Contacts of the helix formed by residues 324 - 335 (chain B) in PDB entry 3K0J
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 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B LYS* 2.8 24.3 + - + +
323B LYS* 1.3 76.4 - - - +
325B GLU* 1.3 58.1 + - + +
326B LEU 3.0 1.3 - - - -
327B LYS* 2.7 31.0 + - - +
328B LYS* 2.8 33.6 + - - +
162F U 3.5 34.0 + - - +
163F C 4.6 2.9 - - - -
172F G 4.7 11.1 + - - +
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Residues in contact with GLU 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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321B ILE* 4.0 14.4 - - + -
322B LYS* 3.0 24.2 + - + +
324B ASP* 1.3 76.1 - - + +
326B LEU* 1.3 56.7 + - - +
328B LYS* 3.3 18.8 + - - -
329B SER* 2.9 36.4 + - - -
378B TYR* 4.1 7.6 + - - +
516D ASN* 4.2 6.6 + - - +
583D ARG* 2.6 37.5 + - - +
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Residues in contact with LEU 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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317B LEU* 4.6 24.0 - - + -
318B ASN 5.4 2.5 - - - +
321B ILE* 3.8 29.1 - - + +
322B LYS 2.7 15.9 + - - +
323B LYS* 3.9 6.3 - - - +
325B GLU* 1.3 78.8 - - - +
327B LYS* 1.3 56.6 + - - +
329B SER* 4.0 2.2 - - - -
330B LEU* 3.0 44.3 + - + +
345B VAL* 4.2 26.5 - - + -
347B ARG* 5.7 3.6 - - + -
353B GLY* 6.1 2.7 - - - +
354B GLN 4.9 2.9 - - - +
377B PHE* 3.6 29.8 - - + -
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Residues in contact with LYS 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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323B LYS* 3.4 14.8 - - - +
324B ASP* 2.7 17.5 + - - +
326B LEU* 1.3 70.2 - - - +
328B LYS* 1.3 58.6 + - - +
329B SER 3.0 1.6 - - - -
330B LEU 4.4 0.2 - - - +
331B HIS* 2.8 35.8 + - - +
342B ASP* 5.3 3.6 + - - -
343B ILE* 3.1 46.4 + - + +
344B LEU* 4.9 2.0 - - - +
345B VAL* 3.8 24.2 - - + +
162F U 3.4 55.4 + - + +
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Residues in contact with LYS 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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324B ASP* 2.8 37.7 + - - +
325B GLU* 3.3 21.0 + - - -
327B LYS* 1.3 75.9 - - - +
329B SER* 1.3 56.5 + - - +
331B HIS* 4.2 2.5 - - - +
332B ALA* 3.4 17.8 + - - +
583D ARG* 3.2 45.3 - - - +
162F U 4.0 28.5 - - - +
163F C 3.0 35.2 + - - +
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Residues in contact with SER 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLU 2.9 19.0 + - - -
328B LYS* 1.3 76.7 - - - +
330B LEU* 1.3 65.6 + - - +
331B HIS 3.1 1.8 - - - -
332B ALA* 3.2 8.8 + - - +
333B ILE* 3.0 24.4 + - - +
377B PHE* 3.8 24.2 - - - -
378B TYR* 3.5 8.2 + - - -
516D ASN* 3.4 12.3 + - - -
581D PRO* 3.9 12.2 - - - +
583D ARG* 3.0 17.6 + - - +
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Residues in contact with LEU 330 (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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314B ILE* 4.2 12.3 - - + -
317B LEU* 4.4 13.0 - - + -
326B LEU* 3.0 29.6 + - + +
327B LYS* 3.1 3.6 + - - +
329B SER* 1.3 76.3 - - - +
331B HIS* 1.3 63.1 + - - +
333B ILE* 3.2 2.3 + - + -
334B PHE* 3.0 53.9 + - + -
343B ILE* 4.2 18.6 - - + +
345B VAL* 4.9 0.7 - - + -
355B ALA* 3.6 31.6 - - + -
357B VAL* 4.9 4.7 - - + -
377B PHE* 3.7 28.7 - - + -
382B MET* 4.6 4.9 - - - -
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Residues in contact with HIS 331 (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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327B LYS 2.8 17.0 + - - +
328B LYS 4.2 3.6 - - - +
330B LEU* 1.3 75.1 - - - +
332B ALA* 1.3 60.7 + - + +
333B ILE 3.0 5.1 + - - -
335B SER* 3.0 58.2 + - - -
340B ILE* 3.9 28.5 - - + +
343B ILE* 3.4 13.2 - - + +
573D GLN* 6.0 0.2 - - - -
162F U 3.5 36.2 + - - +
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Residues in contact with ALA 332 (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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328B LYS 3.4 17.6 + - - +
329B SER* 3.2 6.7 + - - +
331B HIS* 1.3 81.3 - - + +
333B ILE* 1.3 53.6 + - - +
335B SER* 4.9 2.5 - - - -
336B ARG* 4.5 0.2 + - - -
573D GLN* 2.7 65.3 - - - +
574D GLY* 3.1 6.2 - - - +
581D PRO* 6.0 0.2 - - + -
583D ARG* 4.3 15.0 - - + -
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Residues in contact with ILE 333 (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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329B SER 3.0 10.5 - - - +
330B LEU* 3.6 9.4 - - + +
331B HIS 3.0 0.8 - - - -
332B ALA* 1.3 83.1 - - - +
334B PHE* 1.3 74.7 + - + +
335B SER 3.8 0.2 - - - -
336B ARG* 3.0 26.1 + - - +
372B MET* 3.2 30.4 - - + +
375B PHE* 4.6 13.9 - - + -
376B PRO 5.1 0.4 - - - +
377B PHE* 3.1 42.8 - - + -
382B MET* 4.6 4.7 - - + -
573D GLN 4.4 3.1 - - - -
574D GLY* 3.8 21.3 - - - +
581D PRO* 4.3 8.1 - - + -
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Residues in contact with PHE 334 (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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312B ILE* 4.0 7.2 - - + -
314B ILE* 3.2 31.0 - - + -
330B LEU* 3.0 39.2 + - + +
333B ILE* 1.3 83.4 - - + +
335B SER* 1.3 67.7 + - - +
336B ARG* 2.7 5.5 + - - -
337B PHE* 2.7 40.1 + + - +
338B GLY 4.0 1.6 + - - -
340B ILE* 4.0 9.6 - - + -
357B VAL* 4.8 7.9 - - + -
359B PHE* 3.8 19.7 - + + -
368B ALA* 3.8 17.9 - - + -
372B MET* 3.7 23.3 - - + -
382B MET* 3.2 27.1 - - + -
384B ILE* 4.0 1.3 - - + -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B HIS* 3.0 40.0 + - - -
332B ALA* 5.0 4.0 - - - -
333B ILE 3.8 0.2 - - - -
334B PHE* 1.3 75.4 - - - +
336B ARG* 1.3 62.3 + - - +
338B GLY 2.8 27.0 + - - +
340B ILE* 3.9 9.0 - - - +
573D GLN* 5.6 5.8 - - - -
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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