Contacts of the helix formed by residues 293 - 306 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290D SER 3.4 3.2 + - - +
291D PHE 3.1 0.6 - - - -
292D GLU* 1.3 80.1 - - - +
294D TYR* 1.3 64.9 + - - +
295D GLU* 3.9 12.9 + - - +
296D GLN* 2.6 36.7 + - - +
297D ALA* 3.0 22.0 + - - +
354D PHE* 3.7 13.6 - - - -
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Residues in contact with TYR 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D SER* 1.3 74.7 - - - +
295D GLU* 1.3 79.6 + - + +
297D ALA* 3.4 0.7 + - - +
298D ASP* 2.9 54.0 + - + +
354D PHE* 3.6 44.4 - + + +
381D MET* 3.9 22.0 - - + -
384D LYS* 4.1 12.9 + - - +
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Residues in contact with GLU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D SER 4.5 1.1 - - - -
293D SER* 3.9 11.4 + - - +
294D TYR* 1.3 99.4 + - + +
296D GLN* 1.3 59.6 + - + +
298D ASP* 3.8 3.5 - - - +
299D MET* 2.9 32.7 + - - +
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Residues in contact with GLN 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D ASP* 5.1 0.8 + - - -
263D SER* 3.3 43.0 + - - +
264D LYS* 3.8 25.3 - - + +
289D TYR 4.9 3.8 + - - -
290D SER 3.2 14.6 - - - +
292D GLU* 2.9 40.1 + - - +
293D SER* 2.6 27.8 + - - +
294D TYR 3.3 0.4 - - - -
295D GLU* 1.3 75.7 - - + +
297D ALA* 1.3 59.9 + - - +
300D MET* 3.0 30.5 + - - +
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Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D SER* 2.9 22.7 + - - +
291D PHE* 3.9 30.9 - - + -
293D SER 3.0 13.4 + - - +
294D TYR 3.9 1.1 - - - +
296D GLN* 1.3 75.7 - - - +
298D ASP* 1.3 63.6 + - - +
300D MET* 3.4 2.3 + - - +
301D LEU* 3.1 27.0 + - - +
354D PHE* 4.1 4.7 - - + -
381D MET* 3.7 17.7 - - + -
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Residues in contact with ASP 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D TYR* 2.9 37.7 + - + +
295D GLU* 3.8 4.3 - - - +
297D ALA* 1.3 76.0 - - - +
299D MET* 1.3 58.5 + - - +
301D LEU* 3.3 4.1 + - - +
302D ARG* 2.8 32.4 + - - +
381D MET* 3.5 17.2 - - + +
384D LYS* 2.9 30.9 + - - +
385D TYR* 2.9 28.7 + - - -
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Residues in contact with MET 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D SER 3.6 4.7 - - - +
263D SER 3.2 29.8 - - - +
264D LYS* 4.0 16.6 - - - +
265D GLU 3.9 7.2 - - - +
266D LEU* 3.7 33.7 - - + +
295D GLU 2.9 19.6 + - - +
297D ALA 3.3 0.2 - - - -
298D ASP* 1.3 75.1 - - - +
300D MET* 1.3 59.6 + - - +
302D ARG* 3.5 10.5 - - - +
303D ASN* 2.9 35.8 + - - +
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Residues in contact with MET 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D LEU* 4.1 15.7 - - + +
262D SER* 3.3 21.5 + - - +
263D SER 4.1 3.8 - - - +
283D CYS* 4.5 5.2 - - - -
286D VAL* 4.0 20.4 - - + +
287D CYS* 3.9 25.6 - - - -
290D SER* 3.6 29.6 - - - +
296D GLN 3.0 17.5 + - - +
297D ALA 3.9 1.8 - - - +
299D MET* 1.3 75.8 - - - +
301D LEU* 1.3 58.2 + - - +
303D ASN* 3.3 2.4 + - - +
304D ALA* 2.9 29.4 + - + +
314D PHE* 6.4 0.9 - - + -
501D SAH 3.9 36.1 - - + +
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D CYS* 6.2 0.4 - - - -
291D PHE* 5.8 1.3 - - + -
297D ALA 3.1 15.3 + - - +
298D ASP* 3.5 8.7 - - - +
299D MET 3.3 0.2 - - - -
300D MET* 1.3 74.5 - - - +
302D ARG* 1.3 56.4 + - - +
304D ALA* 3.2 2.0 + - - +
305D CYS* 2.6 47.4 + - - +
314D PHE* 3.6 32.3 - - + -
378D LEU* 4.0 23.6 - - + -
381D MET* 3.5 40.4 - - + +
382D ALA* 3.7 20.2 - - + +
385D TYR* 4.0 10.8 - - + -
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Residues in contact with ARG 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D LEU* 3.6 30.4 - - + +
298D ASP* 2.8 16.3 + - - +
299D MET* 3.5 13.8 - - - +
301D LEU* 1.3 77.4 - - - +
303D ASN* 1.3 61.1 + - - +
306D GLU* 2.9 62.3 + - - +
307D ARG 4.6 0.5 + - - -
384D LYS* 4.2 15.6 - - - +
385D TYR* 2.9 55.0 + - + +
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Residues in contact with ASN 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D LEU* 3.4 17.7 - - - +
204D LEU* 4.2 7.4 - - + -
262D SER* 2.8 29.1 + - - +
265D GLU 2.7 24.4 + - - -
266D LEU* 3.6 10.7 - - - +
267D LEU* 2.8 45.6 + - + +
268D ILE 4.7 0.5 + - - -
271D PHE* 5.7 0.7 - - - -
278D PHE* 5.2 3.8 - - - -
299D MET* 2.9 19.0 + - - +
300D MET 3.6 5.2 - - - +
302D ARG* 1.3 76.5 - - - +
304D ALA* 1.3 60.8 + - - +
306D GLU 5.1 0.2 + - - -
307D ARG* 5.5 3.3 + - - +
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Residues in contact with ALA 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D LEU* 5.0 0.9 - - - +
204D LEU* 4.0 6.7 - - + +
278D PHE* 5.6 2.4 - - - -
281D CYS* 3.4 42.3 - - - +
283D CYS* 5.7 0.4 - - + -
300D MET* 2.9 18.6 + - + +
301D LEU 3.8 3.6 - - - +
303D ASN* 1.3 81.0 - - - +
305D CYS* 1.3 62.8 + - - +
307D ARG 5.2 0.6 + - - -
308D LEU* 3.5 11.6 + - - +
314D PHE* 3.7 26.5 - - + -
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Residues in contact with CYS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D LEU* 2.6 30.0 + - - +
304D ALA* 1.3 78.1 - - - +
306D GLU* 1.3 65.0 + - - +
307D ARG 3.3 2.5 - - - -
308D LEU* 3.2 12.7 + - - +
314D PHE* 3.6 38.4 - - - -
382D ALA* 5.4 0.9 - - - -
385D TYR* 3.7 19.1 - - + -
387D MET* 3.7 23.1 - - + -
474D LYS* 3.0 22.0 + - - -
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Residues in contact with GLU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D LEU* 5.0 1.2 - - - +
268D ILE* 4.1 23.0 - - - +
302D ARG* 2.9 66.6 + - + +
305D CYS* 1.3 74.8 - - - +
307D ARG* 1.3 70.1 + - + +
308D LEU 3.5 1.2 + - - +
385D TYR* 4.3 14.1 - - + +
474D LYS* 3.6 15.2 + - - +
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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