Contacts of the helix formed by residues 415 - 431 (chain A) in PDB entry 1DGD
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 GLU 415 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ARG* 5.3 1.6 - - - +
333A MET* 3.9 31.4 - - + +
336A ARG* 2.7 33.1 + - - +
414A SER* 1.3 74.5 - - - +
416A ASP* 1.3 67.7 + - - +
418A ILE* 3.2 5.7 + - - +
419A ASP* 3.0 27.4 + - - +
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Residues in contact with ASP 416 (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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414A SER* 3.1 7.4 + - - +
415A GLU* 1.3 84.5 - - - +
417A GLU* 1.3 54.4 + - + +
419A ASP* 3.1 9.4 + - - +
420A LEU* 2.7 36.4 + - - +
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Residues in contact with GLU 417 (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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35A SER* 2.9 29.0 + - - -
36A PHE* 3.6 28.7 - - + -
46A LEU* 3.5 21.2 - - + +
48A PHE* 4.2 1.9 - - - -
412A THR 4.6 0.9 - - - +
413A VAL* 3.4 10.7 - - + +
414A SER* 2.9 37.0 + - - +
416A ASP* 1.3 78.7 - - + +
418A ILE* 1.3 62.5 + - - +
420A LEU* 3.6 6.9 - - + +
421A GLY* 3.0 19.8 + - - -
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Residues in contact with ILE 418 (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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48A PHE* 4.5 11.5 - - + -
333A MET* 4.2 17.0 - - - +
336A ARG* 3.6 23.8 - - - -
337A LEU* 3.4 41.1 - - + +
359A LEU* 5.0 0.7 - - + -
409A PRO* 4.6 3.8 - - + -
413A VAL* 3.9 24.2 - - + -
414A SER 3.0 16.6 + - - +
415A GLU* 3.5 9.4 - - - +
416A ASP 3.2 0.2 - - - -
417A GLU* 1.3 75.7 - - - +
419A ASP* 1.3 58.5 + - - +
421A GLY* 3.9 0.7 - - - -
422A LEU* 2.9 40.7 + - + +
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Residues in contact with ASP 419 (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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336A ARG* 2.6 45.2 + - - -
415A GLU* 3.0 16.4 + - - +
416A ASP* 3.6 10.0 - - - +
418A ILE* 1.3 77.9 - - - +
420A LEU* 1.3 65.9 + - - +
422A LEU* 2.9 15.2 + - - +
423A SER* 2.9 23.1 + - - -
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Residues in contact with LEU 420 (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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36A PHE* 4.4 27.6 - - + -
46A LEU* 4.3 5.6 - - + -
416A ASP 2.7 19.8 + - - +
417A GLU* 3.6 7.2 - - - +
419A ASP* 1.3 71.0 - - - +
421A GLY* 1.3 58.5 + - - +
423A SER* 3.0 11.4 + - - +
424A LEU* 2.8 62.1 + - + +
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Residues in contact with GLY 421 (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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46A LEU* 3.7 19.9 - - - +
48A PHE* 4.0 15.5 - - - -
391A LEU* 3.9 11.1 - - - +
417A GLU 3.0 13.2 + - - -
418A ILE 3.9 1.1 - - - -
420A LEU* 1.3 76.9 - - - +
422A LEU* 1.3 65.1 + - - +
424A LEU* 4.6 1.3 - - - -
425A LEU* 2.9 25.3 + - - +
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Residues in contact with LEU 422 (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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48A PHE* 4.9 0.4 - - - -
336A ARG* 4.6 5.4 - - - +
337A LEU* 3.9 15.5 - - + -
340A GLY* 3.4 44.0 - - - +
341A LEU* 3.5 20.2 - - + +
344A LEU* 4.1 13.6 - - + +
418A ILE* 2.9 36.9 + - + +
419A ASP* 2.9 16.6 + - - +
421A GLY* 1.3 77.8 - - - +
423A SER* 1.3 56.0 + - - +
425A LEU* 3.6 5.9 - - - +
426A GLY* 3.0 24.1 + - - -
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Residues in contact with SER 423 (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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419A ASP 2.9 11.9 + - - -
420A LEU* 3.2 15.6 + - - +
