Contacts of the helix formed by residues 344 - 363 (chain A) in PDB entry 1F9O
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 ASN 344 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLN* 3.4 24.4 + - - +
268A ARG* 3.7 2.0 - - - -
289A TYR* 3.6 27.6 + - - +
342A SER 3.3 0.4 - - - -
343A SER* 1.3 93.5 + - - +
345A GLY* 1.3 66.9 + - - +
346A ALA 3.5 1.8 - - - -
347A SER* 3.2 14.0 + - - +
348A ASP* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 4.0 4.7 - - - -
268A ARG* 3.7 14.3 - - - +
340A PRO* 4.0 11.4 - - - -
342A SER* 2.9 25.3 + - - -
344A ASN* 1.3 78.3 - - - +
346A ALA* 1.3 61.5 + - - +
348A ASP* 3.6 1.7 - - - +
349A TRP* 3.2 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU 3.7 22.4 - - - +
333A SER* 3.1 24.6 - - - +
339A LYS* 4.1 33.1 - - + +
340A PRO* 3.9 8.2 + - + +
342A SER 5.0 1.4 + - - -
343A SER 5.3 1.0 + - - -
344A ASN 3.5 0.4 - - - -
345A GLY* 1.3 73.2 - - - +
347A SER* 1.3 58.5 + - - +
349A TRP* 3.3 1.6 + - - +
350A ALA* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER 4.8 1.4 + - - -
344A ASN* 3.2 24.1 + - - +
346A ALA* 1.3 75.8 - - - +
348A ASP* 1.3 65.8 + - - +
350A ALA* 3.1 10.2 + - - +
351A LYS* 3.1 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 4.4 0.9 - - - +
268A ARG* 2.6 27.6 + - - +
271A PHE* 3.9 11.7 - - + -
272A PHE* 5.8 0.3 - - - -
289A TYR* 2.6 46.7 + - - -
294A TYR* 4.0 9.4 + - - -
344A ASN* 2.9 24.6 + - - +
345A GLY 3.6 4.3 - - - +
347A SER* 1.3 78.6 + - - +
349A TRP* 1.3 59.0 + - - +
351A LYS* 3.2 15.4 + - - +
352A SER* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ALA* 5.4 0.2 - - + -
264A GLY 2.9 28.3 + - - -
265A ASP* 5.6 0.2 - - - -
267A LEU* 3.8 25.1 - - + -
268A ARG* 3.6 11.7 - - + +
271A PHE* 3.6 30.7 - + - -
296A LEU* 3.8 23.1 - - + -
325A ASN 5.1 0.9 - - - -
328A ALA* 4.9 4.7 - - + -
329A ALA* 3.5 47.4 - - + +
332A LEU* 3.7 31.7 - - + +
333A SER* 3.9 11.0 - - - -
340A PRO* 4.8 4.0 - - + -
345A GLY 3.2 22.2 + - - +
346A ALA 3.6 9.0 - - - +
347A SER 3.2 0.4 - - - -
348A ASP* 1.3 79.5 - - - +
350A ALA* 1.3 58.5 + - - +
351A LYS 3.3 0.2 - - - -
352A SER* 3.6 8.7 - - - -
353A LEU* 3.1 25.5 + - - +
356A GLN* 4.1 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A SER* 3.8 15.3 - - - +
346A ALA 3.1 12.4 + - - +
347A SER* 3.1 15.4 + - - +
349A TRP* 1.3 76.9 - - - +
351A LYS* 1.3 64.0 + - + +
353A LEU* 3.3 15.7 + - - +
354A ASP* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TYR* 6.3 0.2 - - - -
294A TYR* 3.9 40.9 + - + +
347A SER* 3.1 21.0 + - - +
348A ASP* 3.2 15.1 + - - +
350A ALA* 1.3 76.5 - - + +
352A SER* 1.3 63.7 + - - +
354A ASP* 3.5 7.8 + - - +
355A ARG* 3.1 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 3.6 29.9 - - - -
294A TYR* 2.8 28.8 + - - +
295A LEU* 4.7 0.2 - - - -
348A ASP 3.0 11.8 + - - -
349A TRP* 3.7 11.4 - - - -
350A ALA 3.2 0.4 - - - -
351A LYS* 1.3 76.0 - - - +
353A LEU* 1.3 56.0 + - - +
355A ARG* 3.8 0.3 - - - +
356A GLN* 2.7 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PRO* 3.3 35.9 - - + +
329A ALA* 4.0 8.5 - - + +
330A TRP* 4.2 26.9 - - + -
333A SER* 4.7 6.3 - - - +
334A THR* 5.6 2.0 - - + -
349A TRP 3.1 14.3 + - - +
350A ALA* 3.4 11.4 - - - +
351A LYS 3.2 0.2 - - - -
352A SER* 1.3 78.5 - - - +
354A ASP* 1.3 68.0 + - - +
356A GLN* 3.9 2.8 - - - +
357A LEU* 3.3 37.2 + - + +
425A LEU* 4.3 7.4 - - + -
431A ASP* 5.8 0.7 - - - +
433A ARG* 4.9 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA 3.3 12.6 + - - +
351A LYS* 3.5 8.1 + - - +
352A SER 3.3 0.2 - - - -
353A LEU* 1.3 81.7 - - - +
355A ARG* 1.3 62.2 + - - +
357A LEU* 3.5 3.3 + - - +
358A GLU* 3.3 33.2 + - - +
