Contacts of the helix formed by residues 295 - 305 (chain F) in PDB entry 3ECS
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 ALA 295 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294D SER* 4.3 9.9 - - - +
291F LEU* 4.2 16.4 - - + -
292F THR* 3.0 23.5 + - - +
294F SER* 1.3 77.9 + - - +
296F VAL* 1.3 64.9 + - - +
297F SER 3.3 1.7 + - - -
298F ASP* 3.4 14.0 + - + +
299F GLU* 3.5 15.4 + - - +
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Residues in contact with VAL 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F VAL* 4.1 16.8 - - + -
201F VAL 3.6 23.8 - - - +
202F GLU* 4.0 6.3 - - - +
204F GLY* 3.7 13.7 - - - +
235F PHE* 4.2 14.3 - - + -
284F LEU* 4.0 19.7 - - + -
291F LEU* 4.5 15.3 - - + -
292F THR 3.6 3.7 + - - +
293F PRO 3.1 17.0 + - - +
295F ALA* 1.3 78.8 - - - +
297F SER* 1.3 59.1 + - - +
299F GLU* 3.1 7.8 + - - +
300F LEU* 2.8 29.4 + - + +
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Residues in contact with SER 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D GLU 5.1 1.1 + - - -
203D ASN* 4.5 16.2 + - - -
239D PHE* 3.7 24.0 - - - -
294D SER* 4.5 9.9 - - - -
297D SER* 4.5 9.8 + - - -
202F GLU 3.6 19.1 + - - -
293F PRO 4.5 0.6 + - - -
294F SER 3.4 15.1 + - - -
296F VAL* 1.3 80.8 - - - +
298F ASP* 1.3 63.5 + - - +
300F LEU* 3.4 1.7 + - - -
301F ILE* 3.1 29.8 + - - +
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Residues in contact with ASP 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ASN 4.8 2.6 - - - +
278D PRO* 3.8 28.2 - - - +
279D SER* 5.2 1.4 + - - -
293D PRO* 5.4 1.2 - - - +
294D SER* 2.5 29.4 + - - -
295F ALA* 3.4 10.0 + - + +
296F VAL 3.3 0.8 - - - -
297F SER* 1.3 79.3 + - - +
299F GLU* 1.3 63.8 + - + +
301F ILE* 3.4 8.3 + - - +
302F LYS* 3.1 26.3 + - - +
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Residues in contact with GLU 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F PHE* 4.2 8.3 - - + -
288F LEU* 3.8 39.8 - - + +
291F LEU* 3.4 33.4 - - + -
295F ALA 3.5 6.0 + - - +
296F VAL 3.1 7.0 + - - +
298F ASP* 1.3 80.0 - - + +
300F LEU* 1.3 60.8 + - - +
302F LYS* 3.9 25.0 + - - +
303F LEU* 2.9 29.6 + - - +
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Residues in contact with LEU 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D PHE* 3.6 25.6 - - + -
241D LEU* 4.5 1.6 - - + -
200F VAL 4.8 1.1 - - - +
201F VAL 4.9 0.4 - - - -
202F GLU* 3.9 22.7 - - + +
235F PHE* 3.8 29.1 - - + -
236F VAL 3.7 26.5 - - - +
237F ARG* 4.3 10.3 - - - -
296F VAL* 2.8 18.0 + - + +
297F SER* 3.8 6.3 - - - +
298F ASP 3.3 0.2 - - - -
299F GLU* 1.3 74.4 - - - +
301F ILE* 1.3 58.8 + - - +
303F LEU* 3.4 2.1 + - - +
304F TYR* 2.8 61.6 + - + -
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Residues in contact with ILE 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ASN* 4.0 18.8 - - + +
239D PHE* 3.8 16.8 - - + -
240D PRO 5.2 0.4 - - - +
241D LEU* 4.3 12.1 - - + +
275D TYR* 4.8 1.8 - - - +
277D ALA* 5.8 0.2 - - + -
278D PRO* 3.6 34.8 - - + -
297F SER 3.1 16.6 + - - +
298F ASP* 3.4 10.8 - - - +
299F GLU 3.2 0.2 - - - -
300F LEU* 1.3 76.7 - - - +
302F LYS* 1.3 69.3 + - - +
304F TYR* 3.0 2.6 + - - -
305F LEU* 2.8 45.4 + - + +
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Residues in contact with LYS 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F ASP 3.1 13.5 + - - +
299F GLU* 3.9 26.4 + - - +
301F ILE* 1.3 80.4 - - - +
303F LEU* 1.3 57.7 + - - +
305F LEU* 3.4 4.4 + - - -
306F ALA* 3.0 28.4 + - - +
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Residues in contact with LEU 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F LEU* 3.4 43.2 - - + +
232F SER* 4.2 30.7 - - - +
235F PHE* 4.7 5.2 - - + -
288F LEU* 4.6 17.0 - - + -
299F GLU 2.9 20.3 + - - +
300F LEU* 3.4 6.1 - - - +
302F LYS* 1.3 79.4 - - - +
304F TYR* 1.3 69.1 + - + +
306F ALA* 3.2 21.6 - - + +
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Residues in contact with TYR 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D LEU* 3.9 19.1 - - + -
67F SER* 4.0 10.2 - - - -
70F GLU* 3.8 17.7 - - + -
71F LEU* 3.6 31.2 - - + +
74F ARG* 3.1 44.9 + - - +
235F PHE* 2.6 31.6 + - + -
236F VAL* 3.6 9.0 - - - +
237F ARG* 3.7 29.3 + - + +
300F LEU* 2.8 51.9 + - + +
301F ILE 4.0 2.0 - - - +
303F LEU* 1.3 77.2 - - + +
305F LEU* 1.3 58.8 + - - +
306F ALA* 3.1 8.0 + - - +
307F ALA 5.1 0.5 + - - -
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Residues in contact with LEU 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D LEU* 3.7 44.2 - - + +
242D ASN* 5.4 6.1 - - + +
74F ARG* 5.5 3.6 - - - +
301F ILE* 2.8 36.1 + - + +
302F LYS* 3.5 5.4 - - - +
304F TYR* 1.3 78.0 - - - +
306F ALA* 1.3 68.3 + - - +
307F ALA 3.1 13.9 + - - +
308F ALA* 3.5 11.0 - - + +
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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