Contacts of the helix formed by residues 403 - 420 (chain A) in PDB entry 6DWW
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 VAL 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A ASN* 6.2 0.4 - - - +
356A ILE* 3.5 35.0 - - + -
401A GLY 3.6 3.6 + - - +
402A ASP* 1.3 76.6 - - - +
404A ALA* 1.3 60.1 + - - +
405A ASP* 4.0 6.1 - - + +
406A ILE* 3.6 21.5 - - + +
407A ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 404 (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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403A VAL* 1.3 75.2 - - - +
405A ASP* 1.3 70.8 + - - +
407A ALA* 3.4 6.7 + - - +
408A LYS* 3.2 23.0 + - - +
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Residues in contact with ASP 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A THR* 3.8 11.4 - - - +
283A GLU* 3.2 44.0 - - + +
284A LEU* 4.0 21.3 - - + +
356A ILE* 5.7 2.2 - - + -
403A VAL* 3.4 6.9 - - + +
404A ALA* 1.3 85.2 - - - +
406A ILE* 1.3 63.9 + - + +
408A LYS* 3.6 4.1 + - - +
409A LEU* 3.2 17.5 + - - +
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Residues in contact with ILE 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 4.3 9.2 - - + -
356A ILE* 4.0 27.1 - - + -
359A THR* 3.9 29.4 - - + -
360A MET* 4.1 19.3 - - + +
363A ILE* 5.2 3.8 - - + -
402A ASP* 4.1 8.1 - - - +
403A VAL* 3.6 27.6 + - + +
404A ALA 3.4 0.4 - - - -
405A ASP* 1.3 76.3 - - - +
407A ALA* 1.3 66.3 + - - +
408A LYS 3.1 0.2 - - - -
409A LEU* 3.1 11.8 + - + +
410A LYS* 3.0 48.4 + - + +
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Residues in contact with ALA 407 (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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399A ASP 5.6 0.9 - - - +
402A ASP* 4.0 21.0 - - + +
403A VAL 3.0 20.8 + - - +
404A ALA* 3.7 6.7 - - - +
405A ASP 3.4 0.2 - - - -
406A ILE* 1.3 76.6 - - - +
408A LYS* 1.3 61.5 + - - +
410A LYS* 3.7 4.4 + - - +
411A VAL* 3.2 28.5 + - + +
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Residues in contact with LYS 408 (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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280A GLU 3.7 20.8 + - - -
281A THR* 4.1 2.9 - - + -
282A PRO* 4.6 4.2 - - - +
283A GLU* 2.5 40.6 + - - +
404A ALA 3.2 15.5 + - - +
405A ASP* 3.8 6.7 - - - +
406A ILE 3.1 0.4 - - - -
407A ALA* 1.3 75.8 - - - +
409A LEU* 1.3 58.6 + - - +
411A VAL* 3.2 9.3 + - + +
412A ASN* 3.0 38.3 + - - +
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Residues in contact with LEU 409 (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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277A SER 3.9 11.2 - - - +
278A PHE* 4.2 30.3 - - + -
281A THR* 3.7 27.0 - - + +
284A LEU* 4.0 18.4 - - + -
360A MET* 5.0 7.4 - - + -
363A ILE* 5.2 12.8 - - + -
364A LEU* 6.2 0.9 - - + -
405A ASP 3.2 13.7 + - - +
406A ILE* 3.1 21.4 + - + +
408A LYS* 1.3 73.8 - - - +
410A LYS* 1.3 62.7 + - + +
412A ASN* 3.1 2.4 + - - -
413A ILE* 2.9 55.0 + - + +
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Residues in contact with LYS 410 (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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359A THR* 5.7 0.8 - - - +
363A ILE* 4.2 22.8 - - + +
395A ILE 3.9 14.0 + - - -
396A CYS* 3.5 43.0 - - + +
397A SER 3.8 13.3 + - - +
398A PRO* 5.2 2.0 - - + -
399A ASP* 4.3 6.1 - - - +
402A ASP* 3.2 38.3 + - - +
406A ILE* 3.0 27.7 + - + +
407A ALA* 4.0 4.5 - - - +
409A LEU* 1.3 77.5 - - + +
411A VAL* 1.3 61.4 + - + +
414A ILE* 3.1 30.3 + - - +
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Residues in contact with VAL 411 (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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398A PRO* 6.2 4.3 - - + -
407A ALA* 3.2 17.4 + - + +
408A LYS* 3.5 12.3 - - + +
409A LEU 3.1 0.4 - - - -
410A LYS* 1.3 78.1 - - + +
412A ASN* 1.3 71.5 + - - +
414A ILE* 3.2 24.7 - - + +
415A LYS* 3.3 20.0 + - - +
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Residues in contact with ASN 412 (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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277A SER* 3.2 15.6 + - - +
