Contacts of the helix formed by residues 414 - 426 (chain B) 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 GLY 414 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409B LEU* 4.7 1.3 - - - -
413B GLY* 1.3 68.3 - - - -
415B GLU* 1.3 63.5 + - - -
416B ASN* 3.2 15.9 - - - -
417B PHE* 3.4 10.7 + - - +
418B GLU 3.3 15.9 + - - -
464B ASN* 4.2 4.4 - - - +
465B TYR* 3.5 28.6 - - - -
468B VAL* 3.7 16.8 - - - +
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Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 4.6 7.4 - - - +
281B ILE* 3.6 39.4 - - + +
284B ARG* 3.4 34.8 + - - +
388B ALA 5.2 0.5 - - - +
389B GLY* 4.8 3.7 - - - +
405B TYR* 3.3 23.5 - - + +
409B LEU* 3.7 12.7 - - + +
412B TRP* 4.2 3.6 + - - -
413B GLY 2.5 32.1 + - - +
414B GLY* 1.3 73.4 - - - +
416B ASN* 1.3 77.9 + - + +
418B GLU* 3.4 2.6 + - - +
419B ILE* 3.3 18.0 + - - +
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Residues in contact with ASN 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B TRP* 4.0 6.9 - - - +
387B MET* 3.1 18.7 + - + +
388B ALA 3.0 29.0 + - - +
389B GLY* 3.6 14.1 - - - -
405B TYR* 5.0 0.7 - - - -
413B GLY 4.6 0.2 - - - +
414B GLY* 3.4 17.7 - - - -
415B GLU* 1.3 90.7 + - - +
417B PHE* 1.3 90.0 + - - +
419B ILE* 3.4 10.4 - - - +
420B SER* 2.8 27.4 + - - -
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Residues in contact with PHE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ALA 3.6 6.1 - - - -
356B TRP* 3.6 42.2 - + + -
360B MET* 3.3 52.0 - - + -
362B TRP* 3.9 24.7 - + + -
386B ALA* 4.0 12.8 - - + -
414B GLY* 3.8 11.0 - - - +
415B GLU 3.3 0.6 - - - -
416B ASN* 1.3 104.4 + - - +
418B GLU* 1.3 68.1 + - - +
420B SER* 3.1 4.0 + - - -
421B TYR* 3.0 46.5 + + + -
465B TYR* 5.5 1.1 - + - -
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 3.8 14.4 - - - -
406B ASP* 3.0 42.4 + - + +
409B LEU* 4.0 4.5 - - + +
414B GLY 3.3 10.6 + - - +
415B GLU* 3.4 10.1 + - - +
417B PHE* 1.3 79.7 - - - +
419B ILE* 1.3 61.9 + - - +
421B TYR* 3.4 3.1 + - - +
422B LYS* 3.0 61.5 + - - +
468B VAL* 4.0 26.6 - - + +
471B VAL* 5.8 0.9 - - + -
472B TRP* 4.1 18.0 + - + +
498B LEU* 4.6 4.0 - - - +
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Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B MET* 3.9 29.6 - - + -
392B PHE* 5.4 2.5 - - + -
394B ILE* 4.7 4.0 - - + -
399B PHE* 3.3 37.9 - - + -
402B LEU* 4.3 15.0 - - + -
404B LEU 4.0 11.7 - - - +
405B TYR* 3.9 17.7 - - + +
415B GLU 3.3 7.3 + - - +
416B ASN* 3.4 13.0 - - - +
418B GLU* 1.3 79.1 + - - +
420B SER* 1.3 61.0 + - - +
422B LYS* 3.3 9.8 + - - +
423B ILE* 2.9 50.4 + - + +
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Residues in contact with SER 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B PRO 3.6 19.5 - - - -
386B ALA* 3.2 9.6 - - - +
387B MET* 3.1 27.3 + - - +
416B ASN 2.8 20.4 + - - -
417B PHE* 3.1 5.9 + - - -
419B ILE* 1.3 80.8 - - - +
421B TYR* 1.3 66.3 + - - +
423B ILE* 3.4 5.5 + - - +
424B TRP* 3.1 32.0 + - - -
