Contacts of the helix formed by residues 422 - 431 (chain C) in PDB entry 1G3I
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 ASP 422 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370C THR* 3.4 20.0 - - + +
373C ALA* 3.7 7.2 - - - -
420C ASN* 3.8 15.1 - - - +
421C ILE* 1.3 74.5 - - - +
423C ALA* 1.3 66.1 + - - +
424C ALA* 3.5 13.8 - - - +
425C TYR* 2.7 35.2 + - - +
426C VAL* 3.0 24.4 + - - +
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Residues in contact with ALA 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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370C THR* 4.2 1.4 + - - -
372C ASP* 4.1 26.0 - - + +
373C ALA* 4.0 11.7 - - - +
376C LYS* 4.4 13.6 - - + +
422C ASP* 1.3 72.2 - - - +
424C ALA* 1.3 60.7 + - - +
426C VAL* 4.2 0.8 - - - +
427C ALA* 2.9 31.8 + - - +
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Residues in contact with ALA 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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422C ASP* 3.2 13.8 + - - +
423C ALA* 1.3 75.1 - - - +
425C TYR* 1.3 68.5 + - - +
427C ALA* 3.0 7.7 + - - +
428C ASP* 2.9 23.2 + - - +
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Residues in contact with TYR 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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403C LEU* 5.4 7.7 + - + -
406C LYS* 5.3 7.8 - - + +
407C ILE* 3.0 32.0 + - + +
419C VAL* 3.5 17.8 - - + +
420C ASN 4.3 2.7 - - - +
421C ILE* 3.1 46.0 - - + -
422C ASP* 2.7 30.3 + - - +
424C ALA* 1.3 71.3 - - - +
426C VAL* 1.3 59.5 + - - +
428C ASP* 2.9 12.6 + - + +
429C ALA* 2.8 39.7 + - + +
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Residues in contact with VAL 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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373C ALA* 4.0 11.2 - - + +
376C LYS* 3.9 22.0 - - + -
377C ILE* 3.7 28.7 - - + +
403C LEU* 3.7 27.8 - - + -
421C ILE* 3.7 11.4 - - + -
422C ASP 3.0 14.7 + - - +
423C ALA 4.2 0.2 - - - +
425C TYR* 1.3 79.6 - - - +
427C ALA* 1.3 65.6 + - - +
428C ASP 2.9 1.2 + - - -
429C ALA* 4.5 1.8 - - - +
430C LEU* 3.2 42.5 + - + +
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Residues in contact with ALA 427 (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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376C LYS* 4.0 25.1 - - - +
423C ALA 2.9 22.8 + - - +
424C ALA* 3.4 5.8 - - - +
426C VAL* 1.3 76.3 - - - +
428C ASP* 1.3 60.6 + - - +
430C LEU* 4.3 2.5 - - - +
431C GLY* 3.7 14.6 + - - +
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Residues in contact with ASP 428 (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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406C LYS* 5.9 1.6 - - - -
424C ALA 2.9 10.0 + - - +
425C TYR* 2.9 18.3 + - + +
426C VAL 2.9 0.2 + - - -
427C ALA* 1.3 76.0 - - - +
429C ALA* 1.3 70.8 + - - +
430C LEU 2.5 17.9 + - - -
431C GLY* 3.0 14.4 + - - -
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Residues in contact with ALA 429 (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 ARG* 4.1 6.9 - - - +
403C LEU* 3.8 38.4 - - + +
406C LYS* 3.7 27.3 + - + +
425C TYR* 2.8 26.5 + - + +
426C VAL* 4.0 3.8 - - - +
428C ASP* 1.3 80.9 + - - +
430C LEU* 1.3 63.1 + - - +
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Residues in contact with LEU 430 (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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376C LYS* 5.9 1.6 - - + -
380C ALA* 3.8 28.7 - - + -
399C VAL* 3.9 19.3 - - + +
402C ARG* 4.0 38.9 + - + +
403C LEU* 4.0 29.4 - - + +
426C VAL* 3.2 32.2 + - + +
427C ALA* 4.8 2.7 - - - +
428C ASP 2.5 6.6 + - - -
429C ALA* 1.3 82.9 - - - +
431C GLY* 1.3 60.7 + - - +
432C GLU 3.6 3.5 + - - +
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Residues in contact with GLY 431 (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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427C ALA 3.7 11.8 + - - +
428C ASP 3.0 10.9 + - - -
430C LEU* 1.3 78.4 - - - +
432C GLU* 1.3 69.1 + - - +
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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