Contacts of the helix formed by residues 324 - 341 (chain B) in PDB entry 4IYM
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 THR 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B PHE* 5.3 13.2 - - + -
175B ARG* 3.8 31.0 - - - +
322B VAL* 3.5 1.6 - - - +
323B VAL* 1.3 89.4 - - + +
325B LYS* 1.3 65.0 + - - +
326B GLU* 3.3 20.2 + - - +
327B ALA* 2.9 24.3 + - - +
328B GLU* 3.0 22.5 + - - +
361B HIS* 3.5 13.2 - - - -
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Residues in contact with LYS 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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324B THR* 1.3 72.5 - - - +
326B GLU* 1.3 65.4 + - - +
328B GLU* 3.3 17.6 + - - +
329B GLN* 2.9 51.9 + - + +
359B ASN* 5.1 15.0 + - - +
361B HIS* 3.6 23.5 + - + +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 5.9 2.3 - - - -
324B THR* 3.3 21.8 - - - +
325B LYS* 1.3 80.1 + - - +
327B ALA* 1.3 66.1 + - - +
329B GLN* 3.4 6.4 + - - +
330B ARG* 3.0 24.3 + - - +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 6.2 0.7 - - + -
277B GLU* 5.1 2.0 - - - +
322B VAL* 4.6 5.4 - - + -
323B VAL* 4.2 12.1 - - + -
324B THR* 2.9 28.4 + - - +
326B GLU* 1.3 73.8 - - - +
328B GLU* 1.3 64.6 + - - +
330B ARG* 3.1 10.1 + - - +
331B ILE* 2.9 37.6 + - + +
383B PHE 6.0 0.4 - - - +
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Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.7 18.9 - - + +
324B THR 3.0 10.4 + - - +
325B LYS* 3.5 19.4 + - - +
327B ALA* 1.3 75.6 - - - +
329B GLN* 1.3 65.9 + - - +
331B ILE* 3.3 2.8 + - - +
332B ARG* 2.9 72.7 + - - +
360B GLY 4.2 3.3 - - - +
361B HIS* 3.2 35.6 - - - +
362B PHE 3.9 2.8 + - - +
363B ILE* 3.8 14.1 - - + -
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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
----------------------------------------------------------
325B LYS* 2.9 40.8 + - + +
326B GLU* 3.9 5.6 - - - +
328B GLU* 1.3 94.0 - - - +
330B ARG* 1.3 61.9 + - - +
332B ARG* 4.0 18.0 - - - +
333B SER* 3.0 25.5 + - - -
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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
----------------------------------------------------------
326B GLU 3.0 13.8 + - - +
327B ALA* 3.1 11.6 + - - +
329B GLN* 1.3 77.2 - - - +
331B ILE* 1.3 61.3 + - - +
333B SER* 3.5 7.2 + - - -
334B LEU* 3.2 35.7 + - + +
380B THR* 3.3 21.0 - - - +
381B GLU 2.7 23.6 + - - -
382B ILE 3.1 27.7 + - - -
383B PHE* 4.8 3.2 - - - +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.8 28.7 - - + -
327B ALA* 2.9 31.1 + - + +
328B GLU 3.6 4.5 - - - +
330B ARG* 1.3 74.1 - - - +
332B ARG* 1.3 61.2 + - - +
334B LEU* 3.1 5.1 + - - +
335B ILE* 2.9 42.9 + - + +
363B ILE* 3.8 17.9 - - + -
382B ILE* 3.6 39.7 - - + +
383B PHE 3.9 13.2 - - - +
384B GLY* 4.0 2.9 - - - -
385B PRO* 4.4 5.8 - - + -
386B VAL* 4.1 7.4 - - + -
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU* 2.9 46.9 + - + +
329B GLN* 4.0 21.1 - - - +
331B ILE* 1.3 74.5 - - - +
333B SER* 1.3 61.8 + - - +
335B ILE* 3.5 11.5 + - + +
336B ASP* 3.2 29.5 + - - +
350B ARG* 3.1 45.0 + - + +
352B PHE 4.6 5.5 + - - -
362B PHE 2.9 28.1 + - - -
363B ILE* 3.9 20.2 - - + +
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Residues in contact with SER 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLN 3.0 19.5 + - - -
