Contacts of the helix formed by residues 387 - 399 (chain A) in PDB entry 1WDR
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 ASP 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A ARG* 2.8 47.4 + - - +
386A TYR* 1.3 84.9 + - - +
388A ALA* 1.3 65.2 + - - +
389A THR* 3.3 12.8 - - - +
390A ALA* 3.1 23.3 + - - +
391A TYR* 3.2 16.7 + - - -
433A ILE* 5.0 2.9 - - - -
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Residues in contact with ALA 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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387A ASP* 1.3 73.8 - - - +
389A THR* 1.3 62.3 + - - +
391A TYR* 3.2 5.7 + - - +
392A ASN* 2.9 33.3 + - - +
433A ILE* 4.2 12.9 - - + +
493A VAL* 3.7 21.1 - - + -
495A GLY* 3.4 30.7 - - - +
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Residues in contact with THR 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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345A GLU 5.3 0.4 - - - +
347A ARG* 4.5 15.7 - - + -
350A GLU* 3.9 21.3 - - - +
385A ARG* 4.2 0.4 - - - +
387A ASP* 3.2 13.3 + - - +
388A ALA* 1.3 77.6 - - - +
390A ALA* 1.3 64.7 + - - +
392A ASN* 3.4 6.9 + - - +
393A GLN* 3.1 22.5 + - - +
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLU* 4.0 15.7 - - + -
385A ARG* 3.5 51.3 - - + +
387A ASP* 3.1 12.7 + - - +
389A THR* 1.3 80.2 - - - +
391A TYR* 1.4 65.6 + - + +
393A GLN* 3.2 5.0 + - - +
394A ILE* 3.0 27.9 + - + +
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Residues in contact with TYR 391 (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 ARG 3.8 6.5 + - - -
386A TYR* 3.4 27.1 + - - -
387A ASP 3.2 15.7 + - - -
388A ALA 3.2 4.0 + - - +
390A ALA* 1.4 77.2 - - + +
392A ASN* 1.4 58.4 + - - +
394A ILE* 3.2 9.9 + - + +
395A ILE* 2.9 35.5 + - - +
418A TYR* 3.4 40.1 + + - -
425A LEU* 4.0 3.1 - - - +
430A ASN 4.7 1.1 + - - -
433A ILE* 3.7 24.0 - - + -
434A PHE* 3.5 28.6 - + - +
437A PHE* 3.3 48.0 - + + -
493A VAL* 4.1 9.2 - - + -
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Residues in contact with ASN 392 (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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388A ALA* 2.9 25.2 + - - +
389A THR* 3.8 5.9 - - - +
391A TYR* 1.4 75.9 - - - +
393A GLN* 1.3 58.9 + - - +
395A ILE* 3.4 6.5 + - - +
396A LEU* 2.9 29.1 + - - +
489A THR* 3.9 11.5 + - + +
492A LYS* 3.4 32.8 - - + +
493A VAL* 2.9 38.1 + - - +
494A ASP 5.2 0.6 - - - +
495A GLY* 5.6 1.4 + - - -
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Residues in contact with GLN 393 (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 3.3 17.5 - - - +
345A GLU 3.6 20.9 - - - +
346A MET 3.6 16.6 - - - +
347A ARG* 3.1 38.8 + - + +
360A GLN* 3.8 15.6 + - - +
389A THR 3.1 12.5 + - - +
390A ALA 3.2 8.3 + - - +
392A ASN* 1.3 75.5 - - - +
394A ILE* 1.3 65.2 + - - +
396A LEU* 3.4 20.2 + - - +
397A ASN* 3.0 35.5 + - - +
485A TRP* 5.6 0.9 + - - -
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Residues in contact with ILE 394 (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* 3.4 26.0 - - + +
345A GLU* 3.8 17.3 - - + +
381A ASN* 4.3 16.4 - - + +
390A ALA* 3.0 20.4 + - + +
391A TYR* 3.2 17.7 + - + +
