.3 + - - -
354B ARG* 3.4 29.9 - - - +
357B VAL* 3.6 31.2 - - + -
358B ILE* 4.2 13.2 - - + -
427B TYR* 3.2 17.5 - - + +
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B THR* 3.3 6.8 + - - +
273B THR* 1.3 79.8 - - - +
275B HIS* 1.3 58.1 - - + +
277B THR* 3.9 2.2 - - - -
278B LEU* 2.9 39.0 + - + +
296B THR* 5.9 2.7 - - + -
300B LEU* 3.4 16.8 - - + +
324B SER 5.8 1.0 + - - +
348B VAL* 5.1 11.0 - - + -
426B LEU* 3.9 23.3 - - + -
427B TYR* 3.1 14.4 + - - +
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Residues in contact with HIS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ASN* 4.0 21.5 + - + -
248B VAL 3.9 4.7 - - - +
249B SER* 3.4 29.4 - - - -
271B THR* 3.3 17.7 - - - +
272B THR* 2.5 38.7 + - + +
274B ALA* 1.3 78.9 - - + +
276B ALA* 1.3 61.3 + - - +
277B THR 3.4 0.7 + - - -
278B LEU 4.3 2.4 - - - +
296B THR* 4.2 16.3 - - + +
298B PRO 2.6 29.0 + - - -
299B PRO 3.9 6.1 + - - -
300B LEU* 3.9 17.8 + - + +
306B THR* 5.3 0.9 - - - +
307B SER* 3.7 12.3 + - - -
310B LEU* 3.5 16.9 - - + +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B THR* 4.2 14.3 + - + -
272B THR 3.0 17.6 + - - +
273B THR 3.2 4.9 + - - +
275B HIS* 1.3 76.7 - - - +
277B THR* 1.3 63.8 + - + +
307B SER* 3.2 25.5 - - - +
310B LEU* 4.4 4.9 - - - -
311B MET* 3.6 30.1 - - + +
314B LEU* 4.3 10.3 - - + -
358B ILE* 4.4 5.8 - - + -
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Residues in contact with THR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B THR 2.6 20.9 + - - +
274B ALA 3.7 0.7 + - - -
276B ALA* 1.3 87.0 - - + +
278B LEU* 1.3 67.5 + - - +
279B THR* 5.7 0.2 - - - +
307B SER* 3.7 11.6 + - - -
311B MET* 3.8 13.2 - - + -
357B VAL* 3.8 16.3 - - + +
358B ILE* 4.7 4.0 - - + -
361B ARG* 3.8 39.1 + - + +
427B TYR* 3.5 20.6 - - - -
430B MET* 5.2 1.5 - - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ALA* 2.9 24.7 + - + +
275B HIS 4.3 2.4 - - - +
277B THR* 1.3 90.6 - - - +
279B THR* 1.3 64.5 + - - +
282B HIS* 4.3 14.6 - - + +
294B TYR* 3.6 14.4 - - + -
300B LEU* 3.8 19.1 - - + +
301B ARG 5.1 1.0 + - - +
307B SER* 3.8 9.8 + - - -
426B LEU* 3.6 49.1 - - + +
427B TYR* 3.8 18.8 - - + -
430B MET* 5.6 2.9 - - + -
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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
------------------------------------------------------------
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