Contacts of the helix formed by residues 283 - 289 (chain F) in PDB entry 3EGC
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 LEU 283 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80F VAL* 4.3 26.0 - - + -
254F HIS* 3.8 46.4 - - + +
281F ASP* 3.3 17.5 + - + +
282F ASN* 1.3 85.5 + - - +
284F PRO* 1.3 76.2 - - + +
285F TRP* 3.5 30.3 - - + +
286F MET* 3.1 25.4 + - + +
287F ALA* 4.2 0.9 + - - +
333F HIS* 5.4 0.7 + - - -
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Residues in contact with PRO 284 (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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255E ARG* 6.2 1.3 - - - +
258E GLU* 3.5 42.8 - - + +
262E GLN* 4.9 6.7 - - - +
282F ASN* 4.3 5.2 - - - +
283F LEU* 1.3 90.9 - - + +
285F TRP* 1.3 62.3 - - + +
287F ALA* 2.9 21.5 + - + +
288F PHE* 3.8 14.1 - - + -
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Residues in contact with TRP 285 (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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258E GLU* 4.9 1.9 + - - +
285E TRP* 3.3 64.7 - + + -
288E PHE* 3.7 26.0 - + - -
254F HIS* 4.4 6.2 + - + +
257F THR* 4.1 20.2 - - + -
258F GLU* 4.3 24.1 + - + -
261F MET* 4.6 3.1 - - + -
283F LEU* 3.5 32.5 - - + +
284F PRO* 1.3 78.6 - - + +
286F MET* 1.3 84.0 + - + +
288F PHE* 2.7 39.8 + - - +
289F LEU* 3.7 31.1 + - + +
293F LEU* 4.7 0.9 - - + -
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Residues in contact with MET 286 (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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254F HIS* 3.7 25.4 - - + -
257F THR* 4.5 2.7 - - + -
279F SER* 3.5 21.5 - - - +
281F ASP 3.2 27.6 - - - +
283F LEU* 3.3 19.5 - - + +
284F PRO 3.1 0.8 + - - -
285F TRP* 1.3 112.9 - - + +
287F ALA* 1.3 60.1 + - - +
288F PHE 3.2 1.3 + - - -
289F LEU* 3.6 9.2 + - - +
293F LEU* 3.0 49.8 + - + +
295F VAL* 3.2 21.3 - - + -
333F HIS* 4.8 1.1 - - + -
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Residues in contact with ALA 287 (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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265E ASN* 4.9 5.7 - - - +
283F LEU 4.2 0.6 + - - +
284F PRO* 2.9 14.3 + - + +
286F MET* 1.3 78.3 - - - +
288F PHE* 1.3 67.1 + - + +
289F LEU 3.3 6.0 + - - +
292F PRO* 4.2 17.1 - - + +
333F HIS* 3.8 30.2 - - + +
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Residues in contact with PHE 288 (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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258E GLU* 3.6 42.2 - - + -
261E MET* 4.0 38.7 - - + +
262E GLN* 4.2 16.8 - - + -
265E ASN* 5.4 8.3 - - - +
285E TRP* 3.7 36.8 - + - -
289E LEU* 5.2 6.5 - - + +
284F PRO* 3.8 14.4 - - + -
285F TRP* 2.7 30.3 + - + +
287F ALA* 1.3 85.4 - - + +
289F LEU* 1.3 65.1 + - + +
290F ASP* 4.1 0.7 + - - +
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Residues in contact with LEU 289 (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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288E PHE* 5.0 9.0 - - + +
289E LEU* 4.7 17.9 - - + -
261F MET* 4.2 17.9 - - + -
271F TYR* 3.7 16.4 - - + -
285F TRP* 3.7 36.3 - - + +
286F MET* 3.8 12.3 - - - +
287F ALA 3.3 1.5 - - - +
288F PHE* 1.3 84.0 - - + +
290F ASP* 1.3 60.8 + - - +
291F PRO 2.8 25.7 - - - +
292F PRO* 2.8 12.1 - - - +
293F LEU* 3.8 23.1 - - + -
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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