Contacts of the helix formed by residues 406 - 421 (chain C) in PDB entry 1ZXN
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 406 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303C MET* 3.8 12.6 - - - +
402C ALA 4.6 0.6 + - - -
403C ILE 5.0 0.8 + - - -
404C GLY* 3.2 5.0 - - - -
405C CYS* 1.3 80.5 - - - +
407C ILE* 1.3 64.9 + - - +
408C VAL 3.3 3.7 - - - +
409C GLU* 3.5 13.6 + - - +
410C SER* 3.1 22.9 + - - -
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Residues in contact with ILE 407 (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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301C LEU* 5.7 2.2 - - + -
302C THR 5.7 0.9 - - - +
303C MET* 3.8 16.0 - - + -
337C LEU* 3.4 28.3 - - + -
341C VAL* 6.0 0.2 - - + -
356C VAL* 3.7 33.7 - - + +
359C HIS* 3.5 42.0 - - + +
360C MET* 5.3 4.9 - - + -
402C ALA 4.4 0.9 + - - +
405C CYS* 3.2 27.8 - - - -
406C GLY* 1.3 70.9 - - - +
408C VAL* 1.3 73.0 + - - +
410C SER* 3.3 4.6 + - - -
411C ILE* 3.1 20.6 + - + +
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Residues in contact with VAL 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C LEU* 3.9 22.4 - - + +
340C VAL* 4.3 16.4 - - + -
341C VAL* 3.9 29.2 - - + +
344C LYS* 5.0 9.2 - - + +
402C ALA 4.8 0.4 - - - +
403C ILE* 3.5 40.6 - - + +
406C GLY 3.3 1.2 - - - +
407C ILE* 1.3 78.6 - - - +
409C GLU* 1.3 57.8 + - - +
411C ILE* 3.0 12.6 + - - +
412C LEU* 2.8 36.4 + - + +
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Residues in contact with GLU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C GLY* 3.5 16.2 + - - +
407C ILE 3.4 0.4 - - - -
408C VAL* 1.3 80.3 - - - +
410C SER* 1.3 59.2 + - - +
412C LEU* 2.9 22.7 - - - +
413C ASN* 3.4 20.8 + - - +
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Residues in contact with SER 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C MET* 4.9 5.6 - - - -
359C HIS* 4.1 22.2 - - - -
406C GLY 3.1 16.5 + - - -
407C ILE* 3.7 5.2 - - - -
408C VAL 3.1 0.2 - - - -
409C GLU* 1.3 78.3 - - - +
411C ILE* 1.3 62.7 + - - +
413C ASN* 3.3 9.2 + - - +
414C TRP* 3.2 22.4 + - - +
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Residues in contact with ILE 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C VAL* 4.6 18.4 - - + -
355C GLN* 5.8 5.4 - - + +
356C VAL* 5.0 8.7 - - + -
359C HIS* 4.9 9.8 + - + +
407C ILE* 3.1 25.5 + - + +
408C VAL 3.0 6.3 + - - +
410C SER* 1.3 77.4 - - - +
412C LEU* 1.3 57.4 + - - +
414C TRP* 3.5 11.1 + - - +
415C VAL* 3.0 25.5 + - - +
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Residues in contact with LEU 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C VAL* 4.5 17.3 - - + +
344C LYS* 3.8 46.7 - - + +
345C ASN* 4.9 11.9 - - + +
408C VAL* 2.8 37.0 - - + +
409C GLU* 2.9 24.9 - - - +
411C ILE* 1.3 71.5 - - - +
413C ASN* 1.3 66.5 + - - +
414C TRP 3.2 0.9 - - - -
415C VAL* 3.6 7.4 - - + +
416C LYS* 2.9 29.1 + - - +
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Residues in contact with ASN 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C GLU* 3.4 19.4 + - - +
410C SER* 3.3 10.4 + - - +
412C LEU* 1.3 83.3 - - - +
414C TRP* 1.3 58.3 + - - +
416C LYS* 3.3 5.0 + - - +
417C PHE* 2.9 32.0 + - - +
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Residues in contact with TRP 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C GLN* 6.1 5.4 - - + -
359C HIS* 6.1 6.5 - + + +
410C SER 3.2 9.5 + - - +
411C ILE* 3.5 13.2 - - - +
413C ASN* 1.3 82.6 - - - +
415C VAL* 1.3 61.7 + - + +
417C PHE* 3.5 32.5 + + - +
418C LYS* 2.9 38.7 + - + +
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Residues in contact with VAL 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C VAL* 6.2 0.9 - - + -
345C ASN* 4.4 11.2 - - - +
348C GLY* 4.0 2.2 - - - -
349C VAL* 3.4 37.6 + - + +
350C ALA 5.5 2.9 - - - +
351C VAL* 5.7 4.9 - - + +
411C ILE 3.0 17.0 + - - +
412C LEU* 3.9 9.0 - - - +
413C ASN 3.3 0.6 - - - -
414C TRP* 1.3 78.1 - - + +
416C LYS* 1.3 68.3 + - - +
418C LYS* 3.6 5.7 + - - +
419C ALA* 3.2 13.0 + - - +
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Residues in contact with LYS 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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347C GLY 5.5 0.7 - - - -
348C GLY* 4.3 11.8 - - - +
412C LEU 2.9 17.7 + - - +
413C ASN* 3.5 7.6 - - - +
415C VAL* 1.3 72.7 - - - +
417C PHE* 1.3 57.0 + - - +
419C ALA* 2.6 27.4 + - - +
420C GLN* 2.9 14.6 + - - +
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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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413C ASN 2.9 18.1 + - - +
414C TRP* 3.7 40.2 - + + +
416C LYS* 1.3 75.5 - - - +
418C LYS* 1.3 78.9 + - + +
419C ALA 2.8 7.4 + - - -
420C GLN* 2.8 19.6 + - + +
421C VAL* 2.9 33.5 + - + +
423D LEU* 6.4 1.6 - - + -
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Residues in contact with LYS 418 (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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349C VAL* 4.3 16.5 - - + +
414C TRP* 2.9 29.9 + - + +
415C VAL* 3.9 8.1 - - - +
416C LYS 3.2 0.2 + - - -
417C PHE* 1.3 84.1 - - + +
419C ALA* 1.3 56.7 + - - +
421C VAL* 3.0 25.0 - - - +
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Residues in contact with ALA 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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347C GLY 3.8 9.4 - - - +
348C GLY* 3.8 19.5 - - - -
349C VAL* 3.9 12.8 - - + +
415C VAL 3.2 12.0 + - - +
416C LYS* 2.6 19.0 + - - +
418C LYS* 1.3 72.8 - - - +
420C GLN* 1.3 59.9 + - - -
421C VAL 3.4 5.6 + - - +
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Residues in contact with GLN 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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416C LYS 2.9 8.8 + - - +
417C PHE* 2.8 11.9 + - + +
419C ALA* 1.3 77.9 - - - +
421C VAL* 1.3 61.1 + - - +
422C GLN* 4.6 0.3 - - - +
425D LYS* 2.8 31.2 - - + +
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Residues in contact with VAL 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C PHE* 2.9 34.3 + - + +
418C LYS* 3.0 32.8 - - - +
419C ALA 4.0 5.5 - - - +
420C GLN* 1.3 82.4 - - - +
422C GLN* 1.3 71.4 + - - +
423C LEU* 5.6 0.2 - - - -
423D LEU* 4.0 19.7 - - + -
424D ASN 3.1 11.9 - - - +
425D LYS* 4.8 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