Contacts of the helix formed by residues 324 - 338 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A THR* 3.9 13.4 + - + +
323A SER* 1.3 78.0 + - - +
325A ALA* 1.3 61.5 + - - +
326A ALA* 3.7 10.9 + - - +
327A LEU* 2.9 34.6 + - + +
328A THR* 2.9 34.9 + - - -
362A CYS* 3.9 6.2 - - - +
363A GLY 6.0 0.5 - - - -
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A SER 3.4 2.7 + - - -
324A ASN* 1.3 73.1 + - - +
326A ALA* 1.3 58.6 + - - +
328A THR* 3.7 2.3 - - - -
329A LEU* 2.9 28.8 + - - +
361A LEU* 4.2 26.9 - - + -
362A CYS 3.0 25.6 + - - +
363A GLY* 4.7 2.5 - - - +
369A THR* 4.5 11.4 - - + -
372A MET* 4.0 19.9 - - + +
387A VAL* 4.0 4.7 - - - +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ASN* 3.4 6.9 + - - +
325A ALA* 1.3 76.4 - - - +
327A LEU* 1.3 61.4 + - - +
329A LEU* 3.7 6.1 - - + +
330A ARG* 3.0 25.5 + - - +
372A MET* 3.6 28.0 - - + -
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A GLU* 6.4 0.2 - - + -
322A THR* 4.2 14.1 - - + -
324A ASN* 2.9 34.4 + - + +
325A ALA 3.4 0.2 - - - -
326A ALA* 1.3 74.8 - - - +
328A THR* 1.3 58.4 + - - +
329A LEU 3.0 1.1 - - - -
330A ARG* 2.9 40.3 + - - +
331A ASN* 2.6 56.3 + - - +
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A PRO* 5.3 0.3 - - - +
320A GLU 4.3 9.5 - - - +
321A VAL* 3.9 26.9 - - + -
322A THR* 2.6 37.8 + - - +
324A ASN 2.9 15.7 + - - -
325A ALA* 3.7 6.1 - - - -
327A LEU* 1.3 75.5 - - - +
329A LEU* 1.3 56.8 + - - +
331A ASN* 3.5 2.9 + - - +
332A PHE* 2.9 28.5 + - - +
355A LEU* 4.3 8.9 - - + +
357A THR* 5.2 0.9 - - + -
361A LEU* 4.6 10.3 - - + -
387A VAL* 4.3 14.6 - - + -
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ALA 2.9 18.2 + - - +
326A ALA* 3.7 6.1 - - + +
327A LEU 3.0 0.2 - - - -
328A THR* 1.3 75.2 - - - +
330A ARG* 1.3 60.4 + - - +
332A PHE* 4.8 0.4 - - + -
333A CYS* 2.9 31.0 + - + +
372A MET* 4.0 22.7 - - + +
373A ALA* 4.1 24.5 - - - -
374A ASP* 4.3 17.7 - - - +
385A CYS* 4.0 13.0 - - + +
386A SER* 3.8 27.1 - - - +
387A VAL* 3.7 26.5 - - + -
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ALA 3.0 18.0 + - - +
327A LEU* 2.9 32.0 + - - +
329A LEU* 1.3 76.1 - - - +
331A ASN* 1.3 68.1 + - - +
333A CYS* 4.1 3.7 - - + +
334A ASN* 2.9 46.9 + - - +
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Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A PRO* 3.6 4.1 - - + +
320A GLU* 2.7 56.6 + - - +
322A THR* 4.6 3.0 - - - +
327A LEU* 2.6 48.9 + - - +
328A THR* 3.5 3.0 - - - +
330A ARG* 1.3 74.9 + - - +
332A PHE* 1.3 57.8 + - - +
334A ASN* 3.8 6.1 + - - +
335A TRP* 3.2 28.4 + - - +
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Residues in contact with PHE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL* 3.9 23.1 - - + -
319A PRO* 4.0 15.7 - - + -
328A THR 2.9 18.4 + - - +
329A LEU 3.6 4.3 - - - +
331A ASN* 1.3 75.6 - - - +
333A CYS* 1.3 67.2 + - - +
335A TRP* 3.2 13.3 + + - -
336A GLN* 3.0 29.1 + - + +
353A ALA* 3.5 28.3 - - + -
354A ILE 3.7 10.5 - - - -
355A LEU* 3.5 47.3 - - + -
385A CYS* 4.2 12.8 - - + -
386A SER 3.5 25.4 - - - -
387A VAL* 4.1 5.2 - - + -
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Residues in contact with CYS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU* 2.9 22.8 + - + +
330A ARG* 4.2 4.5 - - - +
332A PHE* 1.3 72.6 - - - +
334A ASN* 1.3 64.6 + - - +
336A GLN* 2.8 25.2 + - - +
337A LYS* 3.5 5.5 - - - +
374A ASP* 5.9 2.2 - - - +
382A SER 3.1 28.3 - - - +
383A ARG* 3.4 14.1 - - - -
385A CYS* 2.1 51.1 - - + -
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Residues in contact with ASN 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ARG* 2.9 39.0 + - - +
331A ASN* 3.9 5.7 + - - +
333A CYS* 1.3 77.5 - - - +
335A TRP* 1.3 62.0 - - - +
337A LYS* 3.3 42.0 + - - +
338A GLN* 4.4 0.7 + - - +
382A SER 5.5 0.5 - - - +
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Residues in contact with TRP 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A MET* 4.5 2.5 - - + -
265A VAL* 4.0 23.6 - - + -
310A LEU* 3.8 23.3 - - + -
312A ILE* 4.4 5.8 - - + -
317A LYS 3.2 29.5 + - - -
318A GLY* 3.3 25.4 + - - -
319A PRO* 3.7 14.6 - - + -
331A ASN 3.2 17.2 + - - +
332A PHE* 3.2 28.2 + + - +
334A ASN* 1.3 78.5 - - - +
336A GLN* 1.3 89.4 + - + +
337A LYS 3.4 0.5 + - - -
338A GLN* 3.4 21.0 + - - +
339A HIS* 3.2 40.0 + + - -
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A MET* 3.8 18.6 - - + -
332A PHE* 3.0 24.5 + - + +
333A CYS* 2.8 20.2 + - - +
335A TRP* 1.3 88.6 - - + +
337A LYS* 1.3 63.8 + - - +
339A HIS* 2.8 12.8 + - - +
340A ASN* 3.5 1.2 + - - +
350A TYR* 2.7 48.1 + - - -
353A ALA* 3.9 10.9 - - + +
381A PRO 2.9 27.4 + - - +
382A SER 4.2 0.2 - - - -
384A SER 4.7 1.8 + - - +
385A CYS* 3.2 29.5 - - - -
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Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A CYS 3.5 9.6 - - - +
334A ASN* 3.3 34.1 + - - +
335A TRP 3.3 0.4 - - - -
336A GLN* 1.3 86.8 - - - +
338A GLN* 1.3 58.1 + - - +
339A HIS 3.1 5.0 + - - -
340A ASN* 3.1 23.1 + - - +
381A PRO 4.2 3.4 - - - +
382A SER* 3.5 41.4 + - - +
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ASN 4.4 0.4 + - - +
335A TRP* 3.4 24.1 + - - +
336A GLN 3.2 0.4 + - - -
337A LYS* 1.3 77.0 - - - +
339A HIS* 1.3 92.7 + - + +
340A ASN 3.4 2.6 + - - +
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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