Contacts of the helix formed by residues 317 - 340 (chain B) in PDB entry 1FA0
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 317 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE 5.6 0.2 - - - +
299B ARG* 3.7 9.4 - - - +
315B ASN 3.5 13.7 - - - +
316B ILE* 1.3 81.0 - - - +
318B GLU* 1.3 63.4 + - - +
319B SER* 3.1 2.8 + - - -
320B THR* 2.9 32.8 + - + +
321B LYS* 3.1 18.5 + - - +
387B ARG* 4.2 13.5 - - + +
390B VAL* 3.7 11.6 - - + +
391B MET* 3.7 26.5 - - + -
394B GLU* 3.0 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ARG* 2.7 42.3 + - - +
317B THR* 1.3 74.8 - - - +
319B SER* 1.3 59.6 + - - +
321B LYS* 3.7 22.2 + - - +
322B LYS* 3.2 37.6 + - - +
394B GLU* 2.9 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B THR* 3.1 3.3 + - - -
318B GLU* 1.3 74.6 - - - +
320B THR* 1.3 61.0 + - - +
321B LYS 3.0 1.8 - - - -
322B LYS* 2.8 34.4 + - - +
323B VAL* 3.1 15.6 + - - +
390B VAL* 4.1 1.1 - - - -
394B GLU* 3.1 34.1 + - - +
401B ILE* 3.9 12.9 - - - +
402B ALA 3.4 29.6 + - - -
404B PRO* 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE 3.6 19.1 - - - +
229B GLY* 2.7 32.5 + - - +
230B PHE* 3.8 24.0 - - + -
316B ILE* 3.4 2.8 - - - +
317B THR* 2.9 31.9 + - + +
319B SER* 1.3 75.5 - - - +
321B LYS* 1.3 61.7 + - - +
323B VAL* 3.3 6.8 + - - +
324B ILE* 2.9 30.2 + - - +
404B PRO* 3.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B TRP* 4.4 29.1 + - - +
269B PRO* 6.0 0.8 - - - +
299B ARG* 4.2 22.4 + - + +
300B MET* 3.6 21.1 - - + -
316B ILE* 3.9 12.6 - - + -
317B THR 3.1 14.9 + - - +
318B GLU* 3.7 25.2 + - - +
319B SER 3.0 0.8 - - - -
320B THR* 1.3 83.1 + - - +
322B LYS* 1.3 58.4 + - - +
324B ILE* 3.4 1.8 + - - +
325B LEU* 2.9 56.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU* 3.2 36.8 + - - +
319B SER* 2.8 27.0 + - - +
321B LYS* 1.3 74.5 - - - +
323B VAL* 1.3 51.3 + - - +
325B LEU* 3.1 10.5 + - - +
326B GLN* 2.7 46.3 + - + +
394B GLU* 5.7 3.6 + - - +
400B LYS 3.4 24.6 + - - +
401B ILE* 4.1 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ARG 5.2 0.9 - - - +
222B ALA 5.0 0.4 - - - +
223B VAL* 3.8 22.7 - - + -
230B PHE* 3.8 9.4 - - + -
319B SER 3.1 12.1 + - - +
320B THR* 3.5 12.8 - - - +
322B LYS* 1.3 76.3 - - - +
324B ILE* 1.3 57.4 + - - +
326B GLN* 2.7 36.8 + - - +
327B GLU* 2.8 19.8 + - + +
357B ARG* 5.3 0.2 - - - +
401B ILE* 4.2 10.5 - - + -
403B HIS* 3.5 49.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 6.0 0.4 - - + -
223B VAL* 4.6 12.3 - - + -
229B GLY 4.6 0.2 - - - +
230B PHE* 3.8 18.2 - - + -
231B PRO* 3.4 34.3 - - + -
236B TRP* 4.6 7.4 - - + -
300B MET* 3.8 18.2 - - + -
316B ILE* 4.1 19.5 - - + -
320B THR 2.9 28.2 + - - +
321B LYS* 3.6 4.3 - - - +
323B VAL* 1.3 73.1 - - - +
325B LEU* 1.3 59.9 + - - +
327B GLU* 3.2 3.3 + - - +
328B PHE* 2.9 58.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B SER* 4.3 16.7 - - - +
268B TRP* 4.0 24.5 - - + +
300B MET* 4.6 5.8 - - + -
321B LYS* 2.9 53.3 + - + +
322B LYS* 3.5 7.9 - - - +
324B ILE* 1.3 75.5 - - - +
326B GLN* 1.3 59.2 + - - +
328B PHE* 3.5 19.8 + - + +
329B VAL* 3.2 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LYS* 2.7 24.1 + - + +
323B VAL* 2.7 27.1 + - - +
325B LEU* 1.3 69.9 - - - +
327B GLU* 1.3 67.8 + - + +
329B VAL* 3.2 8.4 + - - +
330B ARG* 3.1 21.3 + - - +
357B ARG* 3.2 34.4 + - - +
358B TYR* 5.2 1.1 + - - -
401B ILE* 4.9 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 3.7 27.1 + - + -
221B ARG* 2.9 56.1 + - + +
223B VAL* 3.6 24.5 - - + -
323B VAL* 2.8 19.6 + - + +
324B ILE 3.6 7.0 - - - +
326B GLN* 1.3 79.5 + - + +
328B PHE* 1.3 57.5 + - - +
330B ARG* 3.4 14.3 + - - +
331B GLY* 2.9 24.4 + - - -
352B ASN* 5.3 2.4 - - - +
357B ARG* 4.8 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 3.7 27.1 - + - -
236B TRP* 3.7 23.6 - + - -
