Contacts of the helix formed by residues 293 - 305 (chain B) in PDB entry 2W27
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 SER 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291B LEU 3.0 14.2 - - - +
292B SER* 1.3 81.0 + - - +
294B ASP* 1.3 61.1 + - - +
295B ASP* 2.8 14.8 + - - +
296B ASP* 2.6 54.3 + - - +
297B PHE* 3.6 7.6 + - - +
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Residues in contact with ASP 294 (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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287B ARG* 4.2 17.0 + - - +
292B SER 3.1 11.6 - - - +
293B SER* 1.3 73.3 - - - +
295B ASP* 1.3 66.0 + - - +
297B PHE* 3.6 15.4 + - - +
298B ILE* 3.6 9.9 + - - +
314B MET* 3.8 21.2 - - - +
322B LEU* 5.2 7.2 - - + +
323B THR* 3.5 27.1 - - + +
389B MET* 4.1 15.6 - - - +
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Residues in contact with ASP 295 (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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293B SER* 2.8 9.3 + - - +
294B ASP* 1.3 79.9 + - - +
296B ASP* 1.3 66.2 + - - +
297B PHE 3.1 2.4 + - - -
298B ILE* 3.2 24.2 + - - +
299B LYS* 3.4 15.3 + - - +
322B LEU 4.9 1.7 - - - +
323B THR* 4.0 16.4 - - - +
324B GLY 3.6 10.7 + - - -
335B TYR* 2.4 37.8 + - + +
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 3.6 28.7 - - + +
292B SER 5.3 0.2 + - - -
293B SER* 2.6 36.3 + - - +
295B ASP* 1.3 72.2 - - - +
297B PHE* 1.3 62.1 + - - +
299B LYS* 3.4 17.4 + - - +
300B LYS* 3.3 28.5 + - - +
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Residues in contact with PHE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL* 3.8 42.4 - - + -
286B LEU* 3.8 36.3 - - + -
287B ARG* 3.9 34.5 - - + +
291B LEU* 4.3 17.0 - - + +
293B SER 3.6 8.5 + - - +
294B ASP 3.6 7.9 - - - +
295B ASP 3.1 0.6 - - - -
296B ASP* 1.3 80.8 - - - +
298B ILE* 1.3 72.1 + - + +
300B LYS* 3.1 5.9 + - - +
301B LEU* 2.9 41.3 + - + +
314B MET* 4.2 11.0 - - - -
385B MET* 4.7 3.8 - - - -
391B LEU* 4.4 8.7 - - + -
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Residues in contact with ILE 298 (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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294B ASP 3.6 7.6 + - - +
295B ASP* 3.2 17.5 - - - +
297B PHE* 1.3 95.6 - - + +
299B LYS* 1.3 64.7 + - - +
301B LEU* 3.7 6.1 - - - +
302B ALA* 3.0 23.9 + - - +
312B ILE* 3.6 26.7 - - + +
313B TYR* 4.8 1.1 - - - -
314B MET* 4.2 19.7 - - + -
323B THR* 3.4 17.7 - - - +
324B GLY 3.1 28.0 - - - +
326B VAL* 3.7 16.7 - - + +
335B TYR* 5.2 0.7 - - + -
391B LEU* 4.3 11.4 - - + -
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Residues in contact with LYS 299 (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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295B ASP* 3.7 16.8 - - - +
296B ASP* 3.4 17.1 + - - +
297B PHE 3.2 0.4 - - - -
298B ILE* 1.3 76.7 - - - +
300B LYS* 1.3 67.7 + - + +
302B ALA* 3.2 14.6 + - - +
303B GLU* 3.2 18.1 + - - +
326B VAL* 3.8 18.2 - - + -
335B TYR* 3.8 45.5 - - + +
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Residues in contact with LYS 300 (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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286B LEU* 3.2 25.1 - - + -
289B ASN* 5.4 4.5 - - - +
291B LEU* 3.1 44.4 - - + +
296B ASP* 3.3 15.8 + - - +
297B PHE 3.1 4.7 + - - +
299B LYS* 1.3 78.7 - - + +
301B LEU* 1.3 64.0 + - - +
303B GLU* 3.1 10.8 + - - +
304B GLU* 2.9 27.1 + - + +
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Residues in contact with LEU 301 (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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279B VAL* 5.3 0.4 - - + +
282B ALA* 3.7 27.4 - - + -
283B VAL* 3.9 9.9 - - + -
286B LEU* 4.2 10.3 - - + +
297B PHE* 2.9 33.8 + - + +
298B ILE* 3.7 8.3 - - - +
299B LYS 3.2 0.2 - - - -
300B LYS* 1.3 76.5 - - - +
302B ALA* 1.3 52.3 + - - +
304B GLU* 2.9 7.6 + - + +
305B LEU* 2.7 61.0 + - + +
312B ILE* 4.2 7.9 - - + -
391B LEU* 3.6 33.9 - - + -
393B ILE* 4.5 4.3 - - + -
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Residues in contact with ALA 302 (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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298B ILE 3.0 17.2 + - - +
299B LYS* 3.2 7.2 + - - +
301B LEU* 1.3 75.3 - - - +
303B GLU* 1.3 53.9 + - + +
305B LEU* 3.2 2.0 - - - +
306B THR* 2.7 36.4 + - - -
312B ILE* 3.5 15.7 - - + +
326B VAL* 3.8 3.8 - - + -
333B TRP* 3.0 47.4 - - + +
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Residues in contact with GLU 303 (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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299B LYS 3.2 13.4 + - - +
300B LYS* 3.1 9.7 + - - +
302B ALA* 1.3 74.2 - - + +
304B GLU* 1.3 71.3 + - + +
306B THR* 3.4 28.5 + - - +
333B TRP* 4.7 18.1 - - + +
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Residues in contact with GLU 304 (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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278B ARG* 3.8 14.6 + - - +
282B ALA* 4.7 10.4 - - + +
286B LEU* 3.6 26.9 - - + +
300B LYS* 2.9 18.9 + - + +
301B LEU* 2.9 19.4 + - + +
303B GLU* 1.3 82.0 - - - +
305B LEU* 1.3 57.1 + - - +
306B THR* 3.4 4.5 + - - +
307B ASP* 5.1 0.3 + - - -
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Residues in contact with LEU 305 (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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275B PHE* 5.3 2.9 - - + -
278B ARG* 3.4 46.4 - - + +
279B VAL* 4.3 14.6 - - + -
282B ALA* 4.8 7.6 - - + -
301B LEU* 2.7 48.4 + - + +
302B ALA* 3.2 4.9 - - - +
304B GLU* 1.3 71.8 - - + +
306B THR* 1.3 62.8 + - - +
307B ASP 3.2 3.5 + - - -
308B CYS* 3.2 12.4 + - - -
309B SER* 3.1 28.2 + - - -
312B ILE* 5.0 1.8 - - + -
393B ILE* 3.8 29.8 - - + -
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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