Contacts of the helix formed by residues 293 - 306 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290C SER 3.5 0.9 + - - +
291C PHE 3.1 0.6 - - - -
292C GLU* 1.3 80.1 - - - +
294C TYR* 1.3 65.7 + - - +
295C GLU* 3.7 12.6 + - - +
296C GLN* 2.8 35.8 + - - +
297C ALA* 3.1 23.0 + - - +
354C PHE* 3.7 14.1 - - - -
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Residues in contact with TYR 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C SER* 1.3 73.6 - - - +
295C GLU* 1.3 79.7 + - + +
297C ALA* 3.3 2.3 + - - +
298C ASP* 2.8 52.5 + - + +
354C PHE* 3.5 44.4 - + + +
381C MET* 3.7 22.4 - - + -
384C LYS* 4.1 11.4 + - - +
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Residues in contact with GLU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C SER 4.5 0.4 - - - -
293C SER* 3.7 11.6 + - - +
294C TYR* 1.3 99.1 + - + +
296C GLN* 1.3 56.5 + - + +
298C ASP* 3.8 3.7 - - - +
299C MET* 2.7 37.1 + - - +
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Residues in contact with GLN 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ASP* 5.2 0.6 + - - -
263C SER* 3.2 48.6 + - - +
264C LYS* 3.9 26.2 - - + +
289C TYR 4.9 4.2 + - - -
290C SER* 3.2 16.1 - - - +
292C GLU* 3.0 44.0 + - - +
293C SER* 2.8 22.3 + - - +
294C TYR 3.4 0.4 - - - -
295C GLU* 1.3 79.9 - - + +
297C ALA* 1.3 56.1 + - - +
299C MET* 3.6 0.3 - - - +
300C MET* 3.0 26.5 + - - +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C SER* 3.0 21.8 + - - +
291C PHE* 4.1 22.0 - - + -
293C SER 3.1 15.2 + - - +
294C TYR 3.5 4.0 - - - +
296C GLN* 1.3 77.0 - - - +
298C ASP* 1.3 61.8 + - - +
300C MET* 3.4 2.1 + - - +
301C LEU* 3.1 26.6 + - - +
354C PHE* 3.9 12.1 - - + -
381C MET* 3.8 16.4 - - + -
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Residues in contact with ASP 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C TYR* 2.8 39.8 + - + +
295C GLU* 3.8 4.3 - - - +
297C ALA* 1.3 72.6 - - - +
299C MET* 1.3 56.8 + - - +
301C LEU* 3.3 4.2 + - - +
302C ARG 2.9 25.3 + - - -
381C MET* 3.6 17.3 - - + +
384C LYS* 2.7 32.0 + - - +
385C TYR* 2.7 34.3 + - - -
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Residues in contact with MET 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C SER 3.5 5.2 - - - +
263C SER 3.1 30.3 - - - +
264C LYS* 3.8 22.4 - - - +
265C GLU 3.5 19.1 - - - +
266C LEU* 3.6 29.6 - - + +
295C GLU 2.7 21.8 + - - +
296C GLN 3.6 0.2 - - - +
298C ASP* 1.3 74.6 - - - +
300C MET* 1.3 55.6 + - - +
302C ARG* 3.4 10.2 + - - +
303C ASN* 2.9 33.7 + - - +
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Residues in contact with MET 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C LEU* 4.0 24.4 - - + +
262C SER* 3.3 15.0 + - - +
263C SER 4.1 3.1 - - - +
283C CYS* 4.6 4.9 - - - -
286C VAL* 4.0 22.4 - - + +
287C CYS* 4.1 15.3 - - - -
290C SER* 3.7 32.1 - - - +
296C GLN 3.0 16.8 + - - +
297C ALA 3.4 1.1 + - - +
298C ASP 3.4 0.2 - - - -
299C MET* 1.3 73.7 - - - +
301C LEU* 1.3 60.9 + - - +
303C ASN* 3.2 2.9 + - - +
304C ALA* 2.9 28.7 + - + +
314C PHE* 6.3 1.6 - - + -
501C SAH 3.7 39.0 - - + +
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C CYS* 6.3 0.2 - - - -
291C PHE* 5.8 1.8 - - + -
297C ALA 3.1 16.6 + - - +
298C ASP* 3.5 8.3 - - - +
300C MET* 1.3 76.6 - - - +
302C ARG* 1.3 57.6 + - - +
304C ALA* 3.2 3.1 + - - +
305C CYS* 2.8 38.0 + - - +
314C PHE* 3.6 31.9 - - + -
378C LEU* 3.8 24.7 - - + -
381C MET* 3.5 50.7 - - + +
382C ALA* 3.7 13.0 - - + +
385C TYR* 3.9 10.5 - - + -
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Residues in contact with ARG 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C LEU* 3.4 45.8 - - + +
268C ILE* 5.1 2.2 - - - +
298C ASP 2.9 10.6 + - - +
299C MET* 3.5 11.8 - - - +
301C LEU* 1.3 77.4 - - - +
303C ASN* 1.3 57.7 + - - +
306C GLU* 2.8 69.2 + - + +
385C TYR* 3.3 42.3 - - + +
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Residues in contact with ASN 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C LEU* 3.5 17.3 - - - +
204C LEU* 4.1 7.9 - - + -
262C SER* 2.7 32.0 + - - +
265C GLU 2.8 20.9 + - - -
266C LEU* 3.7 9.5 - - - +
267C LEU* 2.9 45.8 + - + +
268C ILE 4.5 0.9 + - - -
271C PHE* 5.7 1.4 - - - -
278C PHE* 5.7 0.7 - - - -
299C MET* 2.9 20.7 + - - +
300C MET 3.2 4.7 + - - +
302C ARG* 1.3 77.1 - - - +
304C ALA* 1.3 60.9 + - - +
306C GLU* 4.6 4.9 + - - +
307C ARG* 5.3 4.9 + - - +
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Residues in contact with ALA 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C LEU* 4.7 1.9 - - - +
204C LEU* 3.8 6.9 - - + +
278C PHE* 5.7 1.9 - - - -
281C CYS* 3.4 43.5 - - - +
283C CYS* 6.1 0.2 - - - -
300C MET* 2.9 17.5 + - + +
301C LEU 3.6 4.7 - - - +
302C ARG 3.1 0.4 - - - -
303C ASN* 1.3 78.5 - - - +
305C CYS* 1.3 61.5 + - - +
307C ARG 5.1 0.7 + - - -
308C LEU* 3.6 10.9 + - - +
314C PHE* 3.6 28.7 - - + -
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Residues in contact with CYS 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C LEU* 2.8 25.3 + - - +
304C ALA* 1.3 80.5 - - - +
306C GLU* 1.3 62.8 + - - +
307C ARG 3.3 2.2 - - - -
308C LEU* 3.2 14.0 + - - +
314C PHE* 3.7 33.2 - - - -
382C ALA* 5.5 0.4 - - - -
385C TYR* 3.7 22.0 - - + -
387C MET* 3.7 30.7 - - - -
474C LYS* 2.9 23.9 + - - -
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Residues in contact with GLU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LEU* 4.5 2.8 - - - +
268C ILE* 4.1 23.4 - - - +
302C ARG* 2.8 65.7 + - + +
303C ASN* 4.6 3.3 + - - +
304C ALA 3.7 0.4 - - - -
305C CYS* 1.3 78.7 - - - +
307C ARG* 1.3 78.1 + - + +
308C LEU 3.3 2.5 + - - +
385C TYR* 5.2 8.0 - - + +
474C LYS* 4.3 8.1 + - - +
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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