Contacts of the helix formed by residues 279 - 292 (chain A) in PDB entry 6B3I
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 ASP 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A CYS* 4.6 2.6 - - - +
247A GLU* 3.4 39.7 + - + +
250A PHE* 4.6 0.5 - - - -
275A ARG* 3.0 48.7 + - - +
278A VAL* 1.3 79.1 - - + +
280A LEU* 1.3 62.2 + - - +
281A GLN 3.3 2.9 - - - +
282A GLY* 3.0 6.9 + - - +
283A ILE* 2.9 32.5 + - - +
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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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254A LEU* 5.4 1.6 - - + -
271A ILE 5.1 0.4 - - - +
272A ILE* 4.0 34.8 - - + +
275A ARG 2.9 17.0 + - - +
276A ALA* 3.6 27.8 + - + +
279A ASP* 1.3 76.5 - - - +
281A GLN* 1.3 63.4 + - + +
283A ILE* 3.0 24.5 + - + +
284A LYS* 2.8 39.3 + - + +
295A LEU* 5.1 2.5 - - + -
314A LEU 4.0 21.1 - - - +
315A LEU* 4.5 14.6 - - + -
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Residues in contact with GLN 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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276A ALA 5.1 2.9 + - - +
279A ASP* 3.3 0.8 - - - +
280A LEU* 1.3 81.9 - - + +
282A GLY* 1.3 61.4 + - - +
284A LYS* 3.3 39.3 + - - +
285A ALA* 3.2 22.2 + - - +
314A LEU 5.7 0.3 - - - +
315A LEU 4.8 0.3 - - - +
316A HIS* 4.9 11.3 - - - +
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Residues in contact with GLY 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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247A GLU* 3.7 15.7 - - - +
279A ASP* 3.0 11.3 + - - +
281A GLN* 1.3 75.2 - - - +
283A ILE* 1.3 60.4 + - - +
285A ALA* 3.5 6.3 + - - +
286A LYS* 3.1 34.3 + - - +
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Residues in contact with ILE 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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247A GLU* 4.1 13.9 - - - +
250A PHE* 3.6 25.8 - - + -
251A ALA* 4.1 18.5 - - - +
254A LEU* 3.8 27.1 - - + -
271A ILE* 4.6 4.9 - - + -
275A ARG* 4.0 18.6 - - + -
279A ASP* 2.9 40.8 + - - +
280A LEU* 3.0 17.0 + - + +
282A GLY* 1.3 74.7 - - - +
284A LYS* 1.3 60.8 + - - +
286A LYS* 3.4 1.6 + - - +
287A PHE* 2.9 29.0 + - + +
295A LEU* 5.1 2.0 - - + -
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Residues in contact with LYS 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 LEU* 2.8 25.9 + - + +
281A GLN* 3.3 40.3 + - - +
282A GLY 3.4 0.2 - - - -
283A ILE* 1.3 75.7 - - - +
285A ALA* 1.3 62.4 + - - +
287A PHE* 3.4 7.7 + - - +
288A GLN* 3.1 22.5 + - - +
294A SER* 5.7 0.2 - - - -
295A LEU* 4.4 19.6 + - + +
296A SER* 6.5 0.7 - - - -
315A LEU* 2.6 53.9 + - + +
316A HIS* 4.5 6.9 + - - +
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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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281A GLN 3.2 17.6 + - - +
282A GLY* 3.9 6.5 - - - +
283A ILE 3.2 0.2 - - - -
284A LYS* 1.3 74.2 - - - +
286A LYS* 1.3 66.1 + - + +
288A GLN* 3.2 7.6 + - - +
289A GLU* 3.2 23.5 + - - +
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Residues in contact with LYS 286 (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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245A ASP* 3.2 31.8 + - - +
247A GLU* 3.9 32.6 + - + +
248A ASP* 4.4 11.6 - - + +
251A ALA* 4.4 2.2 - - + -
282A GLY 3.1 20.3 + - - +
283A ILE 4.0 0.7 - - - +
285A ALA* 1.3 78.3 - - + +
287A PHE* 1.3 55.9 + - - +
289A GLU* 3.5 32.0 + - - +
290A LYS* 2.9 31.7 + - - +
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Residues in contact with PHE 287 (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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251A ALA* 3.4 34.0 - - + +
254A LEU* 4.9 1.1 - - + -
255A TYR* 3.8 12.8 - + + -
258A MET* 5.6 0.2 - - - -
283A ILE* 2.9 20.9 + - + +
284A LYS* 3.6 7.9 - - - +
286A LYS* 1.3 74.8 - - - +
288A GLN* 1.3 64.8 + - - +
291A TYR* 3.1 48.5 + + + +
293A LYS* 3.2 30.0 - - + +
294A SER 3.8 2.7 - - - -
295A LEU* 3.4 49.6 - - + -
298A MET* 3.7 29.8 - - + -
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Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A LYS 3.1 13.2 + - - +
285A ALA* 3.2 10.3 + - - +
287A PHE* 1.3 77.8 - - - +
289A GLU* 1.3 58.3 + - - +
292A GLN* 2.9 59.7 + - - +
293A LYS* 3.7 9.2 - - - +
294A SER* 3.2 29.9 + - - +
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Residues in contact with GLU 289 (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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285A ALA 3.2 11.2 + - - +
286A LYS* 3.6 37.0 - - - +
288A GLN* 1.3 81.6 - - - +
290A LYS* 1.3 64.2 + - + +
291A TYR 3.6 0.2 + - - -
292A GLN* 3.9 15.5 + - - +
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Residues in contact with LYS 290 (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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241A ARG* 4.4 2.2 - - - +
248A ASP* 3.0 40.3 + - - +
251A ALA* 4.4 8.7 - - + -
252A GLU* 4.3 17.2 + - - -
286A LYS 2.9 18.7 + - - +
287A PHE* 4.4 0.2 - - - -
288A GLN 3.3 0.2 - - - -
289A GLU* 1.3 81.7 - - + +
291A TYR* 1.3 102.8 + - + +
292A GLN* 5.5 1.0 - - - +
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Residues in contact with TYR 291 (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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251A ALA* 3.6 11.7 - - + -
252A GLU* 3.3 27.2 - - - +
255A TYR* 3.4 57.3 - + + +
287A PHE* 3.1 36.6 + + + +
290A LYS* 1.3 114.6 - - + +
292A GLN* 1.3 67.0 + - - +
293A LYS* 3.0 32.2 + - + +
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Residues in contact with GLN 292 (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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288A GLN* 2.9 30.6 + - - +
289A GLU* 3.9 16.5 + - - +
290A LYS 5.5 0.7 - - - -
291A TYR* 1.3 79.0 - - - +
293A LYS* 1.3 58.2 + - - +
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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