Contacts of the helix formed by residues 323 - 336 (chain B) in PDB entry 1IYH
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 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298B PHE* 4.0 15.8 - - + -
318B GLU* 3.8 4.4 + - - +
319B LEU* 3.1 46.0 + - + +
322B TYR* 1.3 88.3 - - - +
324B ALA* 1.3 67.1 + - - +
325B PRO* 3.3 3.6 - - - -
326B HIS* 3.2 21.6 + - - +
327B LEU* 3.5 8.3 + - - +
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Residues in contact with ALA 324 (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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298B PHE* 3.8 25.5 - - + -
319B LEU 2.9 13.1 + - - +
320B LEU* 3.5 19.3 - - + +
323B ASN* 1.3 71.3 - - - +
325B PRO* 1.3 71.3 - - + +
327B LEU* 3.0 5.9 + - - +
328B MET* 2.8 29.2 + - + +
367B LEU* 3.9 22.0 - - + -
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Residues in contact with PRO 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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320B LEU 3.5 8.5 - - - +
321B THR* 3.3 27.8 - - - +
322B TYR 4.1 0.7 - - - -
323B ASN 3.3 5.8 - - - +
324B ALA* 1.3 93.6 - - + +
326B HIS* 1.3 61.7 + - + +
328B MET* 3.7 8.2 - - + +
329B GLN* 2.9 29.6 + - - +
364B LYS* 6.3 0.2 - - - -
367B LEU* 5.4 0.9 - - + -
371B HIS* 4.5 3.5 + - - +
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Residues in contact with HIS 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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322B TYR 3.1 27.6 + - - -
323B ASN* 3.2 11.6 + - - +
325B PRO* 1.3 81.0 - - + +
327B LEU* 1.3 57.9 + - - +
329B GLN* 3.3 7.7 + - - +
330B ASP* 2.9 36.7 + - - +
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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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294B THR* 4.0 28.0 - - + +
295B LEU* 4.8 8.7 - - + -
298B PHE* 3.6 45.3 - - + -
323B ASN 3.5 5.9 + - - +
324B ALA* 3.0 9.7 + - - +
326B HIS* 1.3 77.3 - - - +
328B MET* 1.3 80.8 + - + +
330B ASP* 3.1 6.3 + - + +
331B LEU* 2.8 45.4 + - + +
648D PHE* 4.3 10.3 - - + -
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Residues in contact with MET 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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295B LEU* 5.8 0.4 - - + -
298B PHE* 5.2 0.2 - - + -
324B ALA* 2.8 25.3 + - + +
325B PRO* 3.7 5.4 - - + +
327B LEU* 1.3 100.7 - - + +
329B GLN* 1.3 57.5 + - - +
331B LEU* 3.4 8.7 + - + -
332B ASP* 2.9 30.3 + - - +
353B TRP* 3.6 29.6 - - + -
360B LEU* 4.4 16.2 - - + -
367B LEU* 3.9 32.3 - - + +
368B LEU* 3.7 11.9 - - + -
371B HIS* 3.5 25.1 - - + +
374B LEU* 3.6 8.2 - - + +
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Residues in contact with GLN 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 PRO 2.9 17.2 + - - +
326B HIS* 3.5 8.5 - - - +
328B MET* 1.3 77.2 - - - +
330B ASP* 1.3 66.6 + - - +
332B ASP* 3.2 11.8 + - - +
333B THR* 2.9 38.8 + - - +
371B HIS* 3.7 19.5 + - + -
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Residues in contact with ASP 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 HIS* 2.9 23.9 + - - +
327B LEU* 3.1 9.8 + - - +
329B GLN* 1.3 79.0 - - - +
331B LEU* 1.3 58.0 + - - +
333B THR* 3.9 5.7 - - - -
334B TYR* 3.0 29.1 + - - +
646D LEU 5.1 1.2 - - - +
647D PRO 3.4 26.1 - - - +
648D PHE* 3.8 33.9 - - + +
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Residues in contact with LEU 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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291B ILE* 4.7 12.8 - - + -
294B THR* 5.4 1.8 - - + -
295B LEU* 3.9 24.7 - - + -
327B LEU* 2.8 35.0 + - + +
328B MET* 3.7 9.6 - - + +
330B ASP* 1.3 73.2 - - - +
332B ASP* 1.3 59.6 + - - +
334B TYR* 3.3 6.5 + - - +
335B LEU* 2.9 31.4 + - - +
341B LEU* 4.8 12.2 - - + +
353B TRP* 3.5 35.7 - - + -
374B LEU* 4.2 12.9 - - + +
648D PHE* 3.7 22.2 - - + -
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Residues in contact with ASP 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 MET 2.9 17.5 + - - +
329B GLN* 3.5 10.8 + - - +
331B LEU* 1.3 77.9 - - - +
333B THR* 1.3 56.3 + - - +
335B LEU* 3.4 2.8 + - - +
336B GLY 3.0 23.6 + - - -
370B ASN 4.3 1.6 - - - +
371B HIS* 2.7 41.9 + - - +
372B PRO* 5.4 0.5 - - - +
373B ARG* 3.2 41.5 + - - +
374B LEU* 4.2 12.3 - - + +
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Residues in contact with THR 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 GLN* 2.9 33.7 + - - +
330B ASP* 3.9 6.0 - - - -
332B ASP* 1.3 77.0 - - - +
334B TYR* 1.3 64.3 + - - +
336B GLY* 3.4 11.1 + - - -
373B ARG* 4.7 4.3 - - - +
647D PRO 6.0 0.4 - - - -
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Residues in contact with TYR 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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287B HIS* 3.8 34.7 + + - +
291B ILE* 3.6 29.1 - - + +
330B ASP 3.0 19.3 + - - +
331B LEU* 3.5 4.0 - - + +
333B THR* 1.3 80.0 - - - +
335B LEU* 1.3 58.8 + - - +
338B ARG* 2.9 33.1 + - - -
341B LEU* 3.4 32.8 + - + -
342B ILE* 3.9 6.1 - - - +
647D PRO* 4.7 13.5 - - + -
648D PHE* 3.7 29.6 - + + -
662D HIS* 5.1 5.9 - + - -
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Residues in contact with LEU 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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331B LEU 2.9 17.9 + - - +
332B ASP* 3.8 4.5 - - - +
334B TYR* 1.3 79.8 - - - +
336B GLY* 1.3 73.6 + - - +
338B ARG* 2.9 52.3 + - - +
339B GLU 4.6 1.8 - - - +
340B TRP* 3.5 29.2 - - - +
341B LEU* 4.0 13.7 - - + +
373B ARG* 3.7 31.4 - - + +
374B LEU* 4.0 16.8 - - + -
377B LEU* 4.4 13.2 - - + -
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Residues in contact with GLY 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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332B ASP 3.0 13.8 + - - -
333B THR 3.4 7.4 + - - -
334B TYR 3.4 2.2 - - - -
335B LEU* 1.3 85.0 - - - +
337B GLY* 1.3 60.7 + - - -
338B ARG* 3.6 3.2 + - - +
373B ARG* 3.2 36.2 + - - +
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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