280A GLU* 3.1 37.9 + - - +
281A THR* 3.1 24.9 + - - +
408A LYS* 3.0 28.9 + - - +
409A LEU 3.1 3.6 + - - +
411A VAL* 1.3 78.3 - - - +
413A ILE* 1.3 61.3 + - - +
415A LYS* 3.3 22.8 + - - +
416A ASN* 3.0 27.4 + - - -
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Residues in contact with ILE 413 (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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273A VAL* 3.9 8.1 - - + +
274A LEU* 4.8 9.2 - - + -
277A SER* 3.3 23.8 - - - +
278A PHE* 5.1 2.7 - - + -
363A ILE* 4.9 4.0 - - + -
364A LEU* 5.8 1.1 - - + -
367A PHE* 4.2 17.5 - - + -
392A VAL* 4.0 18.8 - - + -
396A CYS* 3.6 30.3 - - + -
409A LEU* 2.9 43.1 + - + +
410A LYS 3.9 3.1 - - - +
411A VAL 3.3 0.2 - - - -
412A ASN* 1.3 75.6 - - - +
414A ILE* 1.3 61.5 + - - +
416A ASN 3.3 0.3 + - - -
417A VAL* 2.8 32.1 + - + +
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Residues in contact with ILE 414 (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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392A VAL 4.9 0.4 - - - +
393A LYS* 4.6 25.3 - - + +
396A CYS* 3.6 29.2 - - + +
397A SER* 5.6 0.2 - - - -
398A PRO* 6.0 2.5 - - + -
410A LYS 3.1 14.7 + - - +
411A VAL* 3.2 20.9 - - + +
413A ILE* 1.3 75.3 - - + +
415A LYS* 1.3 65.5 + - + +
417A VAL* 3.8 10.1 + - - +
418A ARG* 3.5 23.0 + - - +
422A GLU* 5.2 0.2 - - - +
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Residues in contact with LYS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLU* 4.9 10.5 + - - +
411A VAL* 3.3 17.8 + - - +
412A ASN* 3.4 26.6 + - - +
413A ILE 3.1 0.6 - - - -
414A ILE* 1.3 82.4 - - + +
416A ASN* 1.3 61.8 + - - +
418A ARG* 2.9 41.6 + - - +
419A ILE* 3.0 30.6 + - + +
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Residues in contact with ASN 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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273A VAL* 3.7 21.2 - - + +
276A ASN* 3.7 12.9 + - - +
277A SER* 2.8 35.8 + - - +
280A GLU* 3.5 26.1 + - - +
412A ASN 3.0 14.6 + - - +
415A LYS* 1.3 73.5 - - - +
417A VAL* 1.3 62.4 + - - +
419A ILE* 3.6 24.0 - - - +
420A ILE* 2.7 45.1 + - + +
421A TRP 3.3 0.9 + - - -
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Residues in contact with VAL 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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270A LEU* 5.7 0.4 - - + -
273A VAL* 3.8 14.1 - - + +
389A ILE* 3.8 22.9 - - + +
392A VAL* 3.5 30.1 - - + -
393A LYS* 4.2 14.6 - - + -
413A ILE 2.8 21.5 + - - +
414A ILE* 3.9 7.0 - - - +
416A ASN* 1.3 76.0 - - - +
418A ARG* 1.3 57.8 + - - +
421A TRP* 3.4 19.3 + - + +
422A GLU* 2.8 43.7 + - - +
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Residues in contact with ARG 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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393A LYS* 5.6 2.9 - - - +
414A ILE* 3.5 14.0 + - - +
415A LYS* 2.9 35.0 + - - +
417A VAL* 1.3 81.4 - - - +
419A ILE* 1.3 79.2 + - - +
420A ILE 3.5 0.2 - - - -
422A GLU* 3.5 24.9 - - + +
423A GLU* 3.2 25.3 + - - +
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Residues in contact with ILE 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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280A GLU* 6.0 0.2 - - - +
415A LYS* 3.0 27.7 + - + +
416A ASN* 3.6 22.7 - - - +
418A ARG* 1.3 108.1 - - - +
420A ILE* 1.3 69.9 + - + +
423A GLU* 3.3 23.0 - - - +
424A ASN* 4.6 0.5 - - - +
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Residues in contact with ILE 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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249A ARG* 4.5 14.1 - - - +
269A LEU* 3.6 18.1 - - + +
272A ASN* 3.6 29.6 - - + -
273A VAL* 3.9 13.7 - - + +
276A ASN* 4.1 19.7 - - - +
416A ASN* 2.7 36.3 + - + +
419A ILE* 1.3 90.7 - - + +
421A TRP* 1.3 58.2 + - - +
423A GLU 4.3 0.7 - - - -
424A ASN* 2.8 23.5 - - - +
6D A 4.9 8.5 - - - +
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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