Contacts of the helix formed by residues 415 - 426 (chain A) in PDB entry 6IWQ
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
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Residue Dist Surf HB Arom Phob DC
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280A LEU* 4.8 6.3 - - - +
281A ILE* 3.7 38.2 - - + +
284A ARG* 2.8 32.7 + - - +
389A GLY* 4.5 3.3 - - - +
405A TYR* 3.2 31.6 + - + -
409A LEU* 3.8 22.1 - - + +
412A TRP* 4.9 1.6 - - - -
413A GLY 3.5 7.7 + - - -
414A GLY* 1.3 88.7 + - - -
416A ASN* 1.3 74.6 + - - +
417A PHE 3.3 0.4 - - - -
418A GLU* 3.7 15.0 - - - +
419A ILE* 3.3 12.3 + - - +
468A VAL* 4.2 3.4 - - - +
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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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362A TRP* 4.2 7.1 - - - +
387A MET* 2.9 25.0 + - + +
388A ALA 3.0 22.2 + - - +
389A GLY* 3.6 15.0 - - - -
405A TYR* 5.0 1.8 - - - -
414A GLY* 3.0 22.7 + - - -
415A GLU* 1.3 80.3 - - - +
417A PHE* 1.3 93.9 + - - +
419A ILE* 3.3 10.2 - - - +
420A SER* 2.8 26.6 + - - -
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Residues in contact with PHE 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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355A ALA 3.6 21.3 - - - -
356A TRP* 3.6 30.5 - + + -
360A MET* 3.7 34.8 - - + -
362A TRP* 3.9 20.6 - + + -
386A ALA* 4.0 12.3 - - + -
414A GLY 3.9 10.1 - - - +
415A GLU 3.3 0.4 - - - +
416A ASN* 1.3 107.4 + - - +
418A GLU* 1.3 66.5 + - - +
420A SER* 3.0 4.5 + - - -
421A TYR* 2.9 57.5 + + + -
465A TYR* 5.5 1.8 - + - -
468A VAL* 4.4 4.3 - - + -
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Residues in contact with GLU 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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405A TYR* 3.8 12.5 - - - -
406A ASP* 3.0 43.5 + - + +
409A LEU* 3.9 5.9 - - + +
415A GLU* 3.5 21.8 + - - +
416A ASN 3.4 0.6 - - - -
417A PHE* 1.3 79.6 - - - +
419A ILE* 1.3 61.5 + - - +
421A TYR* 3.4 3.1 + - - +
422A LYS* 3.0 60.2 + - - +
468A VAL* 4.0 26.7 - - + +
471A VAL* 5.8 0.7 - - + -
472A TRP* 4.1 14.4 + - + +
498A LEU* 3.5 9.9 - - + +
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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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387A MET* 3.9 28.5 - - + -
392A PHE* 5.4 2.0 - - + -
394A ILE* 4.7 4.5 - - + -
399A PHE* 3.3 37.0 - - + -
402A LEU* 4.2 15.9 - - + -
404A LEU 4.0 11.2 - - - +
405A TYR* 3.9 14.1 - - + +
415A GLU 3.3 11.3 + - - +
416A ASN* 3.3 13.9 - - - +
418A GLU* 1.3 79.9 + - - +
420A SER* 1.3 61.1 + - - +
422A LYS* 3.3 10.0 + - - +
423A ILE* 2.9 50.5 + - + +
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Residues in contact with SER 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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385A PRO 3.6 6.3 - - - -
386A ALA* 3.2 23.5 - - - +
387A MET* 3.1 26.9 + - - +
416A ASN 2.8 17.2 + - - -
417A PHE* 3.0 8.6 + - - -
419A ILE* 1.3 82.0 - - - +
421A TYR* 1.3 65.5 + - - +
423A ILE* 4.0 5.3 - - - +
424A TRP* 3.1 31.3 + - - -
430A LEU* 4.5 6.4 - - - +
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Residues in contact with TYR 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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356A TRP* 3.5 40.8 - + - -
