Contacts of the helix formed by residues 426 - 431 (chain C) in PDB entry 3IXK
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 426 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ASN* 4.1 7.3 - - - +
425C LEU* 1.3 80.4 - - - +
427C MET* 1.3 63.0 + - - +
428C GLU* 3.3 2.9 - - - -
429C ASP* 3.1 39.1 + - + +
430C CYS* 3.9 6.5 + - - -
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Residues in contact with MET 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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250C ILE* 3.9 10.0 - - - +
252C VAL* 3.8 19.7 - - + -
336C MET* 3.9 36.3 - - + -
339C VAL 5.2 1.1 - - - +
341C ASN* 3.6 7.4 - - - +
342C GLN 2.9 47.1 - - - +
343C SER* 3.2 11.4 - - - -
424C THR* 3.1 48.0 + - + +
425C LEU 4.1 0.4 - - - -
426C ASP* 1.3 75.1 - - - +
428C GLU* 1.3 64.4 + - - +
430C CYS* 3.0 22.1 + - - +
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Residues in contact with GLU 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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242C ARG* 5.3 1.2 + - - -
250C ILE* 4.3 12.3 - - - +
336C MET* 3.3 25.9 - - - +
426C ASP 3.3 1.1 - - - +
427C MET* 1.3 72.8 - - - +
429C ASP* 1.3 63.9 + - - +
430C CYS 2.9 4.5 - - - -
431C GLY* 2.9 24.1 + - - +
433C ASN* 5.6 1.0 - - - +
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Residues in contact with ASP 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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264C ASP* 5.2 0.3 - - - +
265C CYS* 4.5 4.5 - - - -
266C LYS* 3.1 42.6 + - - +
426C ASP* 3.1 35.3 + - + +
428C GLU* 1.3 80.5 - - - +
430C CYS* 1.3 59.7 + - - +
431C GLY 3.2 0.4 - - - -
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Residues in contact with CYS 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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250C ILE* 3.6 15.7 - - + -
251C ILE 3.9 0.7 - - - +
252C VAL* 3.7 20.9 - - - -
265C CYS* 2.1 48.0 - - - -
266C LYS* 3.4 14.6 - - - +
269C ASN* 3.2 23.3 + - - +
424C THR* 5.8 0.9 - - - -
425C LEU 5.6 1.6 - - - -
426C ASP 4.3 7.0 - - - -
427C MET* 3.0 17.3 + - - +
428C GLU 2.9 2.0 + - - -
429C ASP* 1.3 81.5 - - - +
431C GLY* 1.3 60.6 + - - +
432C TYR 3.6 1.4 + - - -
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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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242C ARG* 3.5 20.6 - - - -
250C ILE* 4.3 11.3 - - - +
266C LYS* 3.9 14.4 + - - -
269C ASN* 4.7 4.5 - - - -
427C MET 4.3 1.0 + - - -
428C GLU 2.9 14.1 + - - +
429C ASP 4.6 0.2 - - - -
430C CYS* 1.3 77.6 - - - +
432C TYR* 1.3 67.4 + - - -
433C ASN* 3.6 11.4 + - - +
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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