Contacts of the helix formed by residues 279 - 292 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B CYS* 4.5 1.9 - - - +
247B GLU* 3.7 33.8 + - + +
250B PHE* 4.3 5.0 - - - -
275B ARG* 2.9 52.7 + - - +
278B VAL* 1.3 79.2 - - + +
280B LEU* 1.3 62.1 + - - +
281B GLN 3.3 2.7 - - - +
282B GLY* 3.2 4.8 + - - +
283B ILE* 2.9 35.3 + - - +
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Residues in contact with LEU 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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254B LEU* 5.5 1.8 - - + -
271B ILE* 6.0 0.2 - - + -
272B ILE* 4.0 25.4 - - + +
275B ARG* 3.0 16.4 + - + +
276B ALA* 3.4 31.8 + - + +
279B ASP* 1.3 77.7 - - - +
281B GLN* 1.3 74.4 + - - +
283B ILE* 3.3 20.7 + - + -
284B LYS* 3.0 29.2 + - + +
295B LEU* 4.8 3.6 - - + -
314B LEU 3.9 21.1 - - - +
315B LEU* 4.3 21.1 - - + -
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Residues in contact with GLN 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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276B ALA 4.8 4.7 + - - +
279B ASP 3.3 0.4 - - - -
280B LEU* 1.3 96.9 - - - +
282B GLY* 1.3 62.1 + - - +
284B LYS* 2.9 34.4 + - - +
285B ALA* 3.2 22.0 + - - +
314B LEU 5.5 0.4 + - - -
315B LEU 5.5 0.2 + - - -
316B HIS* 5.3 8.7 + - - +
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Residues in contact with GLY 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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247B GLU* 3.5 21.5 - - - -
279B ASP* 3.2 9.5 + - - +
281B GLN* 1.3 75.6 - - - +
283B ILE* 1.3 60.5 + - - +
285B ALA* 3.4 5.8 + - - +
286B LYS* 3.0 35.0 + - - +
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Residues in contact with ILE 283 (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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247B GLU* 4.1 20.4 - - + -
250B PHE* 3.6 25.4 - - + -
251B ALA* 3.9 17.2 - - - +
254B LEU* 3.6 28.0 - - + -
271B ILE* 4.6 4.0 - - + -
275B ARG* 3.9 18.6 - - + -
279B ASP* 2.9 36.0 + - - +
280B LEU* 3.5 17.5 - - + +
281B GLN 3.3 0.2 - - - -
282B GLY* 1.3 76.4 - - - +
284B LYS* 1.3 57.0 + - - +
286B LYS 3.4 0.5 + - - -
287B PHE* 2.8 28.7 + - + +
295B LEU* 4.8 2.5 - - + -
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 3.0 28.6 + - + +
281B GLN* 2.9 37.8 + - - +
282B GLY 3.3 0.2 - - - -
283B ILE* 1.3 76.3 - - - +
285B ALA* 1.3 63.0 + - - +
287B PHE* 3.4 7.0 + - - +
288B GLN* 3.1 23.6 + - - +
294B SER* 5.6 0.2 - - - -
295B LEU* 4.1 31.2 + - + +
296B SER* 6.4 1.1 - - - -
315B LEU* 2.7 38.4 + - + +
316B HIS* 4.6 8.3 + - - +
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Residues in contact with ALA 285 (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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281B GLN 3.2 15.9 + - - +
282B GLY* 3.8 7.2 - - - +
284B LYS* 1.3 74.7 - - - +
286B LYS* 1.3 67.2 + - + +
288B GLN* 3.3 6.0 + - - +
289B GLU* 3.1 25.2 + - - +
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Residues in contact with LYS 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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245B ASP* 3.2 31.0 + - - +
247B GLU* 3.7 21.5 - - + +
248B ASP* 4.1 22.6 - - + +
251B ALA* 4.3 2.5 - - + -
282B GLY* 3.0 21.2 + - - +
283B ILE 3.9 3.4 - - - +
285B ALA* 1.3 77.4 - - + +
287B PHE* 1.3 57.6 + - - +
289B GLU* 3.8 24.9 + - - +
290B LYS* 3.0 32.5 + - - +
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Residues in contact with PHE 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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251B ALA* 3.4 38.3 - - + +
254B LEU* 4.6 0.9 - - + -
255B TYR* 3.7 22.9 - + + -
258B MET* 5.4 0.2 - - - -
283B ILE* 2.8 20.3 + - + +
284B LYS* 3.5 8.7 - - - +
285B ALA 3.2 0.2 - - - -
286B LYS* 1.3 76.8 - - - +
288B GLN* 1.3 61.5 + - - +
290B LYS 3.2 0.2 + - - -
291B TYR* 3.0 33.1 + + + -
293B LYS 3.3 19.7 - - - +
294B SER 3.9 0.4 - - - -
295B LEU* 3.4 46.9 - - + -
298B MET* 3.6 40.4 - - + -
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Residues in contact with GLN 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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284B LYS 3.1 16.5 + - - +
285B ALA* 3.3 6.3 + - - +
287B PHE* 1.3 75.6 - - - +
289B GLU* 1.3 59.1 + - - +
292B GLN* 2.9 66.2 + - - +
293B LYS* 3.3 13.4 + - - +
294B SER* 3.3 27.3 + - - +
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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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285B ALA 3.1 16.4 + - - +
286B LYS* 3.9 31.7 + - - +
288B GLN* 1.3 77.3 - - - +
290B LYS* 1.3 61.3 + - + +
292B GLN* 3.5 15.4 + - - -
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ASP* 3.3 37.5 - - - +
251B ALA* 5.1 2.2 - - + -
252B GLU* 3.6 23.6 + - + -
286B LYS 3.0 19.2 + - - +
289B GLU* 1.3 81.5 - - + +
291B TYR* 1.3 103.8 + - + +
292B GLN* 3.8 8.3 + - - +
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Residues in contact with TYR 291 (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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251B ALA* 3.9 11.7 - - + -
252B GLU* 3.3 27.5 - - - +
255B TYR* 3.5 64.7 - + + +
256B LYS* 5.3 0.7 + - - -
287B PHE* 3.0 35.7 + + + +
290B LYS* 1.3 118.0 + - + +
292B GLN* 1.3 70.5 + - - +
293B LYS* 2.9 30.4 + - + +
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Residues in contact with GLN 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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288B GLN* 2.9 28.6 + - - +
289B GLU 3.5 20.6 + - - -
290B LYS 3.8 5.5 + - - +
291B TYR* 1.3 84.2 - - - +
293B LYS* 1.3 60.2 + - + +
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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