Contacts of the helix formed by residues 427 - 442 (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 GLN 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A ASP* 3.0 30.3 + - - +
424A ASP* 3.7 15.9 - - - +
425A LEU 3.3 2.0 - - - -
426A LEU* 1.3 84.8 + - - +
428A LYS* 1.3 59.3 + - - +
429A SER 3.4 2.5 - - - +
430A ASN* 3.2 10.6 + - + +
431A PHE* 2.7 30.3 + - - +
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Residues in contact with LYS 428 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A LEU 3.7 2.6 + - - -
427A GLN* 1.3 73.8 + - - +
429A SER* 1.3 61.4 + - - +
431A PHE* 3.4 2.7 + - - +
432A ASN* 2.9 48.0 + - - +
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Residues in contact with SER 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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427A GLN* 3.4 0.8 - - - +
428A LYS* 1.3 78.8 - - - +
430A ASN* 1.3 73.8 - - - +
432A ASN* 3.2 7.9 + - - +
433A ILE* 3.0 35.2 + - - +
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Residues in contact with ASN 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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386A TYR* 3.7 39.6 - - + +
391A TYR* 4.7 2.9 + - - -
424A ASP* 2.9 36.2 + - - +
425A LEU* 3.7 7.1 - - - +
427A GLN* 3.2 10.3 + - - +
429A SER* 1.3 82.4 - - - +
431A PHE* 1.3 59.2 + - - +
433A ILE* 3.3 11.3 + - - +
434A PHE* 2.9 27.0 + - - +
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Residues in contact with PHE 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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41A GLN* 3.6 44.6 - - + -
42A LEU* 3.9 10.5 - - + -
45A ALA* 3.6 16.6 - - + -
425A LEU* 3.2 22.6 + - + +
426A LEU* 3.4 34.1 - - + +
427A GLN 2.7 19.3 + - - +
428A LYS* 4.0 3.4 - - - +
430A ASN* 1.3 74.8 - - - +
432A ASN* 1.3 57.9 + - - +
434A PHE* 3.2 25.9 + + - +
435A LYS* 2.8 55.0 + - - +
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Residues in contact with ASN 432 (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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428A LYS* 2.9 43.5 + - - +
429A SER* 3.6 7.5 - - - +
431A PHE* 1.3 78.3 - - - +
433A ILE* 1.3 61.2 + - + +
435A LYS* 3.0 32.6 + - - +
436A LYS* 3.2 32.9 + - - +
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Residues in contact with ILE 433 (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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386A TYR 3.9 15.5 - - - +
387A ASP* 5.0 2.0 - - - -
388A ALA* 4.2 22.9 - - + +
391A TYR* 3.7 24.0 - - + -
429A SER* 3.0 24.3 + - - +
430A ASN* 3.8 8.7 - - - +
432A ASN* 1.3 73.5 - - + +
434A PHE* 1.3 65.6 + - - +
436A LYS* 3.0 14.9 + - + +
437A PHE* 2.9 20.3 + - - +
493A VAL* 4.6 8.5 - - + +
495A GLY* 5.7 9.0 - - - +
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Residues in contact with PHE 434 (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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14A VAL* 4.5 3.4 - - + -
16A VAL* 3.7 23.3 - - + -
42A LEU* 4.6 1.6 - - + -
45A ALA* 4.8 2.7 - - + -
47A VAL* 3.6 22.9 - - + -
391A TYR* 3.5 29.8 - + - +
418A TYR* 4.0 25.1 - + + -
425A LEU* 3.8 17.9 - - + -
430A ASN 2.9 17.1 + - - +
431A PHE* 3.5 29.8 - + - +
433A ILE* 1.3 77.3 - - - +
435A LYS* 1.3 64.2 + - - +
437A PHE* 3.1 19.7 + + - +
438A VAL* 2.9 37.6 + - + +
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Residues in contact with LYS 435 (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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44A ALA 5.9 0.2 - - - -
