Contacts of the helix formed by residues 333 - 347 (chain C) in PDB entry 4DVQ
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 ASN 333 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329C GLU* 2.6 46.4 + - - +
330C LEU* 3.2 6.5 + - - +
332C ARG* 1.3 84.6 + - - +
334C PRO* 1.3 65.8 - - - +
335C ASP* 3.1 3.4 - - - -
336C VAL* 2.9 29.8 + - + +
337C GLN 3.0 9.0 + - - -
422C ARG* 5.9 2.6 - - - +
423C TYR* 3.7 27.8 + - + +
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Residues in contact with PRO 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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280A PHE* 6.2 4.3 - - + -
330C LEU 3.8 6.3 - - - +
331C ALA 4.1 8.3 - - - +
332C ARG 3.5 9.4 - - - +
333C ASN* 1.3 87.6 - - - +
335C ASP* 1.3 62.8 + - - +
337C GLN* 3.5 9.5 + - + +
338C GLN* 3.0 28.4 + - - +
341C ARG* 5.1 1.6 + - - -
478C GLN* 5.2 4.9 - - - +
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Residues in contact with ASP 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ASN 3.1 1.2 - - - -
334C PRO* 1.3 79.8 - - - +
336C VAL* 1.3 68.9 + - + +
338C GLN* 3.3 6.0 + - - +
339C ILE* 3.1 31.6 + - + +
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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
----------------------------------------------------------
330C LEU* 4.0 16.8 - - + -
333C ASN* 2.9 23.2 + - + +
335C ASP* 1.3 78.0 - - + +
337C GLN* 1.3 64.1 + - - +
339C ILE* 3.3 14.5 + - + +
340C LEU* 3.1 24.7 + - + +
423C TYR* 3.7 25.4 - - + +
424C ASN* 5.2 2.5 - - - +
425C PRO* 3.6 32.5 - - + -
426C GLN* 5.7 2.5 - - - +
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Residues in contact with GLN 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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330C LEU* 3.0 45.6 - - + +
331C ALA* 4.0 0.2 - - - -
333C ASN 3.0 5.1 + - - -
334C PRO* 3.7 13.0 - - - +
336C VAL* 1.3 78.4 - - - +
338C GLN* 1.3 57.6 + - - +
340C LEU* 3.1 6.6 + - - +
341C ARG* 2.8 56.9 + - - +
468C LEU* 3.8 16.4 - - + +
472C LEU* 3.6 2.2 - - - +
473C VAL* 2.9 53.6 - - - +
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Residues in contact with GLN 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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334C PRO 3.0 18.1 + - - +
335C ASP* 3.7 6.7 - - - +
336C VAL 3.2 0.2 - - - -
337C GLN* 1.3 72.7 - - - +
339C ILE* 1.3 68.7 + - + +
341C ARG* 3.2 35.0 + - - +
342C GLN* 3.0 61.6 + - - +
345C LEU* 6.3 0.6 - - - +
472C LEU* 4.8 3.5 - - - +
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Residues in contact with ILE 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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335C ASP* 3.1 23.2 + - + +
336C VAL* 3.3 13.0 + - + +
338C GLN* 1.3 77.2 - - + +
340C LEU* 1.3 63.1 + - + +
342C GLN* 3.3 11.3 + - - +
343C GLU* 3.1 20.8 + - - +
364C LEU* 3.3 31.9 - - + -
426C GLN* 4.4 22.2 - - - +
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Residues in contact with LEU 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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330C LEU* 3.5 41.1 - - + -
336C VAL* 3.1 16.6 + - + +
337C GLN* 3.1 7.9 + - - +
339C ILE* 1.3 75.9 - - + +
341C ARG* 1.3 58.0 + - - +
343C GLU* 3.3 8.5 + - - +
344C SER* 2.9 30.3 + - - -
364C LEU* 3.4 46.7 - - + +
365C LEU* 3.6 13.4 - - + +
368C ALA* 4.0 17.3 - - + -
425C PRO* 5.0 5.4 - - + -
468C LEU* 3.8 15.2 - - + +
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Residues in contact with ARG 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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334C PRO 5.1 0.8 + - - -
337C GLN* 2.8 48.4 + - - +
338C GLN* 3.2 39.6 + - - +
339C ILE 3.3 0.2 - - - -
340C LEU* 1.3 74.1 - - - +
342C GLN* 1.3 53.3 + - - +
344C SER* 2.8 3.3 + - - -
345C LEU* 2.7 48.9 + - + +
468C LEU* 3.2 38.4 + - + +
471C PHE 3.0 24.0 + - - -
472C LEU* 3.4 24.6 - - - +
502C ILE* 3.5 19.3 - - - -
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Residues in contact with GLN 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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338C GLN* 3.0 54.9 + - - +
339C ILE* 3.7 9.7 - - - +
341C ARG* 1.3 75.9 - - + +
343C GLU* 1.3 64.7 - - - +
345C LEU* 3.9 8.6 - - + +
346C ALA* 2.9 26.2 + - - +
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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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339C ILE 3.1 12.6 + - - +
340C LEU* 3.5 11.0 - - - +
342C GLN* 1.3 77.4 - - - +
344C SER* 1.3 59.1 + - - +
346C ALA* 3.4 5.6 + - - +
347C ALA* 3.2 22.9 + - - +
361C GLU 4.0 11.2 - - - +
362C LEU* 3.4 22.3 - - + +
363C PRO* 3.1 13.9 - - - +
364C LEU* 2.9 39.3 + - + +
365C LEU* 3.1 29.3 + - - +
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Residues in contact with SER 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 LEU 2.9 15.5 + - - -
341C ARG 2.8 11.4 + - - -
343C GLU* 1.3 71.4 + - - +
345C LEU* 1.3 62.7 + - - -
348C ALA* 3.1 25.3 + - - +
362C LEU* 3.8 11.0 - - - +
365C LEU* 4.3 4.3 - - - +
465C HIS* 3.1 48.9 + - - +
468C LEU* 4.1 14.8 - - - +
469C LYS* 4.1 5.7 - - - +
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Residues in contact with LEU 345 (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 GLN* 6.3 0.7 - - - +
341C ARG* 2.7 41.5 + - + +
342C GLN* 4.0 8.3 - - + +
344C SER* 1.3 72.4 - - - +
346C ALA* 1.3 63.5 + - - +
348C ALA* 3.2 18.7 + - + +
349C ALA 4.9 0.2 + - - -
469C LYS* 3.9 34.5 - - + +
502C ILE* 5.6 4.5 - - + -
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Residues in contact with ALA 346 (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 GLN 2.9 19.0 + - - +
343C GLU* 3.7 6.3 - - - +
345C LEU* 1.3 76.6 - - - +
347C ALA* 1.3 58.8 + - + +
348C ALA 3.3 0.7 + - - -
349C ALA* 5.0 2.1 + - - +
350C SER* 5.6 1.2 + - - -
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Residues in contact with ALA 347 (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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343C GLU 3.2 16.5 + - - +
344C SER 3.5 1.5 + - - +
345C LEU 3.2 0.2 - - - -
346C ALA* 1.3 75.0 - - + +
348C ALA* 1.3 63.7 + - - +
349C ALA 3.4 2.4 + - - -
350C SER* 3.5 6.7 + - - -
351C ILE* 3.0 41.8 + - + +
361C GLU* 4.0 26.5 - - + +
362C LEU* 4.0 10.3 - - + -
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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