393A GLN* 1.3 78.1 - - - +
395A ILE* 1.3 57.6 + - - +
397A ASN* 3.2 3.6 + - - +
398A ALA* 2.8 26.2 + - - +
413A MET* 5.3 0.2 - - - +
416A VAL* 3.9 29.7 - - + +
418A TYR* 5.0 4.7 - - + -
437A PHE* 3.6 34.3 - - + -
441A MET* 4.4 1.6 - - - -
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Residues in contact with ILE 395 (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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391A TYR 2.9 23.0 + - - +
392A ASN* 3.8 7.2 - - - +
394A ILE* 1.3 74.1 - - - +
396A LEU* 1.3 61.6 + - - +
398A ALA* 3.2 2.3 + - - +
399A ARG* 3.2 42.3 + - - +
437A PHE* 3.8 11.7 - - + +
440A LYS* 3.7 24.0 - - + +
441A MET* 3.8 26.9 - - + -
489A THR* 3.5 20.0 + - + +
491A MET* 3.7 16.2 - - + +
493A VAL* 3.8 21.1 - - + -
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Residues in contact with LEU 396 (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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347A ARG* 4.7 2.5 - - - +
360A GLN* 5.9 1.3 - - - +
392A ASN 2.9 17.4 + - - +
393A GLN* 3.5 28.7 - - - +
395A ILE* 1.3 77.2 - - - +
397A ASN* 1.3 62.4 + - - +
399A ARG 3.1 6.5 - - - +
400A PRO* 3.1 36.9 - - + +
485A TRP* 4.1 15.5 - - + +
486A LEU* 3.6 36.3 - - + +
487A PRO 4.1 13.5 - - - +
488A GLU* 3.9 20.4 - - - -
489A THR* 3.9 13.6 - - - +
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Residues in contact with ASN 397 (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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343A CYS 4.5 2.0 + - - -
344A LEU* 2.8 49.6 + - + +
346A MET 5.4 0.4 + - - -
360A GLN* 5.3 2.5 - - - +
363A VAL* 3.5 26.0 - - + +
367A LEU* 3.8 7.2 - - + +
393A GLN* 3.0 27.7 + - - +
394A ILE 3.7 4.0 - - - +
396A LEU* 1.3 79.6 - - - +
398A ALA* 1.4 63.1 + - - +
399A ARG 3.4 0.2 + - - -
400A PRO* 3.4 10.7 - - - +
413A MET* 3.4 15.8 - - - +
485A TRP* 2.8 31.8 + - - +
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Residues in contact with ALA 398 (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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12A VAL* 4.2 13.3 - - + +
394A ILE 2.8 16.6 + - - +
395A ILE* 3.5 6.3 - - + +
396A LEU 3.1 0.4 - - - -
397A ASN* 1.4 77.9 - - - +
399A ARG* 1.3 64.2 - - + +
400A PRO* 3.8 0.2 - - - -
412A SER* 3.2 5.0 - - - -
413A MET* 2.9 36.2 + - - -
416A VAL* 4.6 4.7 - - + -
441A MET* 3.7 32.1 - - + -
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Residues in contact with ARG 399 (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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10A ASN* 2.8 54.1 + - - -
12A VAL* 3.8 7.8 - - + +
395A ILE* 3.2 25.7 + - + +
396A LEU* 3.1 9.0 - - - +
398A ALA* 1.3 84.9 - - - +
400A PRO* 1.3 62.5 - - - +
401A GLN 3.2 2.9 - - - -
402A GLY* 2.9 32.7 + - - +
403A VAL* 3.5 16.0 - - - +
409A PRO* 4.3 4.9 - - - -
411A LEU 3.8 6.5 - - - +
412A SER* 4.1 12.8 - - - -
440A LYS 2.8 23.6 + - - -
441A MET* 2.9 24.6 + - - +
443A ALA* 4.1 4.1 - - - +
486A LEU* 4.9 0.3 - - - +
489A THR* 5.2 3.5 + - - +
490A ASP* 5.4 0.8 + - - +
491A MET* 4.0 19.0 - - - +
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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