360A MET* 4.1 2.2 - - + +
417A PHE* 2.9 45.7 + + + +
418A GLU* 4.0 1.3 - - - +
420A SER* 1.3 73.7 - - - +
422A LYS* 1.3 68.2 + - - +
424A TRP* 3.1 3.8 + - - -
425A GLN* 2.8 47.5 + - - +
468A VAL* 3.5 27.4 - - + -
472A TRP* 4.0 20.6 - + + -
473A TRP* 3.3 30.0 + - - -
510A PHE* 3.8 17.7 - + - -
513A PHE* 3.9 12.3 - + - -
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Residues in contact with LYS 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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402A LEU* 2.9 48.0 + - + +
403A GLY 4.3 3.2 + - - -
404A LEU 3.4 18.3 + - - -
406A ASP* 4.1 5.9 - - - +
418A GLU* 3.0 46.7 + - - +
419A ILE* 3.3 13.0 + - - +
421A TYR* 1.3 75.0 - - - +
423A ILE* 1.3 65.1 + - - +
426A CYS* 2.9 30.6 + - - +
472A TRP* 3.2 34.7 - - + +
498A LEU* 4.3 9.1 - - + +
501A PHE* 4.3 12.8 - - + -
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Residues in contact with ILE 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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323A THR 4.1 5.4 - - - +
325A CYS* 3.7 29.2 - - + -
387A MET* 4.9 3.1 - - + -
394A ILE* 4.6 5.2 - - + -
398A PHE* 4.4 6.5 - - + -
402A LEU* 3.5 27.4 - - + -
419A ILE* 2.9 41.3 + - + +
420A SER* 4.0 4.9 - - - +
422A LYS* 1.3 76.6 - - - +
424A TRP* 1.3 58.1 + - - +
426A CYS 4.1 0.3 - - - -
427A GLY 3.7 0.9 + - - -
428A GLY* 2.5 38.7 + - - -
429A LYS 3.4 35.4 - - - +
430A LEU* 4.4 5.4 - - + +
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Residues in contact with TRP 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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383A ARG* 3.6 36.6 - - + -
384A SER 2.9 23.5 + - - -
385A PRO 3.3 15.8 + - - -
420A SER 3.1 22.0 + - - +
421A TYR 3.1 1.4 + - - +
423A ILE* 1.3 82.3 - - - +
425A GLN* 1.3 61.8 + - - +
426A CYS 3.4 0.2 + - - -
427A GLY* 3.6 7.4 + - - -
428A GLY 3.4 26.4 - - - +
429A LYS* 3.9 12.3 - - + -
430A LEU* 3.3 44.8 - - + +
508A LYS* 5.0 0.7 - - - -
512A TRP* 3.5 20.9 - + + -
513A PHE* 3.3 26.9 - + + -
517A ILE* 3.5 34.6 - - + +
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Residues in contact with GLN 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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421A TYR* 2.8 47.1 + - - +
424A TRP* 1.3 74.2 - - - +
426A CYS* 1.3 56.8 + - - +
427A GLY 3.4 1.6 - - - -
472A TRP* 3.7 29.9 + - + +
502A ARG* 3.9 2.3 + - - -
507A CYS* 3.3 1.3 - - + -
508A LYS* 2.6 61.8 + - - +
509A SER 4.2 1.8 - - - +
510A PHE* 3.4 38.1 + - - -
512A TRP* 4.1 6.5 - - + -
513A PHE* 4.1 21.0 - - + -
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Residues in contact with CYS 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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115A PHE* 2.9 40.3 - - + -
402A LEU* 4.8 2.7 - - + -
422A LYS* 2.9 21.9 + - - +
423A ILE* 5.4 0.2 - - - -
424A TRP 3.3 0.2 - - - -
425A GLN* 1.3 75.6 - - - +
427A GLY* 1.3 56.5 + - - +
428A GLY 3.6 2.2 - - - -
472A TRP* 3.8 16.4 - - - -
501A PHE* 4.0 11.0 - - + -
505A HIS* 5.1 4.6 - - + +
507A CYS* 1.7 59.5 - - - +
508A LYS* 5.9 0.2 - - - -
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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