Contacts of the helix formed by residues 283 - 289 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A VAL* 4.3 27.4 - - + -
254A HIS* 3.8 40.6 - - + +
281A ASP* 3.5 17.9 + - + -
282A ASN* 1.3 85.3 - - - +
284A PRO* 1.3 76.3 - - + +
285A TRP* 3.6 31.2 - - + +
286A MET* 3.0 28.9 + - + +
287A ALA* 4.1 1.2 + - - +
333A HIS* 5.5 0.3 + - - -
283B LEU* 6.6 0.2 - - + -
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Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ASN* 4.0 5.4 - - - +
283A LEU* 1.3 90.1 - - + +
285A TRP* 1.3 64.7 + - + +
287A ALA* 2.9 20.0 + - + +
288A PHE* 3.6 17.0 - - + -
255B ARG* 6.1 1.6 - - - +
258B GLU* 3.5 38.4 - - + +
262B GLN* 4.6 9.6 - - - +
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Residues in contact with TRP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A HIS* 4.4 5.0 + - + +
257A THR* 4.0 22.2 - - + -
258A GLU* 4.3 24.7 + - + -
261A MET* 4.6 2.7 - - + -
283A LEU* 3.6 30.8 - - + +
284A PRO* 1.3 78.3 - - - +
286A MET* 1.3 83.2 + - + +
288A PHE* 2.9 35.3 + - + +
289A LEU* 3.7 31.9 + - + +
293A LEU* 4.9 0.7 - - + -
258B GLU* 4.6 3.6 + - - -
285B TRP* 3.2 68.5 - + + +
288B PHE* 4.1 23.8 - + - -
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Residues in contact with MET 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A HIS* 3.7 32.5 - - + -
257A THR* 4.4 2.9 - - - -
279A SER* 3.8 18.4 - - - +
281A ASP 3.3 24.0 - - - +
283A LEU* 3.0 22.5 + - + +
285A TRP* 1.3 109.6 - - + +
287A ALA* 1.3 60.0 + - - +
288A PHE 3.5 0.3 + - - -
289A LEU* 3.7 6.7 + - - +
292A PRO* 3.6 1.6 - - - +
293A LEU* 2.8 54.5 + - + +
295A VAL* 3.4 15.5 - - + -
333A HIS* 4.7 4.0 - - + -
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LEU 4.1 0.6 + - - +
284A PRO* 2.9 13.5 + - + +
286A MET* 1.3 78.8 - - - +
288A PHE* 1.3 65.2 + - + +
289A LEU 3.3 6.6 + - - +
292A PRO* 4.2 15.6 - - + +
333A HIS* 3.9 31.6 - - + +
265B ASN* 4.6 6.6 - - - +
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A PRO* 3.6 15.5 - - + -
285A TRP* 2.9 27.4 + - + +
287A ALA* 1.3 85.1 - - + +
289A LEU* 1.3 68.2 + - + +
290A ASP* 4.0 1.4 + - - +
258B GLU* 3.3 44.0 - - + -
261B MET* 3.7 44.7 - - + +
262B GLN* 3.8 22.4 - - + -
265B ASN* 4.9 11.3 - - - +
285B TRP* 3.8 28.5 - + - -
289B LEU* 5.4 5.3 - - + +
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A MET* 4.3 18.8 - - + -
271A TYR* 3.8 15.7 - - + -
285A TRP* 3.7 38.4 - - + +
286A MET* 3.9 10.5 - - - +
287A ALA 3.3 1.1 - - - +
288A PHE* 1.3 86.2 - - + +
290A ASP* 1.3 59.9 + - - +
291A PRO 2.8 26.5 - - - +
292A PRO* 2.9 12.0 - - - +
293A LEU* 3.8 23.1 - - + -
288B PHE* 5.4 6.5 - - + +
289B LEU* 4.6 19.7 - - + -
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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