430B LEU* 4.5 6.4 - - - +
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Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B TRP* 3.5 41.9 - + - -
360B MET* 3.7 5.1 - - + +
417B PHE* 3.0 45.2 + + + +
418B GLU* 4.0 1.6 - - - +
420B SER* 1.3 73.5 - - - +
422B LYS* 1.3 68.9 + - - +
424B TRP* 3.1 4.1 + - - -
425B GLN* 2.8 47.0 + - - +
468B VAL* 3.5 26.5 - - + -
472B TRP* 4.0 21.1 - + + -
473B TRP* 3.3 27.4 + - - -
510B PHE* 3.8 16.4 - + - -
513B PHE* 3.9 11.9 - + - -
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Residues in contact with LYS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B LEU* 3.1 41.8 + - + +
403B GLY* 4.3 4.8 + - - -
404B LEU 3.3 22.1 + - - -
406B ASP* 4.1 6.9 - - - +
418B GLU* 3.0 44.0 + - - +
419B ILE* 3.6 15.3 - - - +
421B TYR* 1.3 73.3 - - - +
423B ILE* 1.3 64.8 + - - +
426B CYS* 2.9 31.0 + - - +
472B TRP* 3.2 36.3 - - + +
498B LEU* 4.8 8.3 - - - +
501B PHE* 4.1 11.9 - - + -
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B THR 4.2 6.5 - - - +
325B CYS* 3.7 29.6 - - + -
387B MET* 4.9 2.7 - - + -
394B ILE* 4.6 4.9 - - + -
398B PHE* 4.3 5.2 - - + -
402B LEU* 3.3 28.0 - - + -
419B ILE* 2.9 40.6 + - + +
420B SER* 4.0 4.9 - - - +
422B LYS* 1.3 76.6 - - - +
424B TRP* 1.3 57.2 + - - +
426B CYS* 4.1 0.6 - - - -
427B GLY 3.7 0.5 + - - -
428B GLY* 2.5 39.8 + - - -
429B LYS 3.4 35.9 - - - +
430B LEU* 4.4 6.7 - - + +
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Residues in contact with TRP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B ARG* 3.4 36.6 - - + -
384B SER 2.6 25.1 + - - -
385B PRO 3.3 18.8 + - - -
420B SER 3.1 18.8 + - - +
421B TYR 3.1 2.5 + - - +
423B ILE* 1.3 80.1 - - - +
425B GLN* 1.3 62.0 + - - +
426B CYS 3.4 0.2 + - - -
427B GLY* 3.6 7.4 + - - -
428B GLY 3.4 26.9 - - - +
429B LYS* 3.9 13.7 - - + -
430B LEU* 3.3 44.2 - - + +
508B LYS* 5.0 1.0 - - - +
512B TRP* 3.5 22.3 - + - -
513B PHE* 3.3 25.8 - + + -
517B ILE* 3.5 32.9 - - + +
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Residues in contact with GLN 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B TYR* 2.8 46.8 + - - +
424B TRP* 1.3 75.0 - - - +
426B CYS* 1.3 58.1 + - - +
427B GLY 3.4 1.3 - - - -
472B TRP* 3.7 19.2 + - + +
502B ARG* 3.6 13.7 + - - -
507B CYS* 3.3 1.9 - - - -
508B LYS* 2.8 61.3 + - - +
509B SER 4.2 1.6 - - - +
510B PHE* 3.4 38.8 + - - -
512B TRP* 4.1 6.7 - - + -
513B PHE* 4.1 20.3 - - + -
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Residues in contact with CYS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PHE* 3.0 39.5 - - + -
402B LEU* 4.6 3.4 - - + -
422B LYS 2.9 20.9 + - - +
423B ILE* 4.9 0.4 - - - +
424B TRP 3.3 0.2 - - - -
425B GLN* 1.3 77.6 - - - +
427B GLY* 1.3 56.1 + - - +
428B GLY 3.6 2.2 - - - -
472B TRP* 3.8 17.0 - - - -
501B PHE* 3.9 11.7 - - - -
505B HIS* 5.1 3.7 - - + +
507B CYS* 2.1 47.1 - - - +
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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