Contacts of the helix formed by residues 324 - 337 (chain B) in PDB entry 2JIH
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 ASN 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 THR* 3.2 11.0 + - - +
323B SER* 1.3 79.8 + - - +
325B ALA* 1.3 66.1 + - - +
326B ALA* 3.9 11.9 - - - +
327B LEU* 3.0 35.8 + - + +
328B THR* 3.1 25.6 + - - -
362B CYS* 4.2 10.8 + - - -
363B GLY 5.2 3.8 + - - -
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Residues in contact with ALA 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 SER 3.1 6.3 + - - -
324B ASN* 1.3 72.5 - - - +
326B ALA* 1.3 62.1 + - - +
328B THR* 3.4 4.1 + - - +
329B LEU* 3.0 23.9 + - - +
361B LEU* 4.0 32.8 - - + -
362B CYS 3.4 18.2 + - - +
369B THR* 4.6 5.8 - - + -
372B MET* 3.9 27.4 - - + +
387B VAL* 4.3 2.9 - - - +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ASN* 3.4 11.9 - - - +
325B ALA* 1.3 78.9 - - - +
327B LEU* 1.3 58.4 + - - +
329B LEU* 3.1 6.3 + - - +
330B ARG* 2.9 29.0 + - - +
372B MET* 3.6 21.4 - - + +
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Residues in contact with LEU 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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320B GLU* 6.0 2.9 - - - +
322B THR* 4.2 17.3 - - + +
324B ASN* 3.0 23.3 + - + +
325B ALA 3.5 0.2 - - - -
326B ALA* 1.3 79.7 - - - +
328B THR* 1.3 53.4 + - - +
330B ARG* 3.5 32.3 - - - +
331B ASN* 2.8 71.0 + - - +
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Residues in contact with THR 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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319B PRO* 5.8 0.3 - - - +
320B GLU 4.3 8.8 - - - +
321B VAL* 3.7 20.3 - - + -
322B THR* 3.0 38.6 + - - +
324B ASN 3.1 14.0 + - - -
325B ALA* 3.5 6.1 - - - +
326B ALA 3.1 0.8 - - - -
327B LEU* 1.3 76.6 - - - +
329B LEU* 1.3 61.2 + - - +
331B ASN* 3.8 1.0 - - - +
332B PHE* 2.9 31.2 + - - +
355B LEU* 4.3 10.9 - - + +
357B THR* 5.4 1.6 - - + -
361B LEU* 4.7 9.4 - - + -
387B VAL* 4.2 16.2 - - + -
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Residues in contact with LEU 329 (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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325B ALA 3.0 13.4 + - - +
326B ALA* 3.1 8.7 + - - +
328B THR* 1.3 74.2 - - - +
330B ARG* 1.3 57.5 + - - +
332B PHE* 3.1 2.5 + - + +
333B CYS* 2.8 38.3 + - + +
372B MET* 3.6 27.8 - - + -
373B ALA* 3.8 11.0 - - - +
374B ASP* 3.8 28.9 - - - +
385B CYS* 3.7 32.5 - - + +
386B SER* 3.8 15.3 - - - -
387B VAL* 3.6 20.0 - - + -
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Residues in contact with ARG 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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326B ALA 2.9 15.5 + - - +
327B LEU* 3.5 34.3 - - - +
329B LEU* 1.3 78.0 - - - +
331B ASN* 1.3 64.5 + - - +
333B CYS* 3.5 5.0 + - - +
334B ASN* 3.0 50.0 + - - +
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Residues in contact with ASN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PRO* 4.6 1.7 - - - +
320B GLU* 3.4 51.9 + - + +
327B LEU* 2.8 55.9 + - - +
328B THR 3.8 3.8 - - - +
330B ARG* 1.3 79.9 + - - +
332B PHE* 1.3 56.0 + - - +
334B ASN* 3.3 10.2 + - - +
335B TRP* 2.8 34.6 + - - +
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Residues in contact with PHE 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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265B VAL* 3.6 37.7 - - + -
319B PRO* 4.1 13.9 - - + +
328B THR 2.9 18.8 + - - +
329B LEU* 3.5 4.3 - - - +
331B ASN* 1.3 76.0 - - - +
333B CYS* 1.3 59.5 - - - +
335B TRP* 3.2 20.2 + + - +
336B GLN* 2.8 34.0 + - + +
353B ALA* 3.7 26.0 - - + -
354B ILE 3.9 2.5 - - - -
355B LEU* 3.5 53.2 - - + -
385B CYS* 4.4 11.4 - - + -
386B SER 3.6 13.0 - - - -
387B VAL* 4.4 2.7 - - + -
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Residues in contact with CYS 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 LEU* 2.8 21.5 + - + +
330B ARG* 3.8 6.3 - - - +
332B PHE* 1.3 75.2 - - - +
334B ASN* 1.3 61.6 + - - +
336B GLN* 3.2 22.6 + - - +
337B LYS* 3.5 8.1 - - - +
374B ASP* 5.9 2.7 - - - +
382B SER 3.0 30.4 - - - +
383B ARG* 3.6 11.7 - - - -
385B CYS* 2.1 50.5 - - + -
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Residues in contact with ASN 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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330B ARG* 3.0 41.1 + - - +
331B ASN* 3.5 12.2 + - - +
332B PHE 3.3 0.2 - - - -
333B CYS* 1.3 75.9 - - - +
335B TRP* 1.3 65.3 + - - +
337B LYS* 3.5 38.1 + - - +
338B GLN 4.9 0.2 + - - -
382B SER 5.5 1.0 - - - +
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Residues in contact with TRP 335 (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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263B MET* 4.7 1.1 - - + -
265B VAL* 4.1 21.8 - - + -
310B LEU* 3.7 17.0 - - + -
312B ILE* 5.1 3.8 - - + -
317B LYS 3.8 19.4 + - - -
318B GLY* 3.3 30.2 + - - +
319B PRO* 3.7 22.0 - - + -
331B ASN 2.8 21.1 + - - +
332B PHE* 3.4 28.9 - + - +
334B ASN* 1.3 76.9 - - - +
336B GLN* 1.3 79.3 + - + +
337B LYS 3.3 1.0 + - - -
338B GLN* 2.9 45.1 + - - +
339B HIS* 3.2 32.3 + + - -
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Residues in contact with GLN 336 (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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263B MET* 4.1 10.8 - - + -
332B PHE* 2.8 29.5 + - + +
333B CYS* 3.2 28.6 + - - +
335B TRP* 1.3 88.6 - - + +
337B LYS* 1.3 72.4 + - - +
339B HIS* 2.9 15.6 + - - +
340B ASN* 4.6 1.4 - - - +
350B TYR* 3.1 42.0 + - - -
353B ALA* 4.6 5.6 - - + -
381B PRO 2.8 28.3 + - - +
382B SER* 4.3 0.4 - - - +
384B SER 5.0 1.5 + - - -
385B CYS* 3.6 20.2 - - - -
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Residues in contact with LYS 337 (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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333B CYS 3.5 13.0 - - - +
334B ASN* 3.5 37.6 + - - +
335B TRP 3.3 0.8 - - - -
336B GLN* 1.3 88.2 - - - +
338B GLN* 1.3 57.4 + - - +
340B ASN* 3.1 30.2 + - - +
381B PRO 4.8 2.0 - - - +
382B SER* 4.4 28.8 - - - -
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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