Contacts of the helix formed by residues 274 - 283 (chain A) in PDB entry 1B0K
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 HIS 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ASP* 3.1 37.5 + - + -
273A ASN* 1.3 74.4 - - - +
275A ARG* 1.3 85.8 + - - +
277A LYS* 3.6 14.9 - - + +
278A LYS* 3.1 33.5 + - - +
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Residues in contact with ARG 275 (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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246A ASP 2.9 29.8 + - - +
247A SER* 3.7 15.8 + - - +
248A ILE 3.6 21.2 + - - +
249A SER* 3.9 10.9 - - - +
250A CYS* 3.8 11.0 + - - +
253A MET* 4.1 7.6 - - + -
273A ASN* 2.9 17.3 + - - +
274A HIS* 1.3 94.7 + - + +
276A MET* 1.4 59.2 + - - +
278A LYS* 3.5 20.8 - - - +
279A TYR* 3.2 26.5 + - - +
504A GLU* 2.8 38.0 + - - +
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Residues in contact with MET 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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157A PRO* 4.8 1.1 - - + -
173A GLY 3.4 25.1 - - - +
174A LEU* 3.5 36.0 - - + +
175A GLY* 3.6 13.0 - - - +
250A CYS* 4.4 2.7 - - - -
253A MET* 3.9 10.3 - - + -
270A PHE* 3.7 24.7 - - + +
271A PRO 3.4 20.4 - - - +
272A TYR* 3.8 28.9 - - + -
273A ASN* 3.2 15.6 + - - +
275A ARG* 1.4 74.6 - - - +
277A LYS* 1.3 65.0 + - - +
279A TYR* 3.0 4.2 + - - +
280A LEU* 3.0 27.2 + - + +
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Residues in contact with LYS 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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272A TYR* 3.8 18.0 - - + +
273A ASN 3.2 8.7 + - - +
274A HIS* 3.4 17.4 + - + +
276A MET* 1.3 77.1 - - - +
278A LYS* 1.3 62.7 + - - +
280A LEU* 3.4 4.6 + - - +
281A SER* 3.0 32.5 + - - +
289A ALA* 3.8 22.0 + - + +
290A ASN* 3.8 19.4 + - - -
293A ASP* 2.6 32.9 + - - +
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Residues in contact with LYS 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 HIS* 3.1 21.8 + - - +
275A ARG* 3.5 27.6 - - - +
277A LYS* 1.3 81.8 - - - +
279A TYR* 1.4 57.3 + - - +
281A SER* 3.5 8.0 + - - -
282A LYS* 3.2 25.6 + - - +
504A GLU* 3.1 33.8 + - + +
505A LEU* 4.9 7.4 - - + -
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Residues in contact with TYR 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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148A GLN* 4.8 1.9 + - - -
151A LEU* 3.6 40.2 - - + +
152A GLU* 3.5 28.2 + - - +
174A LEU* 3.8 17.7 - - + -
250A CYS* 3.6 27.8 - - + -
251A THR* 3.7 20.1 - - + +
275A ARG 3.2 11.2 + - - +
276A MET 3.0 7.2 + - - +
278A LYS* 1.4 76.3 - - - +
280A LEU* 1.3 63.1 + - - +
282A LYS* 3.3 3.0 + - - +
283A THR* 2.9 39.4 + - + +
285A ARG* 4.0 5.8 - - - -
505A LEU* 3.7 38.3 - - + +
510A PHE* 5.2 3.0 - + - -
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Residues in contact with LEU 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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155A ALA 4.4 3.1 - - - +
157A PRO* 4.0 27.4 - - + -
174A LEU* 4.4 13.9 - - + -
272A TYR* 4.7 3.1 - - + -
276A MET 3.0 19.4 + - - +
277A LYS* 3.6 8.5 - - - +
279A TYR* 1.3 73.9 - - - +
281A SER* 1.3 55.9 + - - +
283A THR* 3.1 12.1 + - - -
285A ARG* 2.8 83.4 + - + +
288A ILE* 4.3 10.3 - - + -
289A ALA* 4.0 27.6 - - + +
292A ALA* 5.6 0.2 - - + -
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Residues in contact with SER 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 LYS* 3.0 18.1 + - - +
278A LYS* 3.6 10.5 - - - -
279A TYR 3.2 0.2 - - - -
280A LEU* 1.3 74.4 - - - +
282A LYS* 1.3 63.2 + - - +
284A GLY* 3.4 12.1 + - - -
286A ALA* 3.7 31.3 - - - +
289A ALA* 4.1 4.2 - - - +
509A GLU* 5.4 0.3 - - - +
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Residues in contact with LYS 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 LYS 3.2 15.9 + - - +
279A TYR 3.3 4.7 + - - +
281A SER* 1.3 75.7 - - - +
283A THR* 1.3 57.6 + - + +
284A GLY 3.3 2.7 + - - -
505A LEU* 4.1 26.0 - - + -
506A PRO* 2.8 24.0 + - + +
507A ARG 3.4 7.1 + - - -
508A ALA 2.6 29.3 + - - +
509A GLU* 2.9 41.4 + - - +
510A PHE* 4.0 26.8 + - + +
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Residues in contact with THR 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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9A HIS* 4.4 6.6 + - - -
152A GLU* 3.7 22.8 - - + +
279A TYR* 2.9 46.8 + - + +
280A LEU* 3.1 5.8 + - - -
282A LYS* 1.3 77.8 - - + +
284A GLY* 1.4 60.8 + - - +
285A ARG* 2.9 32.7 + - - +
395A GLN* 4.6 9.0 - - - +
510A PHE* 4.4 16.6 - - + -
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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