Contacts of the helix formed by residues 300 - 304 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C TRP* 4.9 14.1 - - - -
233C GLU* 5.7 3.1 - - - +
235C ILE* 5.6 9.2 - - + +
256C PHE* 5.8 0.9 - - + -
298C ASN* 2.9 16.8 + - - +
299C HIS* 1.3 95.0 - - + +
301C ASN* 1.3 61.2 + - + +
303C ARG* 3.1 27.7 + - - +
305C HIS* 4.9 2.3 + - - -
306C GLY* 3.3 23.1 + - - -
307C ALA 5.5 1.3 - - - -
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Residues in contact with ASN 301 (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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256C PHE* 3.6 20.0 - - + -
295C PHE* 4.4 3.2 - - - -
297C ASP* 3.2 14.1 - - - +
298C ASN* 2.7 55.8 + - - +
300C ASP* 1.3 74.2 + - + +
302C GLN* 1.3 56.3 + - - -
303C ARG 2.8 11.2 + - - -
304C GLY* 3.2 12.7 + - - -
306C GLY* 4.0 17.0 - - - +
307C ALA 3.4 24.8 + - - +
309C GLY 4.5 1.2 - - - +
312C ILE* 3.4 26.5 - - + +
314C THR* 5.0 0.2 - - - +
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Residues in contact with GLN 302 (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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17C PHE* 4.8 0.7 - - - -
297C ASP* 3.1 25.7 + - - +
298C ASN 3.2 13.4 + - - +
299C HIS 3.9 0.9 - - - +
300C ASP 3.1 1.4 + - - -
301C ASN* 1.3 80.8 + - - +
303C ARG* 1.3 89.8 + - + +
304C GLY 3.4 2.3 + - - -
312C ILE* 4.4 0.4 - - - -
314C THR* 3.4 26.9 + - + +
315C PHE* 4.1 15.0 - - - -
316C TRP* 4.7 2.8 - - - -
339C MET* 3.6 20.9 - - - +
341C SER* 3.5 32.8 + - - -
344C TRP* 3.9 16.2 - - + -
346C ARG* 5.6 1.6 + - - -
385C GLU* 4.6 0.4 + - - -
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Residues in contact with ARG 303 (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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17C PHE* 4.0 8.4 - - - -
58C TRP* 3.7 18.1 - - - +
299C HIS 3.3 15.5 + - - -
300C ASP 3.1 10.7 + - - +
301C ASN 2.8 1.6 - - - -
302C GLN* 1.3 111.9 + - - +
304C GLY* 1.3 57.2 + - - +
305C HIS* 3.6 16.2 + - + -
342C TYR* 3.0 46.4 + - - +
344C TRP* 3.6 35.5 - - + -
346C ARG* 6.5 0.4 - - - -
348C PHE* 4.9 2.9 - - - -
353C ASP* 4.1 20.0 - - - +
356C ASP* 3.1 40.3 + - + +
358C ILE 4.3 1.6 + - - -
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Residues in contact with GLY 304 (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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301C ASN 3.2 9.6 + - - -
302C GLN 3.4 2.8 + - - -
303C ARG* 1.3 77.4 - - - +
305C HIS* 1.3 61.0 + - - +
306C GLY 3.8 1.6 - - - -
309C GLY* 3.5 26.9 - - - -
310C SER* 3.8 7.4 + - - -
348C PHE* 5.3 8.1 - - - -
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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