Contacts of the helix formed by residues 328 - 337 (chain A) in PDB entry 1DNR
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 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ILE* 4.5 0.9 - - - +
319A GLY* 4.0 5.5 + - - -
320A GLU* 2.5 39.1 - - - +
326A SER* 4.7 5.1 + - - -
327A ILE* 1.3 80.4 + - - +
329A ALA* 1.3 64.2 + - - +
330A THR* 3.1 13.2 - - + +
331A ASN* 3.0 44.5 + - - +
350A VAL* 3.6 5.8 - - - +
353A ARG* 4.3 16.5 - - - +
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ILE 3.4 4.0 + - - -
328A ASN* 1.3 68.4 - - - +
330A THR* 1.3 51.3 + - - +
331A ASN 2.9 4.7 - - - -
332A ILE* 2.7 47.9 + - + +
350A VAL* 3.1 16.1 - - + +
351A ALA 3.2 25.6 - - - +
352A PHE* 4.2 9.2 - - - -
353A ARG* 5.1 4.4 - - + +
367A GLU* 4.3 13.4 - - - +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ASN* 3.9 14.8 - - + +
329A ALA* 1.3 79.0 - - - +
331A ASN* 1.3 76.1 + - - +
332A ILE* 3.0 16.3 - - - +
333A LYS* 3.1 35.1 + - - +
353A ARG* 6.2 1.8 - - - +
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Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLY 5.3 0.6 + - - -
318A ILE* 3.4 32.9 - - + +
319A GLY 3.1 24.6 + - - +
320A GLU* 3.2 6.5 + - - -
328A ASN* 3.0 40.6 + - - +
329A ALA 2.9 0.6 + - - -
330A THR* 1.3 87.9 - - - +
332A ILE* 1.3 62.0 + - - +
333A LYS 3.0 1.2 + - - -
334A HIS* 3.1 15.2 + - - +
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Residues in contact with ILE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 3.8 17.5 - - + +
329A ALA* 2.7 43.7 - - + +
330A THR* 3.0 15.5 - - - +
331A ASN* 1.3 77.2 - - - +
333A LYS* 1.3 93.2 + - + +
334A HIS 3.1 0.4 - - - -
335A PHE* 3.2 24.8 + - - +
347A ILE* 6.2 1.6 - - + -
350A VAL* 5.7 3.6 - - + -
367A GLU* 4.8 30.5 - - + +
370A ILE* 4.0 20.9 - - + +
386A TRP* 4.8 21.3 - - + -
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Residues in contact with LYS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A THR* 3.2 38.1 - - - +
331A ASN 3.0 0.6 + - - -
332A ILE* 1.3 87.7 - - + +
334A HIS* 1.3 65.0 + - - +
335A PHE 2.9 2.7 - - - -
336A LYS* 2.8 36.4 + - + +
366A GLN* 6.0 4.6 - - - +
367A GLU* 6.2 2.8 - - - +
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Residues in contact with HIS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A CYS* 4.7 10.7 - - - +
314A ASN 5.8 1.0 + - - -
316A ILE* 3.7 37.5 - - + +
318A ILE* 4.3 8.7 - - + -
331A ASN 3.1 14.8 + - - +
333A LYS* 1.3 77.3 - - - +
335A PHE* 1.3 58.9 + - - +
336A LYS* 3.3 3.7 + - - +
337A ASN* 4.1 8.7 + - - +
338A CYS* 4.1 7.5 - - - -
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Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A ILE* 2.9 24.0 - - + -
318A ILE* 3.4 24.5 - - + -
332A ILE* 3.2 10.2 + - - +
333A LYS 2.9 0.4 + - - -
334A HIS* 1.3 74.4 - - - +
336A LYS* 1.3 62.9 + - - +
337A ASN 3.1 2.9 + - - -
338A CYS* 3.4 26.0 + - + +
341A ILE* 3.3 28.3 - - + -
345A LEU* 2.9 51.6 - - + -
347A ILE* 6.2 0.9 - - + -
370A ILE* 2.9 32.8 - - + +
373A THR* 4.5 0.3 - - - +
374A VAL* 4.4 12.5 - - + +
396A PHE* 4.6 6.3 - + - -
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LYS* 2.8 26.6 + - + +
334A HIS 4.3 2.5 - - - +
335A PHE* 1.3 78.6 - - - +
337A ASN* 1.3 86.8 + - - +
370A ILE* 3.7 12.6 - - - +
371A LEU* 2.7 37.4 - - + +
373A THR* 3.8 0.9 - - - +
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Residues in contact with ASN 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A CYS* 5.4 2.0 - - - -
334A HIS 4.1 5.8 + - - +
335A PHE 3.2 0.8 - - - -
336A LYS* 1.3 107.0 - - - +
338A CYS* 1.3 65.4 + - - +
339A THR* 3.3 7.8 + - - +
373A THR* 4.0 7.3 + - - -
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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