45A ALA* 3.7 35.4 - - + +
431A PHE* 2.8 43.4 + - + +
432A ASN* 3.0 32.8 + - - +
433A ILE 3.2 0.2 - - - -
434A PHE* 1.3 72.8 - - - +
436A LYS* 1.3 57.5 + - + +
438A VAL* 3.3 8.7 + - - +
439A LEU* 3.0 27.8 + - - +
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Residues in contact with LYS 436 (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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432A ASN* 3.2 20.3 + - - +
433A ILE* 3.0 16.3 + - + +
435A LYS* 1.3 74.7 - - + +
437A PHE* 1.4 64.7 + - - +
439A LEU* 3.2 12.8 + - + +
440A LYS* 2.9 29.5 + - + +
493A VAL* 3.4 37.2 - - + +
494A ASP* 4.7 11.8 + - - -
495A GLY* 4.9 8.0 - - - +
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Residues in contact with PHE 437 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.0 22.2 - - + -
391A TYR* 3.3 48.5 - + + -
394A ILE* 3.6 40.6 - - + -
395A ILE* 3.8 9.0 - - + -
416A VAL* 4.5 10.3 - - + -
418A TYR* 4.8 6.7 - + + -
433A ILE 2.9 8.0 + - - +
434A PHE* 3.3 26.9 - + - +
436A LYS* 1.4 76.5 - - - +
438A VAL* 1.3 60.9 + - + +
440A LYS* 3.2 2.4 + - - +
441A MET* 2.8 58.0 + - + +
493A VAL* 3.6 9.9 - - - +
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Residues in contact with VAL 438 (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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14A VAL* 4.3 12.8 - - + -
45A ALA 3.6 21.5 - - - +
46A GLY* 3.7 8.5 - - - +
47A VAL* 4.3 9.0 - - + -
434A PHE* 2.9 47.8 + - + +
435A LYS* 3.7 7.0 - - - +
436A LYS 3.3 0.4 - - - -
437A PHE* 1.3 76.4 - - + +
439A LEU* 1.4 65.3 + - - +
441A MET* 3.3 6.9 + - - +
442A HIS* 2.9 56.3 + - + +
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Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A LYS 3.0 13.9 + - - +
436A LYS* 3.5 13.9 - - + +
438A VAL* 1.4 78.9 - - - +
440A LYS* 1.4 72.4 + - - +
442A HIS* 3.2 12.8 + - - +
443A ALA 3.2 0.2 + - - -
444A ASP* 2.9 65.0 + - - +
445A GLN 3.9 9.6 - - - +
446A ASP* 5.4 4.5 - - - +
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Residues in contact with LYS 440 (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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395A ILE* 3.7 13.0 - - + -
399A ARG* 2.8 24.4 + - - -
436A LYS* 2.9 19.8 + - - +
439A LEU* 1.4 86.4 - - - +
441A MET* 1.3 61.3 + - - +
442A HIS 3.1 1.3 - - - -
443A ALA* 2.9 12.8 + - - +
444A ASP* 2.8 33.4 + - - +
491A MET* 3.3 37.2 - - + +
492A LYS 3.5 21.7 + - - +
493A VAL* 4.0 17.0 - - - -
494A ASP* 4.8 8.6 + - - -
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Residues in contact with MET 441 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.0 42.2 + - + +
13A PRO 4.4 0.2 - - - +
14A VAL* 3.5 27.4 - - + -
394A ILE* 4.4 1.6 - - - -
395A ILE* 3.8 15.0 - - + -
398A ALA* 3.7 18.6 - - + -
399A ARG* 2.9 23.5 + - - +
416A VAL* 3.5 37.2 - - + -
437A PHE* 2.8 47.4 + - + +
438A VAL 3.6 1.6 - - - +
440A LYS* 1.3 75.7 - - - +
442A HIS* 1.3 58.5 + - - +
443A ALA 3.1 0.2 - - - -
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Residues in contact with HIS 442 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.1 50.7 + + + +
12A VAL 3.4 12.5 + - - -
14A VAL* 4.2 2.8 + - - +
46A GLY* 3.0 28.9 - - - -
48A ASP* 2.7 22.0 + - - -
438A VAL* 2.9 33.1 + - + +
439A LEU* 3.4 5.8 - - - +
440A LYS 3.1 0.4 - - - -
441A MET* 1.3 75.9 - - + +
443A ALA* 1.3 69.0 + - - +
444A ASP 3.2 1.1 - - - -
445A GLN* 3.0 34.6 + - - +
447A TYR* 4.2 11.0 + - - +
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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