Contacts of the helix formed by residues 324 - 343 (chain B) in PDB entry 1F89
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 ASP 324 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B SER* 3.1 9.0 + - - +
323B PRO* 1.3 76.1 - - - +
325B LYS* 1.3 63.2 + - - +
326B MET* 3.1 13.3 + - - +
327B ALA* 2.8 41.3 + - + +
328B ASN* 3.1 23.7 + - - -
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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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323B PRO 3.4 5.5 + - - -
324B ASP* 1.3 69.3 + - - +
326B MET* 1.3 62.0 + - + +
328B ASN* 2.9 18.5 + - - +
329B LEU* 2.9 27.6 + - + +
356B ASN* 3.5 33.9 + - + +
367B TYR* 3.5 25.6 + - + -
369B GLU* 3.3 40.9 + - - +
370B VAL* 3.2 24.7 - - - +
378B THR* 5.0 12.4 - - + -
379B SER* 3.2 23.1 - - - -
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Residues in contact with MET 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ASP* 3.1 9.6 + - - +
325B LYS* 1.3 81.0 - - + +
327B ALA* 1.3 57.0 + - - +
329B LEU* 3.4 16.8 + - + +
330B GLN* 2.9 38.4 + - - +
378B THR* 3.7 29.8 - - + -
382B PHE* 5.6 6.4 - - + -
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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
----------------------------------------------------------
322B SER* 4.6 4.5 - - - +
324B ASP* 2.8 35.7 + - + +
326B MET* 1.3 73.4 - - - +
328B ASN* 1.3 59.8 + - - +
330B GLN* 3.7 7.6 - - - +
331B ARG* 3.1 28.9 + - - +
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Residues in contact with ASN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 4.2 4.2 - - - +
320B GLY* 3.8 7.6 - - - -
321B SER 3.4 10.1 + - - +
322B SER* 2.8 57.3 + - - +
324B ASP 3.1 6.9 + - - +
325B LYS 2.9 8.4 + - - +
327B ALA* 1.3 76.5 - - - +
329B LEU* 1.3 65.0 + - - +
331B ARG* 3.2 8.1 + - - +
332B ALA* 2.9 22.5 + - - +
355B PHE* 3.6 14.8 - - - +
356B ASN* 3.0 26.1 - - - +
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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 LYS* 2.9 23.0 + - + +
326B MET* 3.7 33.0 - - + +
328B ASN* 1.3 74.5 - - - +
330B GLN* 1.3 58.6 + - - +
332B ALA* 2.9 7.7 + - - +
333B ALA 2.8 25.6 + - - -
355B PHE* 4.0 24.5 - - + -
356B ASN* 4.1 5.4 - - + -
378B THR* 4.3 9.9 - - + -
379B SER* 3.9 26.7 - - - +
382B PHE* 3.1 50.2 - - + -
383B LEU* 5.2 0.7 - - + -
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Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B MET* 2.9 24.3 + - - +
327B ALA* 3.7 8.7 - - - +
328B ASN 3.3 0.2 - - - -
329B LEU* 1.3 77.4 - - - +
331B ARG* 1.3 57.3 + - - +
333B ALA* 3.2 7.6 + - - +
334B THR* 2.9 32.6 + - - +
382B PHE* 3.6 22.0 - - - -
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.7 11.9 - - + -
319B SER* 3.6 19.6 + - - -
320B GLY* 4.7 3.4 - - - -
327B ALA 3.1 18.9 + - - +
328B ASN* 3.5 7.0 - - - +
329B LEU 3.1 0.2 - - - -
330B GLN* 1.3 72.0 - - - +
332B ALA* 1.3 66.9 + - - +
333B ALA 3.1 1.3 - - - -
334B THR* 3.3 6.4 + - - -
335B PHE* 3.0 45.1 + - + -
555B GLU* 2.6 43.2 + - - -
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.7 18.5 - - + +
328B ASN 2.9 7.2 + - - +
329B LEU* 2.9 8.8 + - - +
331B ARG* 1.3 76.5 - - - +
333B ALA* 1.3 60.7 + - - +
335B PHE* 4.0 1.7 - - - +
336B ILE* 3.0 35.3 + - + +
351B LEU* 4.5 14.4 - - + -
355B PHE* 3.5 33.0 - - + -
382B PHE* 5.3 2.5 - - + -
383B LEU* 5.5 2.2 - - + -
386B LEU* 4.9 0.7 - - + -
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU 2.8 11.7 + - - +
330B GLN* 3.2 14.1 - - - +
332B ALA* 1.3 75.8 - - - +
334B THR* 1.3 66.8 + - - +
336B ILE* 3.1 4.0 + - - +
337B GLU* 3.0 37.9 + - - +
382B PHE* 3.7 21.7 - - + -
386B LEU* 4.0 20.5 - - + +
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Residues in contact with THR 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 GLN* 2.9 19.7 + - - +
331B ARG* 3.5 12.3 - - + -
333B ALA* 1.3 75.2 - - - +
335B PHE* 1.3 67.8 + - + +
