Contacts of the helix formed by residues 339 - 352 (chain A) in PDB entry 1DQU
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 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A HIS* 4.0 36.1 + - - -
261A HIS* 4.1 10.5 - - - -
337A GLY 4.0 0.2 + - - -
338A LYS* 1.3 78.8 - - - +
340A ASN* 1.3 62.2 + - - +
341A LEU* 4.3 5.6 - - - -
342A GLU* 3.0 27.7 + - - +
343A ALA* 2.8 26.7 + - - +
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Residues in contact with ASN 340 (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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261A HIS* 3.8 18.8 + - + +
308A PHE* 3.9 34.2 - - - +
339A SER* 1.3 68.8 - - - +
341A LEU* 1.3 76.6 + - + +
342A GLU 2.6 2.9 + - - -
343A ALA* 2.9 5.2 + - - +
344A ARG* 2.7 53.5 + - - +
357A PHE* 4.5 1.8 - - - -
359A TRP* 3.7 44.1 - - + -
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Residues in contact with LEU 341 (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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339A SER* 4.3 5.8 - - - -
340A ASN* 1.3 83.3 - - - +
342A GLU* 1.3 65.4 + - + +
344A ARG* 3.1 30.3 - - - +
345A ALA* 3.4 5.9 + - - +
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Residues in contact with GLU 342 (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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338A LYS* 3.4 31.3 - - + +
339A SER* 3.0 34.8 + - - +
340A ASN 2.6 3.6 + - - -
341A LEU* 1.3 72.8 - - + +
343A ALA* 1.3 57.4 + - - +
344A ARG 2.8 1.1 - - - -
345A ALA* 2.1 45.2 + - - +
346A ILE* 3.4 11.5 + - - +
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Residues in contact with ALA 343 (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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308A PHE* 3.5 13.0 - - + -
309A ASN* 4.8 1.6 - - - +
331A TYR* 3.4 26.8 - - + +
335A SER* 4.7 8.3 - - - -
338A LYS* 4.7 3.1 - - + +
339A SER 2.8 13.1 + - - +
340A ASN* 3.7 4.3 - - - +
342A GLU* 1.3 79.4 - - - +
344A ARG* 1.3 63.6 + - - +
345A ALA 2.8 0.9 + - - -
346A ILE* 2.9 16.1 + - - +
347A ALA* 2.8 23.9 + - - +
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Residues in contact with ARG 344 (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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308A PHE* 3.2 27.4 - - + -
340A ASN* 2.7 34.8 + - - +
341A LEU* 3.1 29.9 - - - +
342A GLU 2.5 2.6 + - - -
343A ALA* 1.3 73.1 - - - +
345A ALA* 1.3 55.8 + - - +
347A ALA* 3.1 16.6 - - - +
348A LYS* 3.6 7.3 + - - +
355A ILE* 4.3 17.7 + - - +
357A PHE* 2.4 54.5 + - - +
359A TRP* 5.5 0.6 - - - +
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Residues in contact with ALA 345 (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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341A LEU 3.4 4.9 + - - +
342A GLU* 2.1 32.7 + - - +
344A ARG* 1.3 66.0 - - - +
346A ILE* 1.3 71.2 + - + +
347A ALA 3.0 1.5 + - - -
348A LYS* 3.3 7.7 + - - +
349A GLU* 3.3 19.3 + - - +
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Residues in contact with ILE 346 (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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331A TYR* 3.5 29.2 - - + +
334A GLN* 4.6 21.8 - - + +
335A SER* 4.6 14.8 - - - -
338A LYS* 5.0 3.4 - - + -
342A GLU* 3.5 18.2 - - + +
343A ALA* 2.9 29.3 + - - +
345A ALA* 1.3 79.7 - - + +
347A ALA* 1.3 71.4 + - - +
349A GLU* 3.3 12.9 + - + +
350A ILE* 2.8 33.5 + - + +
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Residues in contact with ALA 347 (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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308A PHE* 4.3 0.4 - - + -
312A VAL* 3.7 31.0 - - + -
331A TYR* 4.0 11.6 - - + -
343A ALA 2.8 11.8 + - - +
344A ARG* 3.1 19.3 - - - +
346A ILE* 1.3 81.4 - - - +
348A LYS* 1.3 64.1 + - - +
350A ILE* 2.7 10.8 + - - +
351A ALA* 2.8 19.2 + - + +
355A ILE* 4.0 11.2 - - + -
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Residues in contact with LYS 348 (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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344A ARG 3.6 5.8 + - - +
345A ALA* 3.3 9.1 + - - +
347A ALA* 1.3 77.5 - - - +
349A GLU* 1.3 70.8 + - - +
350A ILE 2.6 1.9 + - - -
352A GLY* 2.6 34.3 + - - +
353A THR* 2.7 31.7 + - - +
354A ASP* 2.6 28.6 + - - +
355A ILE* 4.3 0.9 - - + +
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Residues in contact with GLU 349 (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 LYS* 5.7 5.8 - - - +
334A GLN* 5.6 4.2 + - - +
345A ALA 3.3 7.9 + - - +
346A ILE* 3.3 16.8 + - + +
348A LYS* 1.3 83.3 - - - +
350A ILE* 1.3 77.5 + - + +
352A GLY* 4.4 1.6 + - - -
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Residues in contact with ILE 350 (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* 5.1 7.0 - - + -
321A LEU* 4.8 4.8 - - + +
327A ALA* 4.3 27.6 - - + -
330A LYS* 4.2 27.8 - - + +
331A TYR* 4.2 22.2 - - + +
334A GLN* 4.7 4.5 - - - +
346A ILE* 2.8 33.0 + - + +
347A ALA* 2.7 12.5 + - - +
348A LYS 2.6 2.8 + - - -
349A GLU* 1.3 88.3 - - + +
351A ALA* 1.3 69.4 + - + +
352A GLY* 4.6 0.2 - - - -
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Residues in contact with ALA 351 (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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312A VAL* 6.1 2.2 - - + -
315A ALA* 5.4 5.2 - - + -
316A ILE* 3.8 26.5 - - + -
321A LEU* 3.5 27.8 - - + +
347A ALA* 2.8 18.6 + - - +
348A LYS* 4.9 0.4 - - - -
350A ILE* 1.3 77.8 - - + +
352A GLY* 1.3 58.7 + - - +
353A THR* 3.6 7.8 + - + +
355A ILE* 5.3 6.1 - - + -
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Residues in contact with GLY 352 (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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348A LYS* 2.6 30.3 + - - +
349A GLU 4.9 1.3 - - - -
350A ILE 4.6 0.4 - - - -
351A ALA* 1.3 75.4 - - - +
353A THR* 1.3 62.7 + - - +
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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