Contacts of the helix formed by residues 322 - 341 (chain B) in PDB entry 6FY5
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 PRO 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B TRP* 3.6 32.1 - - + +
320B CYS 3.6 4.0 - - - +
321B PHE* 1.4 86.5 - - + +
323B LYS* 1.3 67.3 + - - +
324B GLN* 4.6 2.9 - - + +
325B THR* 3.1 23.4 + - - +
326B ALA* 3.0 19.6 + - - +
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Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B SER* 5.8 7.4 - - - -
321B PHE 3.5 3.9 + - - +
322B PRO* 1.3 70.6 - - - +
324B GLN* 1.3 57.8 + - - +
326B ALA* 3.3 6.3 + - - +
327B ALA* 2.9 30.3 + - - +
355B ASP* 2.8 30.6 + - - -
357B GLU* 2.8 28.4 + - - +
358B SER* 3.3 20.6 - - - +
361B ILE* 3.6 24.1 - - + +
362B TYR* 4.6 3.3 - - + -
1002B EDO 4.6 16.4 - - - +
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO* 3.2 3.6 - - + +
323B LYS* 1.3 79.0 - - - +
325B THR* 1.3 65.7 + - - +
327B ALA* 3.4 1.6 + - - +
328B GLN* 2.8 59.6 + - - +
361B ILE* 3.6 21.9 - - + +
365B GLU* 2.8 31.6 + - - +
368B LYS* 5.1 3.2 - - - +
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B TRP* 4.9 4.1 + - - +
287B GLU* 3.8 38.1 - - + +
321B PHE* 4.1 13.5 - - + -
322B PRO* 3.1 30.0 + - + +
324B GLN* 1.3 84.9 + - - +
326B ALA* 1.3 65.5 + - - +
328B GLN* 3.8 4.4 - - - +
329B VAL* 2.9 33.0 + - + +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 4.1 13.2 - - + -
314B PHE* 3.8 26.9 - - + -
321B PHE* 4.1 14.0 - - + +
322B PRO 3.0 11.4 + - - +
323B LYS* 3.6 10.3 - - - +
325B THR* 1.3 76.3 - - - +
327B ALA* 1.4 53.5 + - - +
329B VAL* 3.9 0.9 - - - +
330B THR* 2.7 37.8 + - - -
362B TYR* 4.0 7.2 - - - +
1002B EDO 4.4 4.9 - - - +
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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
----------------------------------------------------------
323B LYS 2.9 17.2 + - - +
324B GLN 3.6 4.0 - - - +
326B ALA* 1.4 72.9 - - - +
328B GLN* 1.3 64.6 + - - +
330B THR* 4.0 0.2 - - - -
331B LEU* 3.0 33.2 + - - +
361B ILE* 3.8 18.8 - - + -
362B TYR* 3.6 35.6 + - + -
365B GLU* 4.0 9.9 - - + -
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Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 5.8 1.8 + - - -
324B GLN* 2.8 50.7 + - - +
325B THR* 3.8 5.6 - - - +
327B ALA* 1.3 71.5 - - - +
329B VAL* 1.3 67.4 + - + +
331B LEU* 4.1 2.2 - - - +
332B LYS* 3.0 35.2 + - + +
365B GLU* 4.0 18.5 - - - +
368B LYS* 6.3 0.4 - - - -
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 3.5 53.8 - - + +
290B LEU* 3.8 20.2 - - + -
291B GLU* 3.7 22.2 - - + +
294B ILE* 5.5 0.2 - - + -
325B THR* 2.9 24.5 + - + +
328B GLN* 1.3 79.1 - - + +
330B THR* 1.4 56.6 + - - +
332B LYS* 3.7 13.3 - - - +
333B ALA* 2.9 29.5 + - - +
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 4.5 1.9 - - - +
294B ILE* 4.1 26.5 - - + +
311B PHE* 5.0 3.8 - - + -
314B PHE* 3.2 26.6 - - + -
326B ALA 2.7 22.9 + - - -
327B ALA* 4.0 3.8 - - - -
329B VAL* 1.4 73.9 - - - +
331B LEU* 1.3 57.4 + - - +
333B ALA* 3.4 2.3 + - - +
334B ILE* 3.1 48.4 + - + +
351B PHE* 3.9 17.3 - - + -
362B TYR* 5.0 4.3 - - + -
1001B EDO 5.0 5.4 - - - -
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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
----------------------------------------------------------
197B LEU* 3.9 15.3 - - + +
327B ALA 3.0 21.4 + - - +
328B GLN* 4.2 1.8 - - - +
330B THR* 1.3 74.3 - - - +
332B LYS* 1.3 51.8 + - - +
334B ILE* 3.5 3.3 + - - +
335B SER* 2.8 39.8 + - - -
351B PHE* 3.8 30.3 - - + -
362B TYR* 4.1 20.4 - - + +
365B GLU* 3.6 29.2 - - + +
366B MET* 3.7 33.7 - - + +
369B LEU* 4.5 12.3 - - + +
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Residues in contact with LYS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU* 3.4 31.7 + - - -
