Contacts of the helix formed by residues 293 - 306 (chain B) in PDB entry 5E9W
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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290B SER 3.5 3.0 + - - +
291B PHE 3.2 0.4 - - - -
292B GLU* 1.3 79.5 - - - +
294B TYR* 1.3 64.9 + - - +
295B GLU* 3.8 13.2 + - - +
296B GLN* 2.7 34.5 + - - +
297B ALA* 3.1 21.3 + - - +
354B PHE* 3.7 13.6 - - - -
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Residues in contact with TYR 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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293B SER* 1.3 73.2 - - - +
295B GLU* 1.3 81.1 + - + +
297B ALA* 3.3 0.9 + - - +
298B ASP* 2.8 54.3 + - + +
354B PHE* 3.5 44.0 - + + +
381B MET* 3.7 21.8 - - + +
384B LYS* 4.2 14.1 + - - +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B SER 4.4 0.9 - - - -
293B SER* 3.3 11.5 + - - +
294B TYR* 1.3 100.4 + - + +
296B GLN* 1.3 58.8 + - + +
298B ASP* 3.8 3.6 - - - +
299B MET* 2.8 32.7 + - - +
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Residues in contact with GLN 296 (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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261B ASP* 5.3 0.4 + - - -
263B SER* 3.3 41.4 + - - +
264B LYS* 3.6 27.4 - - + +
289B TYR 5.0 3.8 + - - -
290B SER 3.1 17.3 - - - +
292B GLU* 3.0 43.6 + - - +
293B SER* 2.7 25.3 + - - +
294B TYR 3.3 0.2 - - - -
295B GLU* 1.3 77.3 - - + +
297B ALA* 1.3 55.4 + - - +
299B MET* 3.7 0.2 - - - +
300B MET* 2.9 30.8 + - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B SER* 2.9 22.3 + - - +
291B PHE* 3.9 21.9 - - + -
293B SER 3.1 13.4 + - - +
294B TYR 3.7 3.6 - - - +
296B GLN* 1.3 76.9 - - - +
298B ASP* 1.3 63.0 + - - +
300B MET* 3.5 2.1 + - - +
301B LEU* 3.1 26.9 + - - +
354B PHE* 3.9 20.4 - - + -
381B MET* 3.9 9.0 - - + -
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Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B TYR* 2.8 39.1 + - + +
295B GLU* 3.8 4.9 - - - +
297B ALA* 1.3 72.7 - - - +
299B MET* 1.3 57.8 + - - +
301B LEU* 3.2 5.0 + - - +
302B ARG* 2.8 26.9 + - - +
381B MET* 3.6 17.3 - - + +
384B LYS* 2.9 30.3 + - - +
385B TYR* 2.7 30.6 + - - -
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Residues in contact with MET 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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262B SER 3.7 4.9 - - - +
263B SER 3.2 30.3 - - - +
264B LYS* 4.0 15.3 - - - +
265B GLU 3.8 11.9 - - - +
266B LEU* 3.5 36.1 - - + +
295B GLU 2.8 22.9 + - - +
298B ASP* 1.3 72.4 - - - +
300B MET* 1.3 58.5 + - - +
302B ARG* 4.3 13.0 - - - +
303B ASN* 2.9 30.4 + - - +
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Residues in contact with MET 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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204B LEU* 3.9 29.1 - - + +
262B SER* 3.2 11.6 + - - +
263B SER 4.0 8.5 - - - +
283B CYS* 4.4 4.5 - - - -
286B VAL* 4.0 9.6 - - + +
287B CYS* 3.9 26.7 - - - -
289B TYR 5.5 0.2 - - - -
290B SER* 3.7 29.8 - - - +
296B GLN 2.9 17.6 + - - +
297B ALA 4.0 1.3 - - - +
298B ASP 3.4 0.2 - - - -
299B MET* 1.3 75.9 - - - +
301B LEU* 1.3 58.2 + - - +
303B ASN* 3.4 2.4 + - - +
