Contacts of the helix formed by residues 285 - 290 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A VAL* 4.1 10.2 - - + +
282A ARG* 2.7 86.5 + - + +
283A ALA* 3.4 0.6 - - - -
284A MET* 1.3 74.7 - - - +
286A ALA* 1.3 72.6 + - + +
287A ALA 2.5 17.8 + - - -
288A PHE* 2.7 27.9 + - - -
289A THR* 2.6 44.2 + - + +
298A MET* 4.7 2.9 - - + -
301A LEU* 4.4 5.8 - - + -
324A GLU 6.0 1.8 - - - -
600A CAP 4.2 7.1 + - - -
111H ASN* 6.0 1.8 - - - -
114H GLY* 5.8 1.5 - - - -
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Residues in contact with ALA 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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284A MET 3.4 0.8 - - - +
285A HIS* 1.3 95.5 + - + +
287A ALA* 1.3 51.4 + - - +
288A PHE 3.1 2.4 + - - -
289A THR* 3.1 12.3 - - - -
290A ARG* 3.3 18.7 - - + +
110H GLY 5.6 1.3 - - - +
111H ASN 5.4 0.4 - - - +
113H PHE* 3.7 6.1 - - + +
114H GLY* 3.5 37.2 - - - +
294H HIS* 2.7 27.8 + - - -
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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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284A MET* 3.2 21.4 + - + +
285A HIS 2.5 7.3 + - - -
286A ALA* 1.3 74.9 - - - +
288A PHE* 1.3 58.4 + - + -
113H PHE* 3.7 30.0 - - + +
287H ALA 4.1 0.5 - - - +
288H PHE* 3.3 23.4 - - + +
294H HIS* 3.9 14.8 - - - -
295H GLY* 3.6 18.2 - - - -
296H ILE* 4.6 5.2 - - + -
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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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122A ARG* 4.7 0.2 + - - -
257A VAL* 4.1 21.5 - - + -
284A MET* 4.0 14.1 - - + -
285A HIS* 2.7 11.9 + - - -
287A ALA* 1.3 78.6 - - + +
289A THR* 1.3 83.2 + - + +
290A ARG 3.6 1.6 - - - -
291A ASN* 5.0 2.9 - - - +
294A HIS 3.7 6.7 - - - +
295A GLY* 3.4 5.8 - - - -
296A ILE* 2.8 50.2 + - + +
301A LEU* 3.8 23.3 - - + -
284H MET* 6.5 1.6 - - - -
287H ALA* 3.2 34.3 - - + +
288H PHE* 4.0 20.6 - + + -
294H HIS* 5.7 0.2 - - - -
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Residues in contact with THR 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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122A ARG* 3.8 15.2 + - - -
285A HIS* 2.6 38.8 + - + +
286A ALA* 3.1 2.6 - - - -
288A PHE* 1.3 104.7 - - + +
290A ARG* 1.3 63.0 + - - +
291A ASN 3.6 0.7 - - - -
296A ILE 3.0 20.9 - - - +
298A MET* 4.0 24.6 + - - +
301A LEU* 4.0 12.6 - - + -
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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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122A ARG* 5.7 0.2 - - - -
286A ALA* 3.3 19.8 + - + +
288A PHE 3.6 0.2 - - - -
289A THR* 1.3 81.5 + - - +
291A ASN* 1.3 64.8 + - - +
292A PRO* 3.3 12.0 - - - +
324A GLU* 3.4 47.5 - - + +
113H PHE 2.9 28.4 + - - -
114H GLY* 3.6 7.4 - - - -
115H MET 3.0 29.6 + - - +
116H LYS* 3.6 14.5 + - - +
118H VAL* 3.1 22.5 + - - +
119H LYS* 5.0 7.7 + - - +
294H HIS* 4.0 14.2 - - + +
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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