Contacts of the helix formed by residues 414 - 426 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360C MET* 5.3 0.4 - - - -
409C LEU* 4.0 5.6 - - - +
413C GLY* 1.3 69.9 + - - -
415C GLU* 1.3 59.4 + - - +
416C ASN* 3.6 11.5 + - - -
417C PHE* 4.2 7.9 + - - +
418C GLU* 3.6 9.7 + - - +
464C ASN* 4.5 5.8 - - - -
465C TYR* 3.8 29.1 - - - -
468C VAL* 3.3 26.1 - - - +
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Residues in contact with GLU 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 4.7 5.5 - - - +
281C ILE* 3.3 37.2 - - + -
284C ARG* 2.5 33.0 + - - +
388C ALA 5.2 1.6 - - - +
389C GLY* 4.1 8.2 - - - +
405C TYR* 3.3 32.2 + - + -
409C LEU* 3.9 10.1 - - - -
412C TRP* 4.5 12.2 - - - -
413C GLY* 3.1 21.1 + - - +
414C GLY* 1.3 77.3 - - - +
416C ASN* 1.3 80.4 + - - +
418C GLU* 3.5 2.1 + - - +
419C ILE* 3.4 12.6 + - - +
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Residues in contact with ASN 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C TRP* 4.0 7.5 - - - +
387C MET* 2.9 24.9 + - + +
388C ALA 3.1 23.1 + - - +
389C GLY* 3.6 13.0 - - - -
405C TYR* 5.1 1.3 - - - -
413C GLY 4.6 0.2 - - - -
414C GLY 3.9 12.0 + - - -
415C GLU* 1.3 85.4 - - - +
417C PHE* 1.3 93.2 + - - +
419C ILE* 3.4 9.5 - - - +
420C SER* 2.8 32.7 + - - -
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Residues in contact with PHE 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C ALA 3.5 10.8 - - - -
356C TRP* 3.5 42.8 - + + -
360C MET* 3.7 35.4 - - + -
362C TRP* 3.9 19.5 - + + -
386C ALA* 4.0 12.1 - - + -
414C GLY* 4.5 8.3 - - - +
415C GLU 3.4 0.2 - - - -
416C ASN* 1.3 101.1 + - - +
418C GLU* 1.3 65.0 + - - +
420C SER* 3.2 4.0 + - - -
421C TYR* 3.0 58.0 + + + -
465C TYR* 5.5 2.0 - + - -
468C VAL* 4.4 5.8 - - + -
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Residues in contact with GLU 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C TYR* 3.8 14.0 - - - -
406C ASP* 3.0 42.3 + - + +
409C LEU* 4.2 5.3 - - + +
414C GLY 3.6 17.7 + - - +
415C GLU 3.5 5.1 + - - +
416C ASN 3.4 0.6 - - - -
417C PHE* 1.3 79.5 - - - +
419C ILE* 1.3 62.0 + - - +
421C TYR* 3.4 3.4 + - - +
422C LYS* 3.0 60.1 + - - +
468C VAL* 4.0 24.1 - - + +
472C TRP* 4.1 14.8 + - + +
498C LEU* 3.5 10.0 - - + +
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Residues in contact with ILE 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C MET* 3.9 28.7 - - + -
392C PHE* 5.4 2.0 - - + -
394C ILE* 4.7 4.5 - - + -
399C PHE* 3.3 37.9 - - + -
402C LEU* 4.2 15.5 - - + -
404C LEU 4.0 10.3 - - - +
405C TYR* 3.9 17.3 - - + +
415C GLU 3.4 8.0 + - - +
416C ASN* 3.4 13.0 - - - +
418C GLU* 1.3 78.8 + - - +
420C SER* 1.3 60.6 + - - +
422C LYS* 3.3 9.9 + - - +
423C ILE* 2.9 50.8 + - + +
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Residues in contact with SER 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C PRO 3.6 5.8 - - - -
386C ALA* 3.2 23.3 - - - +
387C MET* 3.1 27.2 + - - +
416C ASN 2.8 19.5 + - - -
417C PHE* 3.2 5.9 + - - -
419C ILE* 1.3 80.6 - - - +
421C TYR* 1.3 66.1 + - - +
423C ILE* 3.4 5.7 + - - +
