Contacts of the helix formed by residues 324 - 328 (chain B) 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 PRO 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303B GLU* 3.4 28.9 - - - +
318B TRP* 3.3 34.1 - - + +
322B THR 3.7 5.8 - - - +
323B THR* 1.3 85.0 - - + +
325B TRP* 1.3 59.6 + - - +
326B ASN* 3.1 15.0 + - - +
327B ILE* 2.8 38.2 - - + +
328B PHE* 3.4 6.5 - - + -
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Residues in contact with TRP 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B THR* 2.8 32.0 + - + -
324B PRO* 1.3 70.1 - - - +
326B ASN* 1.3 64.2 + - - +
327B ILE 2.9 2.3 + - - -
328B PHE* 3.0 15.6 + - - +
350B PRO* 3.7 23.7 - - + +
351B GLN* 3.3 51.3 - - + +
354B LEU* 3.4 29.6 - - + -
368B TYR* 3.5 44.8 + + - -
411B ASP* 4.2 9.9 - - - +
414B ARG* 2.9 18.0 + - - +
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Residues in contact with ASN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ASN* 5.6 2.3 + - - -
324B PRO* 3.5 22.0 - - - +
325B TRP* 1.3 78.7 + - - +
327B ILE* 1.3 79.0 + - - +
328B PHE 3.2 1.8 + - - -
414B ARG* 3.9 18.6 + - - +
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ASN* 6.1 0.4 - - - -
299B ALA* 2.9 37.2 - - - +
300B SER* 3.6 26.3 + - - +
302B THR* 3.6 33.4 - - + +
303B GLU* 4.2 13.5 - - + -
305B PHE* 4.9 0.4 - - + -
324B PRO* 2.8 44.4 - - + +
325B TRP 2.9 0.6 + - - -
326B ASN* 1.3 97.8 - - - +
328B PHE* 1.3 68.5 + - + +
329B PRO* 4.2 0.4 - - - -
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ASN* 5.1 0.2 - - - -
296B ILE* 4.7 6.5 - - + -
300B SER* 3.8 23.6 - - - -
305B PHE* 3.9 25.6 - + - -
309B PHE* 5.6 1.8 - + - -
310B TRP* 5.1 8.5 - + - -
318B TRP* 4.0 21.1 - + - -
323B THR* 4.9 1.1 - - + -
324B PRO* 3.4 26.9 - - + -
325B TRP* 3.0 14.9 + - - +
326B ASN 4.6 0.2 - - - -
327B ILE* 1.3 85.8 - - + +
329B PRO* 1.3 71.7 - - + +
350B PRO* 3.4 18.2 - - + +
353B TYR* 3.9 7.0 - + - +
354B LEU* 3.6 36.8 - - + -
414B ARG* 2.8 26.3 + - - -
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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