Contacts of the helix formed by residues 285 - 290 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C VAL* 4.1 13.2 - - + +
282C ARG* 3.0 78.0 + - + +
283C ALA* 3.2 1.7 + - - -
284C MET* 1.3 78.2 - - - +
286C ALA* 1.3 76.9 + - + +
287C ALA 3.0 5.6 + - - -
288C PHE* 3.0 24.3 + - - -
289C THR* 2.7 51.1 + - + +
298C MET* 4.3 2.7 - - + -
301C LEU* 4.3 6.3 - - + -
324C GLU 5.9 2.9 - - - -
600C CAP 4.5 5.4 + - - -
111F ASN* 6.0 2.7 - - - -
114F GLY* 5.8 2.0 - - - -
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C MET 3.2 1.4 + - - +
285C HIS* 1.3 92.2 - - + +
287C ALA* 1.3 59.9 + - - +
288C PHE 3.1 1.6 + - - -
289C THR* 3.5 11.7 - - - -
290C ARG* 3.5 18.4 + - + +
110F GLY 5.5 0.9 - - - +
111F ASN* 5.4 0.4 - - - +
113F PHE* 3.3 35.2 - - + +
114F GLY* 3.6 11.0 - - - +
294F HIS* 2.8 22.1 + - - -
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Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C MET* 3.0 20.5 + - + +
285C HIS 3.0 0.2 + - - -
286C ALA* 1.3 79.5 - - - +
288C PHE* 1.3 60.1 + - + +
113F PHE* 3.7 24.8 - - + +
287F ALA 4.1 1.0 - - - +
288F PHE* 3.5 28.2 - - + +
294F HIS* 3.9 14.3 - - - +
295F GLY* 3.8 17.8 - - - -
296F ILE* 4.5 7.6 - - + -
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Residues in contact with PHE 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG* 5.3 0.2 - - - -
257C VAL* 4.0 25.1 - - + -
261C TRP* 6.4 0.9 - + - -
284C MET* 4.3 9.2 - - + -
285C HIS* 3.0 10.3 + - - -
287C ALA* 1.3 83.2 - - + +
289C THR* 1.3 78.7 + - + +
290C ARG 3.6 1.6 - - - -
291C ASN* 5.0 1.7 - - - +
294C HIS 3.8 5.4 - - - +
295C GLY* 3.5 6.9 - - - -
296C ILE* 3.0 48.1 + - + -
301C LEU* 3.8 25.6 - - + -
284F MET* 6.1 4.7 - - - -
287F ALA* 3.4 29.8 - - + +
288F PHE* 3.9 23.3 - + + -
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Residues in contact with THR 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG* 2.9 24.7 + - - -
285C HIS* 2.7 48.0 + - - +
286C ALA* 3.5 1.2 - - - -
288C PHE* 1.3 94.3 - - + +
290C ARG* 1.3 62.9 + - - +
291C ASN 3.4 2.0 - - - -
296C ILE 3.1 21.5 - - - +
298C MET* 3.9 19.8 + - - +
301C LEU* 4.0 13.2 - - + -
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Residues in contact with ARG 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG* 4.7 0.7 + - - -
285C HIS* 6.3 0.2 - - + -
286C ALA* 3.5 20.1 + - + +
288C PHE 3.6 0.6 - - - -
289C THR* 1.3 81.8 + - - +
291C ASN* 1.3 58.9 + - - +
292C PRO* 3.1 14.0 - - - +
324C GLU* 3.7 52.1 - - - +
113F PHE 3.1 26.2 + - - -
114F GLY* 3.9 4.9 - - - -
115F MET 3.1 23.7 + - - -
116F LYS* 4.1 6.3 + - - +
118F VAL* 2.8 32.5 + - - +
119F LYS* 4.5 11.4 + - - +
294F HIS* 4.1 17.3 - - + +
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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