239B LEU* 5.3 3.4 - - + -
259B PHE* 4.0 7.6 - + - -
260B PHE* 3.7 16.7 - + - +
263B LEU* 3.5 50.0 - - + -
264B SER* 3.8 15.5 - - - -
268B TRP* 4.9 0.7 - + - -
300B MET* 4.3 11.9 - - + -
324B ILE* 2.9 38.1 + - + +
325B LEU* 3.6 14.1 - - + +
326B GLN 3.1 0.2 - - - -
327B GLU* 1.3 74.3 - - - +
329B VAL* 1.3 67.5 + - - +
331B GLY* 3.0 3.6 + - - -
332B VAL* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B SER* 4.6 12.3 - - - +
325B LEU 3.2 12.5 + - - +
326B GLN* 3.2 9.5 + - - +
328B PHE* 1.3 73.0 - - - +
330B ARG* 1.3 68.0 + - - +
332B VAL* 2.8 19.6 + - + +
333B GLN* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 4.1 11.5 - - - +
221B ARG* 3.2 54.3 - - - +
326B GLN 3.1 12.6 + - - +
327B GLU* 3.5 16.2 - - - +
329B VAL* 1.3 76.5 - - - +
331B GLY* 1.3 57.6 + - - +
333B GLN* 3.0 16.5 + - - +
334B ILE* 2.8 53.6 + - + +
347B ASN 3.3 23.6 + - - -
348B LEU* 3.4 20.0 + - - +
350B GLU* 4.0 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 5.0 1.1 - - - -
260B PHE* 3.7 25.1 - - - -
327B GLU 2.9 14.9 + - - -
328B PHE 3.0 5.8 + - - -
330B ARG* 1.3 77.6 - - - +
332B VAL* 1.3 58.0 + - - +
335B THR* 2.8 33.8 + - - +
348B LEU* 4.3 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PHE* 3.1 41.3 - - - +
261B ILE* 3.4 24.9 - - + +
264B SER* 4.2 7.0 - - - +
328B PHE 2.9 11.4 + - - +
329B VAL* 2.8 12.7 + - + +
331B GLY* 1.3 76.4 - - - +
333B GLN* 1.3 58.7 + - + +
335B THR* 3.9 2.4 + - - -
336B ASN* 2.8 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL* 2.9 30.0 + - + +
330B ARG* 3.0 18.8 + - - +
332B VAL* 1.3 78.6 - - + +
334B ILE* 1.3 67.9 + - + +
336B ASN* 3.4 5.8 + - - +
337B ASP* 3.1 30.6 + - - +
343B LYS* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG* 2.8 71.0 + - + +
333B GLN* 1.3 74.8 - - + +
335B THR* 1.3 57.0 + - - +
337B ASP* 3.0 5.5 + - - +
338B ILE* 2.8 38.1 + - + +
343B LYS* 3.9 32.3 - - + +
347B ASN* 4.3 6.7 - - + +
348B LEU* 3.9 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 4.9 3.8 - - + +
257B ASN* 2.6 37.5 + - - -
260B PHE* 4.1 12.9 - - + -
331B GLY 2.8 23.6 + - - +
332B VAL* 3.9 1.2 + - - -
334B ILE* 1.3 71.8 - - - +
336B ASN* 1.3 63.6 + - - +
338B ILE* 3.7 9.1 - - + +
339B PHE* 3.1 34.5 + - - -
345B TRP* 4.3 12.6 - - + -
348B LEU* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASN* 3.3 25.8 + - - +
261B ILE* 4.4 7.7 - - - +
332B VAL* 2.8 40.0 + - - +
333B GLN* 3.6 6.5 - - - +
334B ILE 3.2 0.6 - - - -
335B THR* 1.3 78.1 + - - +
337B ASP* 1.3 62.8 + - - +
339B PHE* 3.3 8.2 + - - +
340B SER* 3.2 21.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLN* 3.1 17.4 + - - +
334B ILE 3.0 9.1 + - - +
336B ASN* 1.3 75.9 - - - +
338B ILE* 1.3 57.7 + - - +
339B PHE 3.1 0.2 - - - -
340B SER* 3.0 6.2 + - - -
341B ASN 2.8 9.9 + - - -
342B LYS* 2.7 59.1 + - + +
343B LYS* 3.1 45.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.3 24.1 - - + +
334B ILE* 2.8 28.0 + - + +
335B THR* 3.7 11.4 - - - +
336B ASN 3.3 0.2 - - - -
337B ASP* 1.3 75.7 - - - +
339B PHE* 1.3 61.2 + - + +
341B ASN* 3.4 11.1 + - - -
343B LYS* 3.6 19.1 - - + +
344B SER* 3.3 35.2 - - - +
345B TRP* 3.4 54.1 - - + +
348B LEU* 4.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 4.4 11.4 - - + -
25B LEU* 3.9 29.1 - - + +
253B ALA* 3.8 39.5 - - + -
254B VAL* 3.8 23.6 - - + -
257B ASN* 4.4 16.8 - - + -
258B ARG* 5.2 3.8 - - - -
335B THR* 3.1 26.6 + - - +
336B ASN* 3.7 8.3 - - - +
337B ASP 3.1 0.8 - - - -
338B ILE* 1.3 78.1 - - + +
340B SER* 1.3 58.4 + - - +
341B ASN* 3.1 15.3 + - - +
345B TRP* 4.3 15.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASN 3.2 13.6 + - - -
337B ASP* 3.0 18.5 + - - -
339B PHE* 1.3 75.1 - - - +
341B ASN* 1.3 70.9 + - - +
342B LYS* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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