Contacts of the helix formed by residues 324 - 346 (chain B) in PDB entry 2A79
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 SER 324 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B THR 2.6 29.4 + - - -
321B LEU* 3.5 7.3 - - - +
323B ALA* 1.3 70.7 - - - +
325B MET* 1.3 63.4 + - - +
326B ARG 3.3 2.9 - - - +
327B GLU* 3.1 38.0 + - - +
328B LEU* 3.2 8.8 + - - +
408B VAL* 4.8 0.2 - - - -
409B ILE* 4.2 17.4 - - - +
412B ASN* 3.4 24.0 + - - -
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Residues in contact with MET 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 LEU 3.0 14.3 + - - +
322B LYS* 3.9 16.8 - - - +
323B ALA 3.2 4.4 - - - +
324B SER* 1.3 75.9 - - - +
326B ARG* 1.3 73.3 + - + +
327B GLU 3.2 0.3 + - - -
328B LEU* 3.3 8.8 + - - +
329B GLY* 2.9 26.7 + - - -
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Residues in contact with ARG 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ALA 4.8 1.7 + - - +
324B SER 3.3 0.8 - - - -
325B MET* 1.3 89.4 - - + +
327B GLU* 1.3 73.0 + - - +
329B GLY* 3.5 2.5 + - - +
330B LEU* 3.5 25.0 + - - +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B SER* 3.2 29.4 - - - +
325B MET 3.1 0.2 - - - -
326B ARG* 1.3 84.2 - - - +
328B LEU* 1.3 67.2 + - - +
330B LEU* 3.0 30.5 + - - +
331B LEU 3.4 2.9 + - - -
405B PRO* 4.2 14.4 - - + +
408B VAL* 3.2 46.1 - - + +
409B ILE* 4.7 7.4 - - + -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU* 4.7 20.2 - - + -
324B SER* 3.2 8.0 + - - +
325B MET* 3.8 8.7 - - - +
327B GLU* 1.3 79.5 - - - +
329B GLY* 1.3 64.1 + - - +
330B LEU 3.0 1.6 + - - -
331B LEU* 3.0 37.1 + - + +
332B ILE* 3.2 26.9 + - + +
405B PRO* 5.3 0.2 - - - -
409B ILE* 4.8 19.0 - - + +
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Residues in contact with GLY 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 MET 2.9 16.5 + - - -
326B ARG* 3.9 4.5 - - - -
327B GLU 3.1 0.6 - - - -
328B LEU* 1.3 77.4 - - - +
330B LEU* 1.3 57.8 + - - +
332B ILE* 2.9 31.0 - - - +
333B PHE* 3.0 16.5 + - - +
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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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326B ARG 3.5 15.7 - - - +
327B GLU* 3.0 18.9 + - - +
329B GLY* 1.3 77.6 - - - +
331B LEU* 1.3 58.3 + - - +
333B PHE* 3.0 6.4 + - + -
334B PHE* 2.6 68.4 + - + -
405B PRO* 5.1 5.6 - - + -
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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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327B GLU 3.4 2.2 + - - -
328B LEU* 3.0 30.9 + - + +
330B LEU* 1.3 79.2 - - - +
332B ILE* 1.3 61.1 + - + +
334B PHE* 3.8 4.2 - - - +
335B LEU* 2.8 41.4 + - + +
401B THR* 3.9 10.3 - - + +
402B ILE* 3.8 40.8 - - + +
405B PRO* 3.7 25.2 - - + +
409B ILE* 5.9 2.9 - - + -
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Residues in contact with ILE 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 LEU* 3.2 24.2 - - + +
329B GLY* 2.9 34.3 - - - +
331B LEU* 1.3 80.4 - - + +
333B PHE* 1.3 68.4 + - + +
335B LEU* 3.1 14.9 + - + +
336B PHE* 2.9 24.4 + - - +
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Residues in contact with PHE 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 GLY 3.1 15.5 - - - +
330B LEU* 3.0 12.2 + - + +
332B ILE* 1.3 82.2 - - - +
334B PHE* 1.3 65.9 + + + +
336B PHE* 2.8 35.2 + + + +
337B ILE* 3.2 38.0 + - + +
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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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330B LEU* 2.6 66.8 + - + +
331B LEU* 3.9 1.3 - - - +
333B PHE* 1.3 85.8 - + + +
335B LEU* 1.3 61.3 + - - +
337B ILE* 3.6 12.6 + - + +
338B GLY* 3.0 19.8 + - - -
372B MET* 5.3 0.7 - - - +
401B THR* 3.4 30.1 + - + +
404B LEU* 4.8 15.7 - - + -
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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* 2.8 31.7 + - + +
332B ILE* 3.2 14.4 - - + +
334B PHE* 1.3 77.0 - - - +
336B PHE* 1.3 65.5 + - + +
338B GLY* 3.3 1.7 + - - -
339B VAL* 2.9 53.8 + - + +
369B VAL* 4.7 15.0 - - + -
372B MET* 4.2 13.9 - - + +
373B THR* 5.2 13.7 - - + -
401B THR* 4.3 5.8 - - + +
402B ILE* 5.9 5.4 - - + -
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Residues in contact with PHE 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 ILE 2.9 10.6 + - - +
