Contacts of the strand formed by residues 343 - 348 (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 SER 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B TRP* 4.4 0.5 - - - -
334B TYR* 5.9 0.2 - - - -
335B LEU 3.4 9.8 + - - -
336B MET* 3.8 0.2 - - - -
337B GLY* 2.9 24.2 + - - +
340B THR* 3.5 9.7 + - - -
342B GLN* 1.3 79.7 - - - +
344B PHE* 1.3 64.1 + - - +
421B PRO* 3.4 5.0 - - - +
422B PHE* 2.7 38.4 + - - -
424B THR* 2.8 35.6 + - - -
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Residues in contact with PHE 344 (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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237B TRP* 3.5 46.7 - + + -
238B TYR 3.4 26.5 - - - -
239B THR* 3.8 26.0 - - + -
334B TYR* 3.2 5.5 - - - +
335B LEU* 2.9 49.6 + - + -
336B MET 4.4 1.1 - - - -
342B GLN 4.2 5.6 - - - -
343B SER* 1.3 81.9 - - - +
345B ARG* 1.3 65.1 + - - +
346B ILE* 4.4 2.2 - - + -
402B PHE* 3.9 22.0 - + + -
418B VAL* 3.9 11.0 - - + -
419B GLU 3.2 20.0 - - - +
422B PHE* 3.9 7.1 - - - -
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Residues in contact with ARG 345 (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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255B GLU* 4.0 6.9 + - - -
332B SER* 3.7 17.9 + - - +
333B LEU 3.2 9.6 - - - +
334B TYR* 3.0 46.1 + - + -
344B PHE* 1.3 75.3 - - - +
346B ILE* 1.3 63.8 + - - +
347B THR* 4.0 8.1 + - - +
417B ALA 3.7 0.3 - - - +
418B VAL* 3.3 6.2 - - - +
419B GLU* 2.6 61.4 + - - +
422B PHE* 3.9 28.8 - - + -
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Residues in contact with ILE 346 (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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331B ILE 3.5 1.6 - - - +
332B SER* 3.5 3.0 - - - -
333B LEU* 2.9 47.8 + - + +
335B LEU* 4.0 11.0 - - + -
344B PHE* 4.4 9.2 - - + -
345B ARG* 1.3 78.6 - - - +
347B THR* 1.3 62.3 + - - +
348B ILE* 4.0 4.3 + - + +
381B MET* 3.8 28.7 - - + -
385B ILE* 3.9 17.7 - - + -
389B PHE* 3.9 13.7 - - + -
402B PHE* 4.1 26.0 - - + -
417B ALA 3.3 3.8 - - - -
418B VAL* 3.9 20.6 - - + -
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Residues in contact with THR 347 (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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330B VAL* 3.8 34.5 - - + -
331B ILE 3.3 7.2 - - - +
332B SER* 3.3 17.5 + - - +
345B ARG* 4.0 15.2 + - - +
346B ILE* 1.3 75.4 - - - +
348B ILE* 1.3 62.3 + - - +
349B LEU* 5.3 0.9 - - + -
389B PHE* 3.6 4.2 - - - -
415B THR 4.9 6.3 - - - +
416B ALA* 3.3 25.4 - - - +
417B ALA* 2.8 25.4 + - - +
419B GLU* 4.2 5.4 + - - -
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Residues in contact with ILE 348 (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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282B LEU* 5.1 4.5 - - + -
330B VAL* 3.6 4.7 - - - +
331B ILE* 2.9 46.3 + - + +
333B LEU* 5.8 1.6 - - + -
346B ILE* 4.5 6.3 - - + +
347B THR* 1.3 80.1 - - - +
349B LEU* 1.3 67.2 + - - +
352B GLN* 3.6 18.2 - - + +
353B TYR* 3.9 23.6 - - + -
384B VAL* 4.2 16.8 - - + +
385B ILE* 3.5 36.6 - - + -
389B PHE* 4.1 17.5 - - + -
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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