424C TRP* 3.1 32.2 + - - -
430C LEU* 4.5 6.0 - - - +
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Residues in contact with TYR 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C TRP* 3.5 40.6 - + - -
360C MET* 4.1 1.5 - - + +
417C PHE* 3.0 46.0 + + + +
418C GLU* 4.0 1.3 - - - +
420C SER* 1.3 73.5 - - - +
422C LYS* 1.3 68.6 + - - +
424C TRP* 3.1 3.2 + - - +
425C GLN* 2.8 47.1 + - - +
468C VAL* 3.5 26.2 - - + -
472C TRP* 4.0 20.4 - + + -
473C TRP* 3.3 31.5 + - - -
510C PHE* 3.8 17.7 - + - -
513C PHE* 3.9 11.7 - + - -
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Residues in contact with LYS 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C LEU* 2.9 47.4 + - + +
403C GLY 4.3 3.0 + - - -
404C LEU 3.4 18.1 + - - -
406C ASP* 4.1 5.9 - - - +
418C GLU* 3.0 45.6 + - - +
419C ILE* 3.6 13.7 - - - +
421C TYR* 1.3 73.9 - - - +
423C ILE* 1.3 64.1 + - - +
426C CYS* 2.9 31.1 + - - +
472C TRP* 3.2 36.3 - - + +
498C LEU* 4.3 9.3 - - + +
501C PHE* 4.3 13.2 - - + -
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Residues in contact with ILE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C THR 4.1 5.2 - - - +
325C CYS* 3.7 29.4 - - + -
387C MET* 4.9 2.7 - - + -
394C ILE* 4.6 4.5 - - + -
398C PHE* 4.4 6.1 - - + -
402C LEU* 3.5 27.1 - - + -
419C ILE* 2.9 41.5 + - + +
420C SER* 4.0 5.4 - - - +
421C TYR 3.2 0.2 - - - -
422C LYS* 1.3 76.8 - - - +
424C TRP* 1.3 57.0 + - - +
426C CYS 4.1 0.2 - - - -
427C GLY 3.7 0.9 + - - -
428C GLY* 2.5 39.5 + - - -
429C LYS 3.4 36.1 - - - +
430C LEU* 4.4 5.8 - - + +
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Residues in contact with TRP 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C ARG* 3.8 33.9 - - + -
384C SER 2.9 22.8 + - - -
385C PRO 3.3 15.8 + - - -
420C SER* 3.1 21.7 + - - +
421C TYR 3.1 2.7 + - - +
423C ILE* 1.3 81.0 - - - +
425C GLN* 1.3 63.1 + - - +
426C CYS 3.4 0.3 + - - -
427C GLY* 3.6 7.4 + - - -
428C GLY 3.4 26.9 - - - +
429C LYS* 3.9 13.0 - - + -
430C LEU* 3.3 44.7 - - + +
508C LYS* 5.0 0.9 - - - +
512C TRP* 3.5 21.2 - + - -
513C PHE* 3.3 27.4 - + + -
517C ILE* 3.5 36.5 - - + +
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Residues in contact with GLN 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C TYR* 2.8 47.1 + - - +
424C TRP* 1.3 73.5 - - - +
426C CYS* 1.3 56.8 + - - +
427C GLY 3.4 1.3 - - - -
472C TRP* 3.7 31.0 + - + +
502C ARG* 3.9 2.3 + - - -
507C CYS* 3.3 2.0 - - + +
508C LYS* 2.8 57.7 + - - +
509C SER 4.2 1.8 - - - +
510C PHE* 3.4 39.3 + - - -
512C TRP* 4.1 6.3 - - + -
513C PHE* 4.1 20.9 - - + -
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Residues in contact with CYS 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PHE* 3.0 39.7 - - + -
402C LEU* 4.8 2.9 - - + -
422C LYS 2.9 21.6 + - - +
423C ILE* 4.1 0.4 - - - -
425C GLN* 1.3 76.0 - - - +
427C GLY* 1.3 57.3 + - - +
428C GLY 3.6 2.2 - - - -
472C TRP* 3.8 17.3 - - - -
501C PHE* 4.0 10.5 - - - -
505C HIS* 5.1 3.5 - - + +
507C CYS* 2.1 48.2 - - - +
508C 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