Contacts of the helix formed by residues 300 - 304 (chain E) in PDB entry 1KXT
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 ASP 300 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58E TRP* 4.0 22.5 - - - -
233E GLU* 5.7 3.9 - - - +
235E ILE* 6.0 4.3 - - - +
298E ASN* 2.8 18.6 + - - +
299E HIS* 1.3 92.3 - - + +
301E ASN* 1.3 64.0 + - - +
302E GLN 3.2 1.8 - - - -
303E ARG* 3.3 21.3 + - - +
305E HIS 5.3 0.7 - - - +
306E GLY* 4.5 12.0 - - - -
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Residues in contact with ASN 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E PHE* 4.1 14.3 - - + -
295E PHE* 4.3 5.5 - - - -
296E VAL 4.9 1.0 + - - -
297E ASP* 3.4 10.0 - - - +
298E ASN* 2.6 49.6 + - - +
300E ASP* 1.3 71.0 + - + +
302E GLN* 1.3 58.7 + - - +
303E ARG 2.8 9.8 + - - -
304E GLY* 3.5 14.5 + - - +
306E GLY* 3.5 10.1 - - - -
307E ALA* 3.2 27.0 + - + +
309E GLY 4.9 0.7 - - - +
312E ILE* 3.0 42.2 - - + +
314E THR* 5.0 0.3 - - - +
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Residues in contact with GLN 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E PHE* 4.7 0.2 - - - -
297E ASP* 3.0 29.0 + - - +
298E ASN 3.0 11.3 + - - +
299E HIS 3.6 1.1 - - - +
301E ASN* 1.3 82.2 + - - +
303E ARG* 1.3 86.9 + - + +
304E GLY 3.5 3.4 + - - -
314E THR* 3.7 23.3 - - + +
315E PHE* 4.1 17.2 - - + -
316E TRP* 4.5 7.6 - - - -
339E MET* 3.6 21.2 - - - +
341E SER* 3.5 33.5 + - - -
344E TRP* 4.0 13.6 - - + -
346E ARG* 5.5 1.4 + - - -
385E GLU* 4.6 0.2 + - - -
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Residues in contact with ARG 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E PHE* 3.8 13.1 - - - -
58E TRP* 3.3 27.6 - - + +
299E HIS 3.1 17.9 + - - +
300E ASP 3.5 11.9 - - - +
301E ASN 2.8 2.4 - - - -
302E GLN* 1.3 103.0 + - - +
304E GLY* 1.3 58.2 + - - +
305E HIS* 3.6 11.1 + - + -
306E GLY 5.2 0.2 - - - -
342E TYR* 3.5 32.1 + - - -
344E TRP* 3.5 45.7 - - + -
353E ASP* 5.4 4.6 - - - +
356E ASP* 3.0 50.1 + - + +
358E ILE 4.1 2.6 + - - -
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Residues in contact with GLY 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301E ASN 3.5 10.9 + - - +
302E GLN 3.5 2.8 + - - -
303E ARG* 1.3 74.8 - - - +
305E HIS* 1.3 52.6 + - - -
306E GLY* 2.4 23.8 + - - -
309E GLY 4.0 18.2 - - - +
310E SER* 6.1 1.1 - - - -
348E PHE* 6.2 4.5 - - - -
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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