Contacts of the helix formed by residues 332 - 345 (chain C) in PDB entry 5DO7
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 SER 332 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C PHE* 4.0 16.2 - - - -
286C ASP* 4.2 11.6 + - - -
328C ALA 3.4 11.4 + - - -
329C TYR 2.8 18.5 + - - -
331C LYS* 1.3 75.9 - - - +
333C ALA* 1.3 78.5 + - - +
334C ILE* 3.2 14.3 + - - +
335C CYS* 2.8 22.2 + - - +
336C HIS* 2.8 10.6 + - - -
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Residues in contact with ALA 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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331C LYS 3.8 0.6 + - - -
332C SER* 1.3 75.3 + - - +
334C ILE* 1.3 65.1 + - + +
336C HIS* 2.9 11.7 + - - +
337C LYS* 2.8 22.9 + - - +
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Residues in contact with ILE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C PHE* 4.0 12.8 - - + -
274C CYS 4.0 17.0 - - - +
279C GLU* 3.1 41.7 - - + +
283C PHE* 3.9 32.5 - - + -
329C TYR* 5.0 0.4 - - + -
332C SER* 3.2 6.1 + - - +
333C ALA* 1.3 78.6 - - + +
335C CYS* 1.3 64.0 - - - +
337C LYS* 2.9 10.1 + - + +
338C THR* 2.8 41.5 + - + -
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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
----------------------------------------------------------
283C PHE* 4.8 0.4 - - - -
329C TYR* 2.4 90.3 + - + +
330C LYS* 4.1 10.1 - - - +
332C SER* 2.8 14.8 + - - +
334C ILE* 1.3 74.1 - - - +
336C HIS* 1.3 67.7 + - - +
338C THR* 3.6 5.8 + - - -
339C LEU* 3.5 15.6 - - - +
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Residues in contact with HIS 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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330C LYS 5.1 0.8 + - - -
331C LYS 4.8 4.4 + - - +
332C SER 2.8 11.2 + - - +
333C ALA* 2.9 12.7 + - - +
335C CYS* 1.3 75.1 - - - +
337C LYS* 1.3 65.4 + - - +
339C LEU* 2.8 32.4 + - + +
340C LYS* 3.0 47.7 + - + -
343C GLU* 5.8 0.2 - - - -
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Residues in contact with LYS 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TYR* 5.3 3.6 - - - -
262C LYS* 5.5 5.1 - - - +
279C GLU* 5.6 5.4 - - - +
333C ALA 2.8 15.2 + - - +
334C ILE* 2.9 13.6 + - - +
336C HIS* 1.3 71.1 - - - +
338C THR* 1.3 76.4 + - + +
340C LYS* 2.8 19.9 + - - +
341C ASN* 2.8 55.2 + - - +
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Residues in contact with THR 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C SER 5.3 3.1 + - - -
74C LEU* 5.3 3.9 - - - +
75C TYR* 4.0 13.4 - - - +
262C LYS* 3.3 33.0 - - - +
274C CYS* 4.7 9.6 - - - +
275C GLY* 5.9 0.2 - - - -
279C GLU* 5.5 1.1 - - - +
329C TYR* 3.8 13.1 + - - +
334C ILE* 2.8 36.9 + - + +
335C CYS 3.6 7.1 + - - -
337C LYS* 1.3 82.5 - - + +
339C LEU* 1.3 67.5 + - - +
341C ASN* 2.8 21.7 + - - +
342C ILE* 3.2 9.3 + - - +
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Residues in contact with LEU 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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41C LEU* 3.8 30.3 - - + -
42C HIS* 4.4 13.0 - - + +
73C SER* 5.1 13.5 - - - +
74C LEU* 6.4 0.9 - - - +
335C CYS 3.5 11.4 - - - +
336C HIS* 2.8 30.9 + - + +
338C THR* 1.3 81.0 + - - +
340C LYS* 1.3 63.6 + - - +
342C ILE* 2.7 31.7 + - - +
343C GLU* 3.0 30.0 + - - +
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Residues in contact with LYS 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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336C HIS* 3.0 43.6 + - + +
337C LYS* 2.8 17.3 + - - +
339C LEU* 1.3 73.2 - - - +
341C ASN* 1.3 59.7 + - - +
343C GLU* 2.8 26.2 + - + +
344C ARG* 2.8 58.2 + - + +
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Residues in contact with ASN 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TYR* 3.3 48.1 + - + -
337C LYS* 2.8 59.1 - - - +
338C THR* 2.8 8.9 + - - +
340C LYS* 1.3 78.3 - - - +
342C ILE* 1.3 60.3 + - - +
344C ARG* 3.9 13.0 + - - +
345C MET* 3.4 16.1 + - - +
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Residues in contact with ILE 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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39C GLY* 3.6 18.4 - - - -
40C ILE 3.9 10.5 - - - +
41C LEU* 3.5 43.3 - - + +
73C SER* 5.8 0.4 - - - -
74C LEU* 3.5 28.0 - - - +
75C TYR* 3.8 19.3 - - + -
114C TYR* 4.6 20.0 - - + +
338C THR 3.2 4.1 + - - +
339C LEU* 2.7 29.2 + - - +
341C ASN* 1.3 75.8 - - - +
343C GLU* 1.3 68.6 + - + +
345C MET* 3.6 12.2 + - - +
346C LYS* 3.7 13.0 + - - +
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Residues in contact with GLU 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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41C LEU* 5.6 5.5 - - + +
336C HIS* 5.8 0.2 - - - -
339C LEU* 3.0 38.3 + - + +
340C LYS* 2.8 24.9 + - + +
342C ILE* 1.3 83.3 - - + +
344C ARG* 1.3 57.8 + - + +
345C MET 3.2 0.2 - - - -
346C LYS* 2.8 60.7 + - + +
347C HIS* 4.1 5.2 + - - -
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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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340C LYS* 2.8 52.3 + - + +
341C ASN* 3.9 12.2 + - - +
342C ILE 3.4 0.4 - - - -
343C GLU* 1.3 73.5 - - + +
345C MET* 1.3 60.7 + - + +
346C LYS 3.1 0.2 - - - -
347C HIS* 3.1 34.7 + - + +
348C LEU 3.9 2.9 + - - -
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Residues in contact with MET 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C SER* 3.3 41.1 - - - +
75C TYR* 3.6 33.2 - - + +
114C TYR* 5.5 9.2 - - + +
116C ASN* 4.4 2.2 - - - +
117C GLY* 3.2 41.1 - - - +
341C ASN 3.4 2.1 + - - +
342C ILE* 3.8 12.1 - - - +
343C GLU 3.2 0.4 - - - -
344C ARG* 1.3 77.7 - - + +
346C LYS* 1.3 63.3 + - - +
347C HIS 3.1 0.9 - - - -
348C LEU* 4.0 31.7 + - + +
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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