Contacts of the helix formed by residues 283 - 289 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258C GLU* 6.1 0.4 - - - +
283C LEU* 6.6 0.2 - - + -
80D VAL* 4.0 26.2 - - + -
254D HIS* 3.6 41.3 - - + +
281D ASP* 3.5 16.5 + - + -
282D ASN* 1.3 86.0 + - - +
284D PRO* 1.3 76.5 - - + +
285D TRP* 3.0 32.7 + - + +
286D MET* 3.0 29.1 + - + +
287D ALA* 4.0 1.4 + - - +
333D HIS* 5.5 0.3 + - - -
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Residues in contact with PRO 284 (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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255C ARG* 6.1 1.3 - - - +
258C GLU* 3.5 42.6 - - + +
262C GLN* 4.8 8.3 - - - +
282D ASN* 4.0 5.6 - - - +
283D LEU* 1.3 92.5 - - + +
285D TRP* 1.3 61.0 + - + +
287D ALA* 3.0 18.2 + - + +
288D PHE* 3.4 19.9 - - + -
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Residues in contact with TRP 285 (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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258C GLU* 5.4 2.0 - - - +
285C TRP* 3.2 66.2 - + + +
288C PHE* 3.9 26.0 - + - -
254D HIS* 4.5 5.1 + - + +
257D THR* 4.2 21.1 - - + -
258D GLU* 4.2 24.4 + - + -
261D MET* 4.6 3.8 - - + -
283D LEU* 3.0 31.5 + - + +
284D PRO* 1.3 74.6 - - + +
286D MET* 1.3 80.2 + - + +
287D ALA 3.0 4.7 - - - -
288D PHE* 2.7 42.1 + - + +
289D LEU* 3.6 32.4 + - + +
293D LEU* 4.8 0.9 - - + -
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Residues in contact with MET 286 (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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254D HIS* 3.7 25.8 - - + -
257D THR* 4.4 3.8 - - + -
279D SER* 3.6 21.1 - - - +
281D ASP 3.3 13.9 - - - +
283D LEU* 3.0 22.0 + - + +
285D TRP* 1.3 108.8 - - + +
287D ALA* 1.3 59.5 + - - +
288D PHE 3.4 0.7 + - - -
289D LEU* 3.7 9.1 + - - +
292D PRO* 3.6 1.7 - - - +
293D LEU* 2.8 50.2 + - + +
295D VAL* 3.2 30.5 - - - -
333D HIS* 4.7 4.0 - - + -
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Residues in contact with ALA 287 (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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265C ASN* 4.7 6.2 - - - +
283D LEU 4.0 0.8 + - - +
284D PRO* 3.0 13.8 + - + +
285D TRP 2.9 1.8 + - - -
286D MET* 1.3 79.5 - - - +
288D PHE* 1.3 64.8 + - + +
289D LEU 3.3 1.7 - - - +
292D PRO* 4.0 20.7 - - + +
333D HIS* 3.8 30.2 - - + +
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Residues in contact with PHE 288 (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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258C GLU* 3.5 42.4 - - + -
261C MET* 3.8 46.9 - - + +
262C GLN* 4.1 18.6 - - + -
265C ASN* 5.0 10.5 - - - +
285C TRP* 3.9 25.6 - + - -
289C LEU* 5.5 5.3 - - + +
284D PRO* 3.4 18.2 - - + -
285D TRP* 2.7 37.1 + - + +
287D ALA* 1.3 76.4 - - + +
289D LEU* 1.3 69.4 + - + +
290D ASP* 5.4 0.3 - - - +
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Residues in contact with LEU 289 (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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288C PHE* 5.3 7.0 - - + +
289C LEU* 4.6 18.8 - - + -
261D MET* 4.3 19.7 - - + -
271D TYR* 3.8 12.8 - - + -
285D TRP* 3.6 39.3 - - + +
286D MET* 4.0 12.3 - - - +
287D ALA 3.3 1.7 - - - +
288D PHE* 1.3 86.6 - - + +
290D ASP* 1.3 60.0 + - - +
291D PRO 3.4 12.3 - - - +
292D PRO* 3.0 24.1 - - - +
293D LEU* 3.9 22.9 - - + -
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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