330B ARG* 3.6 7.4 - - - -
331B ILE 3.2 0.2 - - - -
332B ARG* 1.3 77.2 - - - +
334B LEU* 1.3 60.3 + - - +
336B ASP* 3.5 10.1 + - - +
337B SER* 3.3 20.4 + - - -
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG* 3.2 54.2 + - + +
331B ILE 3.1 7.0 + - - +
333B SER* 1.3 74.3 - - - +
335B ILE* 1.3 65.2 + - - +
337B SER* 2.7 22.5 + - - +
338B GLY 3.1 5.4 + - - -
376B ASP* 4.2 25.1 - - + +
377B ILE* 3.2 12.9 - - + +
380B THR* 4.1 24.9 - - + +
382B ILE* 4.1 32.1 - - + -
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Residues in contact with ILE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 2.9 28.7 + - + +
332B ARG* 3.7 13.7 - - + +
334B LEU* 1.3 74.6 - - - +
336B ASP* 1.3 63.2 + - - +
338B GLY 3.1 10.0 + - - -
339B ILE* 3.2 12.0 + - + +
345B LEU* 4.3 11.7 - - + -
350B ARG* 3.8 30.5 - - + -
363B ILE* 4.3 11.2 - - + -
366B CYS* 3.5 25.8 - - - -
368B PHE* 3.4 24.3 - - + -
377B ILE* 4.8 0.4 - - - -
382B ILE* 5.8 0.4 - - + -
386B VAL* 3.7 27.8 - - + -
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Residues in contact with ASP 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ARG 3.2 15.0 + - - +
333B SER* 3.6 12.1 - - - +
334B LEU 3.3 0.4 - - - -
335B ILE* 1.3 78.2 - - - +
337B SER* 1.3 58.3 + - - +
339B ILE* 3.3 9.3 + - - +
340B GLU* 2.9 36.3 + - + +
350B ARG* 3.5 29.3 + - - -
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B SER 3.3 8.9 + - - -
334B LEU* 2.7 23.8 + - - +
336B ASP* 1.3 75.5 - - - +
338B GLY* 1.3 59.8 + - - +
340B GLU* 3.8 8.5 - - - +
341B GLN* 2.8 52.1 + - - +
376B ASP* 3.7 23.9 - - - +
377B ILE* 4.1 1.7 - - - +
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Residues in contact with GLY 338 (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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334B LEU 3.1 2.8 + - - -
335B ILE 3.1 9.1 + - - -
337B SER* 1.3 83.3 + - - +
339B ILE* 1.3 60.5 + - - +
341B GLN* 3.4 4.9 + - - +
342B GLY 3.3 3.8 + - - -
343B ALA* 3.1 24.0 + - - +
368B PHE* 3.8 14.8 - - - -
375B MSE 5.3 0.9 - - - -
377B ILE* 3.8 24.0 - - - -
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Residues in contact with ILE 339 (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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335B ILE 3.2 13.6 + - - +
336B ASP* 3.3 8.9 + - - +
338B GLY* 1.3 74.2 - - - +
340B GLU* 1.3 73.3 + - - +
342B GLY* 3.2 13.5 + - - -
343B ALA 4.3 8.2 - - - +
345B LEU* 3.8 26.7 - - + +
350B ARG* 3.2 44.0 - - - +
368B PHE* 3.8 6.4 - - + -
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASP* 2.9 29.0 + - + +
337B SER* 3.3 7.8 + - - +
339B ILE* 1.3 82.2 - - - +
341B GLN* 1.3 62.8 + - + +
342B GLY* 3.3 0.9 + - - -
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Residues in contact with GLN 341 (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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337B SER* 2.8 28.2 + - - +
338B GLY* 4.1 2.8 - - - +
339B ILE 3.2 0.4 - - - -
340B GLU* 1.3 79.2 - - + +
342B GLY* 1.3 55.9 + - - +
343B ALA 3.7 2.0 - - - -
374B ASP 5.1 2.9 - - - -
375B MSE 3.2 32.8 - - + +
376B ASP* 3.0 51.4 + - - +
377B ILE 4.8 0.2 + - - -
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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