Contacts of the helix formed by residues 330 - 344 (chain C) 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 330 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329C TYR* 3.8 28.9 - - - +
331C VAL* 3.8 29.8 - - - +
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Residues in contact with VAL 331 (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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330C ARG* 3.8 28.9 - - - +
332C GLU* 3.8 27.8 - - - +
334C CYS* 4.4 12.8 - - - +
357C ALA* 4.4 23.3 - - - +
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Residues in contact with GLU 332 (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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331C VAL* 3.8 26.2 - - - +
333C THR* 3.7 29.4 - - - +
335C CYS* 4.5 13.5 - - - +
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Residues in contact with THR 333 (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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332C GLU* 3.7 26.7 - - - +
334C CYS* 3.7 29.8 - - - +
336C VAL* 4.2 18.8 - - - +
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Residues in contact with CYS 334 (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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331C VAL* 4.4 16.2 - - - +
333C THR* 3.7 30.1 - - - +
335C CYS* 3.8 23.3 - - - +
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Residues in contact with CYS 335 (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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332C GLU* 4.5 16.6 - - - +
334C CYS* 3.8 25.6 - - - +
336C VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 336 (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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333C THR* 4.2 17.3 - - - +
335C CYS* 3.8 29.4 - - - +
337C ILE* 3.8 25.1 - - - +
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Residues in contact with ILE 337 (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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336C VAL* 3.8 27.4 - - - +
338C GLY* 3.8 30.3 - - - +
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Residues in contact with GLY 338 (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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337C ILE* 3.8 29.6 - - - +
339C ASN* 3.8 26.0 - - - +
341C TYR* 4.5 14.8 - - - +
350C ALA* 4.1 26.0 - - - +
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Residues in contact with ASN 339 (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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338C GLY* 3.8 23.6 - - - +
340C TYR* 3.7 30.1 - - - +
342C SER* 4.4 15.0 - - - +
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Residues in contact with TYR 340 (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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339C ASN* 3.7 29.4 - - - +
341C TYR* 3.8 26.0 - - - +
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Residues in contact with TYR 341 (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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338C GLY* 4.5 12.6 - - - +
340C TYR* 3.8 26.0 - - - +
342C SER* 3.8 29.4 - - - +
344C ARG* 4.0 22.7 - - - +
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Residues in contact with SER 342 (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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339C ASN* 4.4 19.5 - - - +
341C TYR* 3.8 25.6 - - - +
343C LEU* 3.7 29.8 - - - +
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Residues in contact with LEU 343 (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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342C SER* 3.7 29.4 - - - +
344C ARG* 3.8 26.0 - - - +
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Residues in contact with ARG 344 (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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341C TYR* 4.0 19.1 - - - +
343C LEU* 3.8 24.2 - - - +
345C SER* 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