Contacts of the helix formed by residues 378 - 389 (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 LEU 378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A CYS* 3.8 24.9 - - + -
365A ILE* 4.3 7.4 - - + -
375A ALA* 3.9 20.5 + - + -
376A ASP 3.5 4.0 + - - -
377A GLY* 1.4 72.7 - - - +
379A GLY* 1.3 66.7 + - - +
381A LYS* 2.8 22.7 + - + +
382A ILE* 2.8 31.5 + - + +
432A ALA* 3.7 36.1 - - + +
433A LEU* 3.8 25.8 - - + -
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Residues in contact with GLY 379 (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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365A ILE* 5.0 8.3 - - - +
375A ALA* 4.7 5.6 + - - +
377A GLY* 3.3 0.6 - - - -
378A LEU* 1.3 78.3 - - - +
380A ALA* 1.3 63.9 + - - +
382A ILE* 3.0 11.6 + - - +
383A THR* 2.8 28.6 + - - -
395A ILE* 3.8 23.6 - - - -
397A GLN* 6.1 0.4 - - - -
403A GLY* 6.1 0.2 - - - -
405A PHE* 4.0 5.5 - - - -
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Residues in contact with ALA 380 (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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377A GLY* 3.5 13.1 + - - +
378A LEU 3.2 0.4 - - - -
379A GLY* 1.3 75.0 - - - +
381A LYS* 1.3 63.7 + - - +
383A THR* 3.8 8.5 - - - -
384A ARG* 3.1 23.4 + - - +
395A ILE* 4.8 5.1 - - + +
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Residues in contact with LYS 381 (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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377A GLY 3.3 16.4 + - - +
378A LEU* 2.8 19.6 + - + +
380A ALA* 1.3 76.5 - - - +
382A ILE* 1.3 62.3 + - - +
384A ARG* 2.9 35.9 + - - +
385A GLU* 2.8 33.1 + - + +
432A ALA* 2.9 38.7 + - + +
433A LEU 4.3 8.9 + - - -
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Residues in contact with ILE 382 (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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350A CYS* 4.8 0.9 - - - -
365A ILE* 4.6 20.4 - - + -
378A LEU* 2.8 41.7 - - + +
379A GLY* 3.3 6.5 - - - +
381A LYS* 1.3 76.4 - - - +
383A THR* 1.3 62.5 + - - +
385A GLU* 3.3 3.2 + - - +
386A CYS* 2.9 24.9 + - - -
405A PHE* 3.5 21.3 - - + -
425A LEU* 4.4 11.0 - - + -
428A ALA* 3.8 2.3 - - - +
429A ILE* 4.1 42.6 - - + +
432A ALA* 3.9 17.9 - - + -
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Residues in contact with THR 383 (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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379A GLY 2.8 21.1 + - - -
380A ALA* 3.8 6.5 - - - -
382A ILE* 1.3 75.5 - - - +
384A ARG* 1.3 62.2 + - - +
386A CYS* 3.1 9.0 + - - +
387A MET* 3.0 23.5 + - + +
393A MET* 4.2 29.4 - - + +
394A ASN* 5.4 0.2 - - - -
395A ILE* 4.0 16.8 - - + +
405A PHE* 3.4 19.4 - - - -
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Residues in contact with ARG 384 (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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380A ALA 3.1 14.1 + - - +
381A LYS* 2.9 38.3 + - - +
383A THR* 1.3 73.9 - - - +
385A GLU* 1.3 85.2 + - - +
387A MET* 3.3 7.5 + - - +
388A ASN* 3.1 33.9 + - - +
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Residues in contact with GLU 385 (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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381A LYS* 2.8 26.2 + - + +
382A ILE 3.9 0.9 - - - +
384A ARG* 1.3 96.3 + - - +
386A CYS* 1.3 67.0 + - - +
388A ASN* 3.1 18.3 + - - +
389A LEU* 2.8 28.8 + - + +
428A ALA* 3.5 33.2 - - + +
431A ARG* 3.7 36.8 + - + +
432A ALA* 4.7 6.3 - - + +
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Residues in contact with CYS 386 (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* 2.9 24.8 + - - -
383A THR* 3.2 11.0 - - - +
385A GLU* 1.3 74.4 - - - +
387A MET* 1.3 57.9 - - - +
389A LEU* 2.7 26.6 + - - +
390A GLY 2.8 10.0 + - - -
391A LEU* 3.0 38.1 + - + +
393A MET* 4.0 21.5 - - + -
424A LEU 5.1 0.4 - - - -
425A LEU* 4.1 17.0 - - - -
428A ALA* 3.5 17.0 - - - +
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Residues in contact with MET 387 (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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25A GLU* 4.6 20.9 - - - +
26A PRO* 6.2 1.8 - - + -
27A MET* 3.7 22.4 - - + +
43A ARG* 3.0 20.2 + - - +
45A ILE* 3.0 54.7 - - + -
383A THR* 3.0 9.4 + - + +
384A ARG* 3.7 9.9 - - - +
385A GLU 3.2 0.2 - - - -
386A CYS* 1.3 81.8 - - - +
388A ASN* 1.3 57.7 + - - +
390A GLY* 2.9 16.3 + - - +
391A LEU 4.0 3.1 - - - +
392A SER* 4.3 20.2 - - - +
393A MET 5.4 0.9 - - - -
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Residues in contact with ASN 388 (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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43A ARG* 4.0 14.3 + - - +
384A ARG* 3.1 37.1 + - - +
385A GLU* 3.1 28.6 + - - +
387A MET* 1.3 78.0 - - - +
389A LEU* 1.3 61.3 - - + +
390A GLY 3.4 1.0 + - - -
431A ARG* 5.0 6.3 - - - +
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Residues in contact with LEU 389 (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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43A ARG* 5.7 0.2 - - - -
385A GLU* 2.8 19.3 + - + +
386A CYS* 2.7 10.0 + - - +
388A ASN* 1.3 75.9 - - - +
390A GLY* 1.3 58.8 + - - +
424A LEU* 3.7 40.4 - - + +
427A GLN* 4.0 25.8 - - + +
428A ALA* 3.4 39.3 - - + +
431A ARG* 4.4 23.8 - - - +
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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