328B GLN* 3.0 26.6 + - + +
329B VAL* 3.7 13.7 - - - +
331B LEU* 1.3 73.6 - - - +
333B ALA* 1.3 63.2 + - - +
335B SER* 3.4 6.2 + - - -
336B ALA* 3.2 28.1 + - + +
369B LEU* 5.2 2.2 - - - +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU* 3.8 32.5 - - + +
294B ILE* 3.8 23.6 - - + -
295B LYS* 4.5 10.3 - - + +
298B LEU* 4.8 2.0 - - - -
329B VAL 2.9 18.0 + - - +
330B THR 3.8 4.5 - - - +
331B LEU 3.4 0.2 - - - -
332B LYS* 1.3 75.6 - - - +
334B ILE* 1.3 61.9 + - - +
336B ALA* 3.8 4.3 - - - +
337B HIS* 3.1 24.5 + - - +
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 3.6 29.8 - - + -
294B ILE* 3.7 13.9 - - + -
298B LEU* 3.8 17.0 - - + -
311B PHE* 3.8 21.3 - - + -
330B THR* 3.1 27.3 + - + +
331B LEU* 4.0 4.0 - - - +
332B LYS 3.4 0.2 - - - -
333B ALA* 1.3 72.9 - - - +
335B SER* 1.3 60.8 + - - +
337B HIS* 3.2 3.3 + - - +
338B PHE* 3.0 45.9 + - + +
349B VAL* 4.1 4.0 - - + -
351B PHE* 3.5 32.1 - - + -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 4.2 19.3 - - - -
197B LEU* 5.2 1.3 - - - -
331B LEU 2.8 25.2 + - - -
332B LYS* 3.4 7.4 + - - -
334B ILE* 1.3 73.6 - - - +
336B ALA* 1.4 54.2 + - - +
338B PHE 3.4 0.5 + - - -
339B ASP* 2.8 51.4 + - - +
369B LEU* 3.5 29.8 - - - +
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU* 5.7 2.2 - - - +
295B LYS* 5.6 6.3 - - - -
332B LYS* 3.2 19.2 + - + +
333B ALA* 3.8 4.9 - - - +
335B SER* 1.4 77.1 + - - +
337B HIS* 1.3 65.2 + - - +
339B ASP* 4.6 4.2 - - - +
340B ASP* 3.3 24.8 + - - +
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Residues in contact with HIS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LYS* 4.7 18.4 - - + +
298B LEU* 3.7 30.3 - - + +
299B SER* 4.6 7.8 + - - -
302B GLU* 2.8 44.4 + - - -
333B ALA 3.1 18.5 + - - +
334B ILE 3.2 5.6 + - - +
336B ALA* 1.3 80.1 - - - +
338B PHE* 1.3 73.0 + + - +
340B ASP* 3.5 17.1 - - - +
341B SER* 3.9 6.2 + - - +
344B SER* 5.1 2.0 - - - -
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Residues in contact with PHE 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 3.7 14.8 - - + -
193B LEU* 3.3 15.6 - - - +
195B GLN* 3.3 58.8 + - + +
197B LEU* 4.6 2.0 - - + -
298B LEU* 4.5 5.2 - - + -
302B GLU* 4.0 2.2 - - - -
334B ILE* 3.0 31.6 + - + +
337B HIS* 1.3 90.0 - + - +
339B ASP* 1.3 60.2 + - - +
340B ASP 3.3 2.2 - - - -
341B SER 3.3 4.3 - - - +
344B SER* 3.9 12.1 - - - -
346B LEU* 3.6 44.0 - - + -
348B ASN 5.7 0.2 - - - -
349B VAL* 3.3 31.0 - - + -
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Residues in contact with ASP 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LYS* 2.9 41.3 + - - -
191B LEU* 4.0 19.8 - - - +
192B VAL* 3.9 10.7 - - + +
193B LEU* 3.3 17.3 + - - +
335B SER* 2.8 38.0 + - - +
336B ALA* 4.6 3.8 - - - +
338B PHE* 1.3 73.8 - - - +
340B ASP* 1.4 62.6 + - - +
341B SER 3.5 0.4 - - - -
370B ASP 4.9 1.6 - - - +
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Residues in contact with ASP 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 4.3 0.4 - - - +
336B ALA 3.3 19.1 + - - +
337B HIS* 3.5 8.9 - - - +
338B PHE 3.3 0.2 - - - -
339B ASP* 1.4 78.6 - - - +
341B SER* 1.3 69.3 + - - +
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.6 8.3 - - - -
195B GLN* 3.6 6.2 + - - -
337B HIS 3.9 3.7 + - - +
338B PHE* 3.3 16.5 - - - +
339B ASP 3.5 0.8 - - - -
340B ASP* 1.3 92.4 + - - +
342B SER* 1.3 56.9 + - - +
343B ALA* 3.1 31.7 + - - +
344B SER* 4.8 6.8 - - - -
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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
------------------------------------------------------------
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