Contacts of the helix formed by residues 283 - 290 (chain A) in PDB entry 1DKF
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 THR 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A VAL* 2.9 42.2 + - - +
279A LYS* 3.6 13.7 + - + +
280A GLN* 3.1 19.1 + - - +
282A PHE* 1.3 82.2 - - + +
284A LEU* 1.3 58.3 + - - +
285A VAL 3.3 3.1 - - - -
286A GLU* 3.4 12.2 + - + +
287A TRP 3.0 13.3 + - - -
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Residues in contact with LEU 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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247A VAL* 5.0 0.2 - - - -
280A GLN 3.1 10.5 + - - +
281A LEU* 3.4 22.2 + - + +
283A THR* 1.3 76.4 - - - +
285A VAL* 1.3 61.6 + - + +
287A TRP* 3.3 27.7 + - + -
288A ALA* 2.9 26.9 + - - +
306A LEU* 4.1 15.3 - - + -
310A TRP* 3.6 36.8 - - + -
313A LEU* 4.0 15.0 - - + -
314A LEU* 4.1 19.5 - - + -
376A ARG* 4.5 8.7 - - - +
456A LEU* 5.6 5.2 - - + -
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Residues in contact with VAL 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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281A LEU 4.6 2.5 + - - +
282A PHE 4.8 0.4 + - - -
283A THR 3.3 0.2 - - - -
284A LEU* 1.3 73.9 - - - +
286A GLU* 1.3 69.7 + - - +
288A ALA* 3.4 6.4 + - - +
289A LYS* 2.9 43.3 + - + +
306A LEU* 4.0 4.3 - - + -
456A LEU* 3.9 22.2 - - + -
459A MET* 3.6 48.5 - - + +
460A LEU* 3.6 33.2 - - + +
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Residues in contact with GLU 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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247A VAL* 4.7 4.9 - - + -
282A PHE 5.3 0.6 + - - +
283A THR* 3.4 18.9 + - + +
285A VAL* 1.3 83.9 - - - +
287A TRP* 1.3 67.5 + - - +
289A LYS* 3.0 42.8 + - - +
290A ARG* 3.2 38.1 + - - +
459A MET* 5.9 2.0 - - - +
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Residues in contact with TRP 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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243A ALA* 3.3 41.9 - - + +
244A GLU* 3.2 19.2 + - - -
247A VAL* 3.9 17.6 - - + +
283A THR 3.0 11.2 + - - +
284A LEU* 3.4 28.7 - - + +
286A GLU* 1.3 78.5 - - - +
288A ALA* 1.3 81.5 + - + +
290A ARG* 3.0 23.8 + - - +
291A ILE* 3.6 27.2 + - + +
313A LEU* 3.8 27.1 - - + -
373A GLY 4.7 0.4 - - - -
376A ARG* 3.2 50.2 - - + +
377A ALA* 4.2 3.1 - - - -
380A LEU* 3.9 26.5 - - + -
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Residues in contact with ALA 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 LEU 2.9 19.5 + - - +
285A VAL* 3.8 5.6 - - - +
287A TRP* 1.3 94.9 - - + +
289A LYS* 1.3 57.3 + - - +
291A ILE* 2.9 26.9 + - - +
294A PHE* 3.2 39.4 - - + +
306A LEU* 4.2 12.6 - - + -
380A LEU* 4.3 3.4 - - + -
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Residues in contact with LYS 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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285A VAL* 2.9 33.2 + - + +
286A GLU* 3.0 43.5 + - - +
288A ALA* 1.3 76.8 - - - +
290A ARG* 1.3 61.0 + - + +
291A ILE 3.5 4.9 + - - +
294A PHE* 3.9 5.8 - - + -
295A SER* 3.1 30.4 + - - +
302A GLN* 5.6 1.6 - - - +
459A MET 5.1 4.6 + - - -
460A LEU* 5.0 9.8 + - + -
462A ALA* 5.6 3.6 + - - -
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Residues in contact with ARG 290 (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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239A LYS* 3.4 17.3 - - - +
242A GLU* 5.2 10.8 + - + +
243A ALA* 3.6 15.8 - - + +
246A ALA* 3.7 32.8 - - - +
286A GLU* 3.2 38.0 + - - +
287A TRP* 3.0 9.0 + - - +
289A LYS* 1.3 75.9 - - + +
291A ILE* 1.3 59.7 + - - +
292A PRO* 3.2 12.5 - - - +
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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