422A LEU* 1.3 74.4 - - - +
424A LEU* 1.3 69.6 + - - +
426A GLY* 3.1 4.2 + - - -
427A GLN* 3.1 37.6 + - - +
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Residues in contact with LEU 424 (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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46A LEU* 5.0 2.2 - - + -
386A CYS* 5.4 0.2 - - - -
389A LEU* 3.7 42.0 - - + +
390A GLY 4.2 14.4 - - - +
391A LEU* 4.2 21.1 - - + -
420A LEU* 2.8 51.5 + - + +
421A GLY* 4.0 5.2 - - - +
423A SER* 1.3 71.9 + - - +
425A LEU* 1.3 57.5 + - - +
427A GLN* 3.2 20.2 + - - +
428A ALA* 2.8 30.9 + - - +
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Residues in contact with LEU 425 (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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48A PHE* 6.4 1.3 - - + -
341A LEU* 4.0 17.3 - - + -
344A LEU* 3.4 24.5 - - + -
351A ILE* 5.9 1.3 - - + -
363A VAL* 5.8 5.8 - - + -
382A ILE* 4.4 7.2 - - + -
386A CYS* 4.1 20.0 - - - -
391A LEU* 4.0 8.7 - - + +
393A MET* 4.1 22.9 - - + -
405A PHE* 5.5 3.1 - - + -
407A ILE* 5.3 5.2 - - + -
421A GLY 2.9 18.8 + - - +
422A LEU* 3.6 6.1 - - + +
424A LEU* 1.3 76.4 - - - +
426A GLY* 1.3 64.0 + - - +
428A ALA 3.3 0.5 + - - -
429A ILE* 3.1 37.5 + - + +
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Residues in contact with GLY 426 (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 LEU* 3.9 24.8 - - - +
348A PHE* 4.0 8.8 - - - -
422A LEU 3.0 12.2 + - - -
423A SER 3.1 3.5 + - - -
425A LEU* 1.3 77.8 - - - +
427A GLN* 1.3 61.2 + - - +
429A ILE* 3.1 4.6 + - - +
430A GLU* 2.9 25.5 + - - +
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Residues in contact with GLN 427 (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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389A LEU* 4.0 22.7 - - + +
423A SER* 3.1 31.5 + - - +
424A LEU* 3.7 19.5 - - - +
426A GLY* 1.3 76.8 - - - +
428A ALA* 1.3 63.3 + - - +
430A GLU* 3.1 21.8 + - - +
431A ARG* 2.9 31.0 + - - +
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Residues in contact with ALA 428 (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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382A ILE* 3.8 5.4 - - + +
385A GLU* 3.5 9.9 - - + +
386A CYS* 3.5 36.1 - - - +
389A LEU* 3.4 23.5 - - + +
424A LEU 2.8 17.1 + - - +
425A LEU 4.0 2.0 - - - +
427A GLN* 1.3 74.3 - - - +
429A ILE* 1.3 64.0 + - - +
431A ARG* 3.2 4.1 + - - +
432A ALA* 3.0 23.4 + - - +
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Residues in contact with ILE 429 (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 LEU* 4.7 3.1 - - + -
348A PHE* 3.9 33.4 - - + -
350A CYS* 4.0 14.8 - - - -
351A ILE* 4.2 20.4 - - + -
365A ILE* 5.8 2.5 - - + -
382A ILE* 4.1 20.2 - - + -
425A LEU* 3.1 40.6 + - + +
426A GLY* 3.6 4.9 - - - +
428A ALA* 1.3 72.8 - - - +
430A GLU* 1.3 68.7 + - - +
432A ALA* 3.2 12.9 + - - +
433A LEU* 3.0 30.6 + - + +
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Residues in contact with GLU 430 (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 PHE* 4.0 16.6 - - + -
426A GLY 2.9 16.9 + - - +
427A GLN* 3.1 36.4 + - - +
429A ILE* 1.3 81.2 - - - +
431A ARG* 1.3 66.6 + - + +
432A ALA 3.4 0.2 + - - -
433A LEU* 3.7 18.2 + - - +
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Residues in contact with ARG 431 (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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385A GLU* 3.7 31.9 + - + +
388A ASN* 5.0 7.1 - - - +
389A LEU* 4.4 30.4 - - - +
427A GLN* 2.9 25.5 + - - +
428A ALA* 3.4 6.3 - - - +
430A GLU* 1.3 84.7 + - + +
432A ALA* 1.3 59.7 + - - +
433A LEU* 3.5 4.8 + - - +
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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