Contacts of the helix formed by residues 279 - 292 (chain B) in PDB entry 6CNB
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 TYR 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B CYS* 3.2 37.3 - - + +
274B GLY* 5.5 2.2 - - - -
276B ASP 3.5 3.8 + - - +
277B SER* 3.6 23.8 - - - -
278B SER* 1.3 76.3 - - - +
280B GLN* 1.3 67.3 + - - +
281B ASP* 3.3 2.0 + - - -
282B ILE* 3.4 16.6 + - + +
283B PHE* 3.5 8.8 + - - +
354B ARG* 4.6 12.6 - - - -
357B VAL* 4.0 24.5 - - + +
358B MET* 3.5 55.9 + - + +
361B TYR* 4.3 23.4 - + + -
365B MET* 4.9 7.8 - - - +
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Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B MET* 3.7 28.5 - - + +
273B CYS* 3.4 11.4 - - - -
275B ASN 3.3 22.3 + - - +
276B ASP* 2.9 41.9 + - - +
277B SER 4.7 1.4 - - - +
278B SER 2.7 8.9 + - - +
279B TYR* 1.3 76.1 - - - +
281B ASP* 1.3 64.4 + - + +
283B PHE* 3.6 1.2 + - - +
284B ALA* 3.5 14.1 + - - +
2I LEU* 5.7 1.1 - - + -
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Residues in contact with ASP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264A ARG* 5.6 9.9 - - - +
278B SER* 2.8 19.2 + - - +
280B GLN* 1.3 76.9 - - - +
282B ILE* 1.3 95.3 + - - +
283B PHE 3.0 1.6 + - - -
284B ALA* 3.0 16.5 + - - +
285B VAL* 3.3 19.3 + - + +
2I LEU* 5.4 4.9 - - - -
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B GLY* 4.9 8.1 - - - +
278B SER* 5.1 3.1 - - - +
279B TYR* 3.4 13.3 + - + +
281B ASP* 1.3 100.3 + - - +
283B PHE* 1.3 60.8 + - - +
285B VAL* 3.9 15.2 - - - +
286B ASN* 4.2 2.4 + - - +
357B VAL* 3.7 23.3 - - + -
360B MET* 3.7 30.1 - - + +
361B TYR* 4.3 36.6 - - + +
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Residues in contact with PHE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE* 5.1 4.0 - - + -
253B ILE* 4.6 4.9 - - + -
254B ALA* 5.6 4.7 - - + -
257B LEU* 5.7 0.7 - - + -
268B ILE* 3.5 34.5 - - + -
269B MET* 4.0 21.5 - - + -
272B VAL* 3.5 24.2 - - + -
273B CYS* 4.5 9.9 - - + -
279B TYR 3.5 11.7 + - - +
280B GLN 4.3 1.3 - - - +
281B ASP 3.1 0.4 - - - -
282B ILE* 1.3 78.4 - - - +
284B ALA* 1.3 69.0 + - - +
285B VAL 3.1 2.5 - - - -
286B ASN* 2.9 48.7 + - + +
287B LEU* 3.2 18.6 + - + -
353B THR* 4.5 16.6 - - + -
357B VAL* 4.6 18.1 - - + +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B MET* 4.6 8.7 - - - -
280B GLN 3.5 9.5 + - - +
281B ASP* 3.0 8.1 + - - +
283B PHE* 1.3 79.9 - - - +
285B VAL* 1.3 57.0 + - + +
287B LEU* 2.7 32.2 + - + +
288B GLU* 2.9 12.0 + - - +
2I LEU* 3.6 42.9 - - + +
11I MET* 5.9 0.3 - - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261A GLN* 5.0 3.1 - - - +
1265A ARG* 3.2 51.3 + - + +
237B ASN 4.7 4.7 - - - +
238B GLY* 4.3 18.6 - - - +
239B LYS* 6.4 0.2 - - + -
281B ASP* 3.6 17.0 - - + +
282B ILE* 3.9 11.7 - - - +
284B ALA* 1.3 77.4 - - - +
286B ASN* 1.3 63.7 + - - +
288B GLU* 3.3 16.4 - - - +
