Contacts of the helix formed by residues 285 - 290 (chain I) in PDB entry 3KDO
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 HIS 285 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E ASN* 6.2 1.6 - - - -
114E GLY* 5.9 1.3 - - - -
257I VAL* 3.9 14.5 - - + +
282I ARG* 2.9 78.6 + - + +
283I ALA* 3.3 0.8 + - - -
284I MET* 1.3 73.8 + - - +
286I ALA* 1.3 75.1 + - + +
287I ALA 2.8 11.9 + - - -
288I PHE* 2.8 27.3 + - - -
289I THR* 2.6 55.6 + - + +
298I MET* 4.4 3.6 - - + -
301I LEU* 4.3 5.2 - - + -
323I LEU* 6.2 1.1 - - + -
600I CAP 4.3 5.6 - - - -
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Residues in contact with ALA 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E GLY 5.5 1.1 - - - +
111E ASN* 5.2 0.9 - - - +
113E PHE* 3.5 10.3 - - + +
114E GLY* 3.5 36.1 - - - +
294E HIS* 2.9 20.4 + - - -
284I MET 3.3 1.2 - - - -
285I HIS* 1.3 94.4 + - + +
287I ALA* 1.3 59.4 + - - +
288I PHE 3.1 1.2 + - - -
289I THR* 3.4 12.1 - - - +
290I ARG* 3.4 17.1 - - + +
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Residues in contact with ALA 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E PHE* 3.8 25.2 - - + +
287E ALA 4.1 1.0 - - - +
288E PHE* 3.5 27.8 - - + +
294E HIS* 3.9 19.4 - - - +
295E GLY* 4.0 12.0 - - - -
296E ILE* 4.4 11.2 - - + -
284I MET* 3.1 17.3 + - + +
285I HIS 2.8 1.0 + - - -
286I ALA* 1.3 77.8 - - - +
288I PHE* 1.3 59.8 + - + +
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Residues in contact with PHE 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E MET* 6.4 2.9 - - - -
287E ALA* 3.5 34.1 - - + +
288E PHE* 4.0 20.0 - + + -
122I ARG* 5.0 0.2 + - - -
257I VAL* 4.1 18.8 - - + -
261I TRP* 6.4 0.7 - + - -
284I MET* 4.2 8.7 - - + -
285I HIS* 2.8 20.9 + - - -
287I ALA* 1.3 82.6 - - + +
289I THR* 1.3 77.7 + - + +
290I ARG 3.6 1.6 - - - -
291I ASN* 5.0 1.5 - - - +
294I HIS 3.9 5.4 - - - +
295I GLY* 3.4 7.0 - - - -
296I ILE* 2.9 51.7 + - + -
301I LEU* 3.7 24.9 - - + -
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Residues in contact with THR 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I ARG* 2.9 24.8 + - - -
285I HIS* 2.6 48.7 + - + +
286I ALA* 3.4 2.8 - - - +
288I PHE* 1.3 95.0 - - + +
290I ARG* 1.3 62.7 + - - +
291I ASN 3.6 1.6 - - - -
296I ILE 3.2 21.3 - - - +
298I MET* 4.0 17.0 + - - +
301I LEU* 3.9 13.0 - - + -
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Residues in contact with ARG 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E PHE 2.8 36.8 + - - -
114E GLY* 3.5 8.9 - - - -
115E MET 3.1 22.4 + - - +
116E LYS* 4.1 7.1 + - - +
118E VAL* 2.9 27.2 + - - +
119E LYS* 4.6 11.7 + - - +
294E HIS* 4.1 13.9 - - + +
122I ARG* 4.7 0.9 + - - -
286I ALA* 3.4 21.4 + - + +
288I PHE 3.6 0.4 - - - -
289I THR* 1.3 80.7 + - - +
291I ASN* 1.3 65.5 + - - +
292I PRO* 3.3 10.4 - - - +
324I GLU* 3.9 49.3 - - - +
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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