Contacts of the helix formed by residues 416 - 422 (chain C) in PDB entry 6ZGI
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 416 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A TYR* 5.9 0.2 - - - -
369A TYR* 3.6 19.6 + - - -
408C ARG* 6.1 0.2 - - - -
409C GLN* 3.5 11.7 - - - -
415C THR* 1.3 85.6 + - - +
417C LYS* 1.3 61.6 + - - -
418C ILE 3.3 2.9 - - - -
419C ALA 3.3 0.9 + - - -
420C ASP* 2.9 31.7 + - - -
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Residues in contact with LYS 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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369A TYR* 3.8 48.4 - - + +
373A SER* 6.1 0.4 - - - -
403C ARG* 4.1 8.4 - - - +
406C GLU* 2.3 34.1 + - + +
409C GLN* 3.7 4.9 + - - +
416C GLY* 1.3 72.6 - - - -
418C ILE* 1.3 67.7 + - + +
420C ASP* 4.5 0.7 - - - +
421C TYR* 2.9 37.1 + - + +
422C ASN* 3.2 10.2 + - - -
453C TYR* 3.8 34.3 - - + -
454C ARG 4.8 2.5 - - - +
455C LEU* 4.2 20.6 - - + -
495C TYR* 4.1 2.4 + - - -
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Residues in contact with ILE 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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350C VAL* 4.4 20.0 - - + -
402C ILE* 4.6 6.1 - - + -
406C GLU* 3.6 40.6 - - + +
409C GLN* 3.2 14.8 + - + +
410C ILE* 3.9 28.0 - - + -
417C LYS* 1.3 91.8 - - + +
419C ALA* 1.3 57.6 + - - +
422C ASN* 3.2 31.8 + - + +
423C TYR* 2.8 33.9 + - + +
453C TYR* 4.8 1.8 - - + -
495C TYR* 4.1 6.5 - - - +
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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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409C GLN* 3.4 20.4 + - - +
411C ALA 5.8 0.4 - - - +
414C GLN* 3.5 30.1 - - + +
415C THR 3.9 11.0 - - - +
416C GLY 3.3 2.5 + - - +
418C ILE* 1.3 78.0 - - - +
420C ASP* 1.3 62.3 + - - +
423C TYR 3.4 14.3 - - - +
424C LYS* 3.4 29.9 + - + +
461C LEU 5.6 0.3 - - - +
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Residues in contact with ASP 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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365A TYR* 5.2 0.5 + - - -
369A TYR* 3.1 19.4 + - - -
414C GLN 4.4 2.6 - - - +
415C THR* 3.6 18.6 + - - -
416C GLY 2.9 24.1 + - - +
417C LYS* 4.3 0.7 - - - +
419C ALA* 1.3 84.4 - - - +
421C TYR* 1.3 84.8 + - + +
422C ASN 3.8 0.2 - - - -
424C LYS* 5.5 1.8 + - - -
459C SER 4.5 0.2 - - - +
460C ASN* 3.5 28.8 + - - +
461C LEU* 3.0 30.7 + - - +
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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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366A SER* 4.6 8.3 - - - -
369A TYR* 4.0 31.0 - + - -
351C TYR* 5.9 0.2 - - - +
417C LYS* 2.9 18.3 + - + +
420C ASP* 1.3 92.8 + - + +
422C ASN* 1.3 65.8 + - - +
454C ARG* 3.7 34.6 + - + -
455C LEU 3.3 33.2 - - - -
456C PHE* 4.4 0.4 - - - -
457C ARG* 3.5 43.1 + - + +
459C SER 4.3 2.5 - - - -
460C ASN* 4.1 12.5 + - - -
461C LEU* 3.3 17.7 - - - +
467C ASP* 5.2 1.7 - - - +
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Residues in contact with ASN 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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350C VAL* 3.6 37.9 - - + +
351C TYR* 3.6 16.4 - - - +
353C TRP* 3.7 20.1 + - - -
417C LYS* 3.2 19.6 + - - +
418C ILE* 3.2 21.9 + - - +
420C ASP 3.8 0.6 - - - -
421C TYR* 1.3 82.8 - - - +
423C TYR* 1.3 63.9 + - - +
453C TYR* 4.5 1.2 - - - +
454C ARG* 3.2 43.6 + - - +
461C LEU* 3.8 11.7 - - - +
465C GLU 4.3 0.3 - - - +
466C ARG* 5.6 0.7 - - - -
467C ASP 5.8 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