289B GLU* 4.3 1.6 + - - +
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Residues in contact with ASN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B GLY 3.6 17.5 + - - +
239B LYS* 5.2 1.8 - - - +
240B ILE* 3.1 40.9 + - + +
252B PRO* 4.9 0.7 - - - +
253B ILE* 3.1 24.0 + - - +
254B ALA* 4.6 9.7 + - - +
282B ILE 4.2 0.8 + - - +
283B PHE* 2.9 27.0 + - + +
285B VAL* 1.3 79.0 - - - +
287B LEU* 1.3 60.1 + - - +
288B GLU 2.8 7.3 + - - -
289B GLU* 3.1 33.3 + - - +
290B SER 4.2 1.0 + - - -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ALA* 4.6 14.6 - - + -
265B ASP* 3.5 26.9 - - - +
266B LEU* 4.5 10.3 - - + -
268B ILE* 4.7 7.2 - - + -
269B MET* 4.5 20.0 - - + +
283B PHE* 3.2 24.4 + - + +
284B ALA* 2.7 24.3 + - + +
286B ASN* 1.3 76.9 - - - +
288B GLU* 1.3 63.3 + - - +
290B SER* 3.5 13.9 + - - -
291B SER* 3.8 4.7 + - - +
2I LEU* 5.5 3.4 - - + -
11I MET* 3.5 35.2 - - + -
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257A PHE* 3.1 29.0 - - - -
1258A TYR* 3.0 37.4 - - + -
1261A GLN* 4.7 18.3 - - + +
1265A ARG* 5.2 3.8 - - - +
284B ALA 2.9 8.1 + - - +
285B VAL* 3.3 17.0 - - - +
286B ASN 2.8 1.4 + - - -
287B LEU* 1.3 77.1 - - - +
289B GLU* 1.3 57.7 + - + +
290B SER 3.0 0.2 - - - -
291B SER* 2.6 42.2 + - - -
292B LYS* 3.4 4.9 + - + -
11I MET* 4.0 13.4 - - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B LYS* 3.1 30.6 - - + +
240B ILE 4.6 1.0 + - - -
241B TYR* 3.0 32.1 + - - -
252B PRO* 3.6 28.1 - - + +
255B ILE* 5.7 0.3 - - - +
285B VAL 4.3 1.1 + - - +
286B ASN* 3.1 21.7 + - - +
288B GLU* 1.3 78.2 - - + +
290B SER* 1.3 61.2 + - - +
292B LYS* 3.1 39.6 - - + +
293B LEU* 3.9 8.7 + - - +
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Residues in contact with SER 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO* 5.7 0.4 - - - -
254B ALA* 3.7 29.1 - - - +
255B ILE* 4.3 19.9 + - - +
258B LYS* 3.8 18.8 + - - +
265B ASP* 6.0 0.7 - - - -
286B ASN 4.2 0.4 + - - -
287B LEU* 3.5 9.0 + - - -
288B GLU 2.8 2.0 + - - -
289B GLU* 1.3 81.0 - - - +
291B SER* 1.3 64.0 + - - -
293B LEU* 3.1 12.0 + - - +
294B ASP 3.3 27.9 + - - +
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Residues in contact with SER 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257A PHE* 6.4 0.4 - - - -
1258A TYR* 4.5 3.5 + - - -
265B ASP* 4.6 3.3 + - - -
287B LEU* 4.0 8.5 + - - +
288B GLU* 2.6 25.8 + - - -
290B SER* 1.3 74.9 - - - +
292B LYS* 1.3 57.7 + - - -
293B LEU* 3.0 8.9 + - - +
10I ASN* 5.7 1.0 + - - -
11I MET* 3.6 31.5 - - - +
13I LEU* 5.0 13.2 - - - -
27I ARG* 5.1 12.2 - - - +
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258A TYR* 3.3 42.1 + - + +
288B GLU* 3.4 5.3 + - + +
289B GLU* 3.1 37.9 - - + +
291B SER* 1.3 76.7 - - - +
293B LEU* 1.3 62.1 + - + +
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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