333B PHE* 2.8 17.9 + + + +
335B LEU* 1.3 79.3 - - + +
337B ILE* 1.3 69.5 + - + +
339B VAL* 2.8 7.1 + - + +
340B ILE* 2.8 50.6 + - + +
365B PHE* 5.4 8.3 - + - -
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Residues in contact with ILE 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 PHE* 3.2 42.1 + - + +
334B PHE* 3.9 13.7 - - + +
336B PHE* 1.3 76.4 - - + +
338B GLY* 1.3 56.6 + - - +
340B ILE* 3.9 7.8 - - - +
341B LEU* 3.0 36.2 + - + +
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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 PHE 3.0 14.9 + - - -
335B LEU 3.6 3.1 - - - -
336B PHE 2.9 2.0 + - - -
337B ILE* 1.3 74.9 - - - +
339B VAL* 1.3 57.6 + - - +
341B LEU* 3.1 5.3 + - - +
342B PHE* 2.8 42.9 + - - -
372B MET* 3.8 16.6 - - - -
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Residues in contact with VAL 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 LEU* 2.9 39.2 + - + +
336B PHE* 2.8 9.7 + - + +
338B GLY* 1.3 71.5 - - - -
340B ILE* 1.3 55.7 + - + +
343B SER* 2.6 53.4 + - - +
365B PHE* 3.7 30.5 - - + +
368B ALA* 3.5 17.9 - - + -
369B VAL* 3.7 17.5 - - + +
372B MET* 3.8 14.5 - - - -
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Residues in contact with ILE 340 (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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336B PHE* 2.8 57.1 + - + +
337B ILE* 3.9 7.6 - - - +
339B VAL* 1.3 74.5 - - + +
341B LEU* 1.3 58.6 + - - +
343B SER* 4.1 2.9 - - - -
344B SER* 2.9 28.2 + - - -
365B PHE* 3.4 38.7 - - + -
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Residues in contact with LEU 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 ILE* 3.0 24.9 + - + +
338B GLY* 3.7 5.2 - - - +
340B ILE* 1.3 79.5 - - - +
342B PHE* 1.3 67.7 + - + +
344B SER* 2.8 19.2 + - - +
345B ALA* 3.1 17.5 + - + +
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Residues in contact with PHE 342 (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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338B GLY* 2.8 28.1 + - - +
339B VAL 4.2 0.7 - - - +
341B LEU* 1.3 86.3 - - + +
343B SER* 1.3 58.4 + - - +
344B SER 2.9 9.9 + - - -
345B ALA* 4.3 0.7 - - + +
346B VAL* 3.2 30.2 + - - +
367B TRP* 4.3 7.4 - - + -
368B ALA* 4.5 4.0 - - + -
372B MET* 3.6 17.3 - - + -
390B VAL* 3.4 28.3 - - + -
393B LEU* 3.5 20.9 - - + -
394B CYS* 3.6 38.8 - - + -
397B ALA* 3.5 33.9 - - + -
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Residues in contact with SER 343 (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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339B VAL* 2.6 42.0 + - - +
340B ILE 4.1 1.6 - - - -
342B PHE* 1.3 71.3 - - - +
344B SER* 1.3 56.5 + - - +
346B VAL* 5.3 0.4 - - - -
347B TYR* 3.1 22.2 + - - +
361B ILE* 3.9 6.8 - - - +
364B ALA* 2.8 48.1 + - - +
365B PHE* 3.7 18.6 - - - -
367B TRP* 5.1 1.8 - - - -
368B ALA* 3.2 3.1 - - - +
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Residues in contact with SER 344 (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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340B ILE 2.9 15.6 + - - -
341B LEU* 2.8 28.2 + - - +
342B PHE 2.9 0.4 - - - -
343B SER* 1.3 80.1 - - - +
345B ALA* 1.3 62.8 + - - +
346B VAL 3.2 1.8 - - - -
347B TYR* 3.6 7.0 - - - +
348B PHE* 3.0 43.0 + - - -
361B ILE* 5.4 3.4 - - - -
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Residues in contact with ALA 345 (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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341B LEU* 3.1 17.3 + - + +
342B PHE* 3.3 1.1 + - + +
344B SER* 1.3 81.7 + - - +
346B VAL* 1.3 60.9 + - - +
348B PHE* 4.0 6.5 + - - +
349B ALA* 3.8 17.8 + - - +
390B VAL* 3.5 34.0 - - + +
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PHE 3.2 17.3 + - - +
343B SER* 5.2 1.3 - - - -
345B ALA* 1.3 73.2 - - - +
347B TYR* 1.3 58.8 + - - +
348B PHE 3.2 2.2 - - - -
349B ALA* 4.4 3.1 - - - +
350B GLU* 2.6 52.0 + - + +
358B PHE* 5.3 4.7 - - + -
364B ALA* 6.1 1.6 - - + -
367B TRP* 3.6 26.7 - - + -
382B PRO* 4.6 9.6 - - + -
386B GLY 4.8 0.2 - - - -
387B GLY* 3.7 23.8 - - - +
390B VAL* 3.5 29.8 - - + -
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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