337B GLU* 3.2 18.6 + - - +
338B ARG* 3.2 49.5 + - + +
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Residues in contact with PHE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B VAL* 3.8 23.1 - - + +
318B LEU* 3.6 11.4 - - + -
331B ARG* 3.0 38.5 + - + +
332B ALA 4.2 1.6 - - - +
334B THR* 1.3 80.9 - - + +
336B ILE* 1.3 60.5 + - - +
338B ARG* 3.5 34.0 + - - +
339B ALA* 3.1 19.8 + - - +
555B GLU* 3.4 45.5 - - + -
556B GLU* 5.0 7.9 - - - -
557B ILE* 3.2 36.0 - - + +
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Residues in contact with ILE 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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316B VAL* 4.3 8.5 - - + -
332B ALA* 3.0 18.8 + - + +
333B ALA* 3.1 6.5 + - - +
335B PHE* 1.3 76.3 - - - +
337B GLU* 1.3 64.5 + - - +
339B ALA* 3.2 5.9 + - + +
340B MET* 3.1 26.8 + - + +
349B VAL* 4.1 20.4 - - + -
351B LEU* 3.7 30.1 - - + -
386B LEU* 4.1 21.1 - - + -
390B PHE* 4.2 14.8 - - + -
392B ILE* 4.1 23.3 - - + -
394B LEU* 4.4 9.0 - - + -
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Residues in contact with GLU 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 ALA* 3.0 33.6 + - - +
334B THR* 3.2 14.4 + - - +
336B ILE* 1.3 77.7 - - - +
338B ARG* 1.3 58.0 + - + +
340B MET* 3.4 2.8 + - - +
341B LYS* 2.9 29.4 + - - +
386B LEU* 4.7 5.9 - - - +
389B LYS* 4.7 13.7 + - - +
390B PHE* 3.8 26.6 - - + -
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Residues in contact with ARG 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 THR* 3.2 33.9 + - + +
335B PHE* 3.7 37.6 - - - +
336B ILE 3.2 0.2 - - - -
337B GLU* 1.3 76.4 - - + +
339B ALA* 1.3 59.9 + - - +
341B LYS* 3.7 6.2 - - - +
342B GLU* 2.9 38.2 + - + +
557B ILE* 3.9 10.5 - - + -
559B TYR* 4.5 0.2 - - - -
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Residues in contact with ALA 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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314B ALA* 4.2 22.9 - - + -
316B VAL* 4.8 4.7 - - + -
335B PHE 3.1 14.5 + - - +
336B ILE* 3.4 15.0 - - + +
337B GLU 3.2 0.4 - - - -
338B ARG* 1.3 77.0 - - - +
340B MET* 1.3 63.3 + - - +
342B GLU* 3.4 0.5 + - - -
343B GLN* 2.9 33.3 + - - +
346B THR* 4.4 1.5 + - - -
349B VAL* 5.2 2.2 - - + -
557B ILE* 3.7 9.2 - - + +
559B TYR* 3.8 14.2 - - - -
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Residues in contact with MET 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ILE* 3.1 19.0 + - + +
337B GLU 3.8 3.6 - - - +
339B ALA* 1.3 76.8 - - - +
341B LYS* 1.3 58.1 + - - +
343B GLN 3.8 2.0 - - - -
344B PRO* 3.1 43.2 - - - +
346B THR* 3.9 29.6 - - - +
349B VAL* 4.2 8.1 - - - -
390B PHE* 3.4 43.3 - - + -
391B LYS* 4.8 4.3 - - + +
392B ILE* 3.3 35.2 - - + -
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Residues in contact with LYS 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 GLU 2.9 17.5 + - - +
338B ARG* 3.7 7.9 - - - +
340B MET* 1.3 78.1 - - - +
342B GLU* 1.3 70.7 + - + +
343B GLN 3.5 0.3 + - - -
344B PRO* 3.7 12.5 - - - +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ARG* 2.9 21.6 + - + +
341B LYS* 1.3 86.2 - - + +
343B GLN* 1.3 59.4 + - - +
344B PRO* 3.8 4.1 - - - +
557B ILE* 5.2 3.3 - - - +
559B TYR* 2.9 37.3 + - + +
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Residues in contact with GLN 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LYS* 3.4 32.3 - - + +
313B VAL 3.2 25.5 + - - -
339B ALA 2.9 12.4 + - - +
340B MET* 3.3 7.2 - - - +
342B GLU* 1.3 79.7 - - - +
344B PRO* 1.4 63.4 - - - +
345B ASP* 3.7 16.2 - - - +
346B THR* 2.6 39.2 + - - +
559B TYR* 3.4 32.5 - - + +
560B ALA 4.4 2.1 + - - +
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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
------------------------------------------------------------
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