304B ALA* 2.9 29.1 + - + +
314B PHE* 6.4 0.2 - - + -
501B SAH 3.8 36.6 - - + +
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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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287B CYS* 6.1 0.4 - - - -
291B PHE* 5.7 1.6 - - + -
297B ALA 3.1 16.1 + - - +
298B ASP* 3.5 8.1 - - - +
299B MET 3.2 0.2 - - - -
300B MET* 1.3 72.7 - - - +
302B ARG* 1.3 57.7 + - - +
304B ALA* 3.1 2.6 + - - -
305B CYS* 2.6 47.3 + - - +
314B PHE* 3.5 35.0 - - + -
378B LEU* 3.8 24.2 - - + -
381B MET* 3.5 50.0 - - + +
382B ALA* 3.8 9.2 - - + +
385B TYR* 4.0 11.7 - - + -
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Residues in contact with ARG 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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266B LEU* 3.9 44.1 - - + +
268B ILE* 5.0 1.4 - - - +
298B ASP* 2.8 12.0 + - - +
299B MET* 3.2 16.3 + - - +
301B LEU* 1.3 77.1 - - - +
303B ASN* 1.3 64.3 + - - +
306B GLU* 2.9 69.2 + - - +
307B ARG* 4.7 0.3 + - - +
385B TYR* 3.2 40.3 + - - +
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Residues in contact with ASN 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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202B LEU* 3.5 16.5 - - - +
204B LEU* 4.2 7.0 - - + -
262B SER* 2.8 30.2 + - - +
265B GLU 2.6 25.6 + - - +
266B LEU* 3.5 10.6 - - - +
267B LEU* 2.9 44.8 + - + +
268B ILE* 4.8 0.5 + - - +
271B PHE* 5.8 0.7 - - - -
278B PHE* 5.2 4.2 - - - -
299B MET* 2.9 19.1 + - - +
300B MET 3.7 4.0 - - - +
302B ARG* 1.3 77.5 - - - +
304B ALA* 1.3 60.6 + - - +
306B GLU 4.9 0.5 + - - -
307B ARG* 5.4 5.4 + - - +
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Residues in contact with ALA 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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202B LEU* 5.0 0.5 - - - +
204B LEU* 4.0 6.5 - - + -
278B PHE* 5.7 2.1 - - - -
281B CYS* 3.3 43.8 - - - +
283B CYS* 5.7 0.4 - - + -
300B MET* 2.9 19.1 + - + +
301B LEU 3.7 3.4 - - - +
303B ASN* 1.3 80.0 - - - +
305B CYS* 1.3 61.3 + - - +
306B GLU 3.9 0.2 - - - -
307B ARG 5.3 0.8 + - - -
308B LEU* 3.6 12.8 + - - +
314B PHE* 3.8 26.2 - - + +
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Residues in contact with CYS 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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301B LEU* 2.6 28.7 + - - +
304B ALA* 1.3 74.5 - - - +
306B GLU* 1.3 63.2 + - - +
307B ARG 3.3 2.0 - - - -
308B LEU* 3.3 10.5 + - - +
314B PHE* 3.5 43.1 - - - -
382B ALA* 5.4 0.9 - - - -
385B TYR* 3.7 19.7 - - + -
387B MET* 3.7 22.7 - - - -
474B LYS* 3.0 24.6 + - - -
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Residues in contact with GLU 306 (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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266B LEU* 4.9 0.7 - - - +
268B ILE* 4.2 16.6 - - - +
302B ARG* 2.9 67.9 + - - +
304B ALA 3.9 0.2 - - - -
305B CYS* 1.3 74.8 - - - +
307B ARG* 1.3 74.2 + - + +
308B LEU 3.5 1.7 + - - +
385B TYR* 4.4 14.6 - - + -
474B LYS* 3.7 14.9 + - - +
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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