Contacts of the helix formed by residues 298 - 314 (chain O) in PDB entry 5KHU
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 ARG 298 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299O SER* 3.7 30.1 - - - +
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Residues in contact with SER 299 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298O ARG* 3.7 29.8 - - - +
300O LEU* 3.8 28.0 - - - +
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Residues in contact with LEU 300 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299O SER* 3.8 26.5 - - - +
301O ARG* 3.8 29.4 - - - +
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Residues in contact with ARG 301 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300O LEU* 3.8 26.7 - - - +
302O TYR* 3.8 29.8 - - - +
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Residues in contact with TYR 302 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301O ARG* 3.8 29.8 - - - +
303O ALA* 3.8 26.0 - - - +
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Residues in contact with ALA 303 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302O TYR* 3.8 26.9 - - - +
304O ALA* 3.8 29.8 - - - +
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Residues in contact with ALA 304 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303O ALA* 3.8 26.0 - - - +
305O LEU* 3.7 28.9 - - - +
307O LEU* 4.4 17.0 - - - +
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Residues in contact with LEU 305 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304O ALA* 3.7 26.2 - - - +
306O ASN* 3.7 28.9 - - - +
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Residues in contact with ASN 306 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305O LEU* 3.7 29.6 - - - +
307O LEU* 3.8 25.8 - - - +
309O ALA* 4.3 18.6 - - - +
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Residues in contact with LEU 307 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304O ALA* 4.4 17.7 - - - +
306O ASN* 3.8 24.9 - - - +
308O ALA* 3.7 30.1 - - - +
310O LEU* 4.7 12.6 - - - +
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Residues in contact with ALA 308 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307O LEU* 3.7 29.8 - - - +
309O ALA* 3.8 26.0 - - - +
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Residues in contact with ALA 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306O ASN* 4.3 15.9 - - - +
308O ALA* 3.8 24.9 - - - +
310O LEU* 3.7 28.7 - - - +
312O CYS* 4.4 17.9 - - - +
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Residues in contact with LEU 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307O LEU* 4.7 16.8 - - - +
309O ALA* 3.7 29.8 - - - +
311O HIS* 3.8 26.7 - - - +
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Residues in contact with HIS 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310O LEU* 3.8 29.2 - - - +
312O CYS* 3.8 24.9 - - - +
314O PHE* 4.5 16.8 - - - +
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Residues in contact with CYS 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309O ALA* 4.4 19.1 - - - +
311O HIS* 3.8 26.9 - - - +
313O ARG* 3.8 28.3 - - - +
315O GLY* 4.1 19.1 - - - +
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Residues in contact with ARG 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312O CYS* 3.8 23.6 - - - +
314O PHE* 3.8 29.4 - - - +
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Residues in contact with PHE 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311O HIS* 4.5 16.6 - - - +
313O ARG* 3.8 26.2 - - - +
315O GLY* 3.7 28.7 - - - +
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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