433A ARG* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ILE* 5.5 2.2 - - - +
292A ALA 4.6 1.6 + - - -
293A HIS* 3.0 42.9 + - - +
294A TYR* 4.1 24.7 - - + +
295A LEU* 3.9 11.0 - - + -
351A LYS 3.1 18.2 + - - +
352A SER 3.8 2.7 - - - +
354A ASP* 1.3 75.5 - - - +
356A GLN* 1.3 64.8 + - - +
358A GLU* 3.2 10.7 + - - +
359A PHE* 3.1 21.1 + - - +
392A PHE* 3.7 22.0 - - + -
393A TYR* 3.7 47.9 + - - +
395A MET* 5.4 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR 4.4 0.2 - - - +
295A LEU* 3.8 12.6 - - + -
296A LEU* 4.4 6.4 - - - +
324A GLN* 3.3 30.1 - - + +
325A ASN 2.8 41.0 + - - +
326A PRO* 3.2 12.1 - - + +
329A ALA* 3.9 18.0 - - - +
349A TRP* 4.1 7.7 - - - -
352A SER* 2.7 44.1 + - - +
353A LEU* 3.9 4.7 - - - +
355A ARG* 1.3 72.8 - - - +
357A LEU* 1.3 62.2 + - - +
359A PHE* 3.1 5.8 + - - +
360A TYR* 3.1 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PRO* 4.4 23.6 - - + -
353A LEU* 3.3 28.4 + - + +
354A ASP 4.0 3.8 - - - +
355A ARG 3.3 0.2 - - - -
356A GLN* 1.3 77.6 - - - +
358A GLU* 1.3 61.3 + - - +
360A TYR* 3.8 6.7 + - + +
361A GLN* 3.4 22.0 + - - +
422A VAL* 4.8 7.4 - - + -
425A LEU* 4.2 15.0 - - + -
431A ASP* 4.6 2.0 - - - +
433A ARG* 3.6 57.4 - - + +
434A ALA 4.7 5.2 - - - +
437A LEU* 4.2 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ASP* 3.3 24.8 + - - +
355A ARG* 3.2 14.5 + - - +
356A GLN 3.1 0.6 - - - -
357A LEU* 1.3 76.0 - - + +
359A PHE* 1.3 55.8 + - - +
361A GLN* 3.4 2.9 + - - +
362A TRP* 2.8 36.0 + - - +
392A PHE* 3.8 9.5 - - + -
393A TYR* 2.6 31.4 + - - -
433A ARG* 6.4 1.8 - - - -
472A TRP* 3.0 39.9 + - + -
474A PRO* 4.3 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 3.8 22.0 - - + -
319A ASN* 3.7 12.6 - - + -
320A HIS 4.0 4.7 - - - -
321A PHE* 3.8 22.4 - - + -
324A GLN* 4.2 17.0 - - + -
355A ARG 3.1 11.6 + - - +
356A GLN 3.3 10.3 - - - +
358A GLU* 1.3 77.5 - - - +
360A TYR* 1.3 63.9 + + - +
362A TRP* 3.2 26.9 + + - +
363A LEU* 3.1 39.6 + - + +
373A GLY* 3.4 23.1 - - - -
374A ALA* 3.6 14.4 - - + -
392A PHE* 3.6 28.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 3.9 22.0 - + + -
324A GLN* 3.5 23.1 + - + -
326A PRO* 3.4 34.4 - - + +
356A GLN 3.1 29.5 + - - +
357A LEU* 4.0 7.9 - - + +
358A GLU 3.3 0.2 - - - -
359A PHE* 1.3 76.4 - - + +
361A GLN* 1.3 63.6 + - - +
363A LEU* 3.1 13.1 + - - +
364A GLN* 3.2 9.9 + - - +
370A ILE* 3.9 13.8 - - + +
418A SER* 2.6 40.9 + - - -
419A MET* 4.1 19.5 - - - -
422A VAL* 3.5 16.2 - - + -
437A LEU* 3.5 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU 3.4 14.4 + - - +
358A GLU* 3.4 4.1 + - - +
359A PHE 3.3 0.2 - - - -
360A TYR* 1.3 80.4 - - - +
362A TRP* 1.3 63.2 + - - +
363A LEU 3.3 0.2 + - - -
364A GLN* 3.0 32.1 + - - +
433A ARG 4.7 1.2 - - - +
436A LYS* 4.2 18.5 - - - +
437A LEU* 3.5 19.1 - - + +
472A TRP* 4.4 13.9 - - + -
478A TYR* 3.4 53.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLU 2.8 18.5 + - - +
359A PHE* 3.2 10.9 + + - +
361A GLN* 1.3 77.8 - - - +
363A LEU* 1.3 84.9 + - + +
373A GLY 3.9 1.3 - - - -
374A ALA* 3.7 16.8 - - + -
390A SER* 4.3 0.9 - - - -
391A THR* 3.7 23.7 + - - -
392A PHE* 3.5 37.7 - + + -
397A TYR* 3.6 34.5 - + + -
469A PRO* 3.2 26.8 - - + +
470A ASP 2.8 28.6 + - - -
472A TRP* 3.5 38.0 - + + +
478A TYR* 5.3 0.4 - - - -
481A ASN* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 3.8 8.5 - - + -
359A PHE* 3.1 42.8 + - + +
360A TYR 3.1 3.1 + - - -
362A TRP* 1.3 106.1 - - + +
364A GLN* 1.3 62.0 + - - +
365A SER 3.3 1.7 + - - -
370A ILE* 3.7 8.7 - - + -
371A ALA* 2.8 58.2 + - + +
372A GLY 3.8 1.1 - - - +
373A GLY* 3.8 10.3 - - - +
397A TYR* 3.7 28.0 - - + -
469A PRO* 4.5 3.6 - - + -
481A ASN* 4.3 1.1 - - - -
484A LEU* 3.7 2.2 - - - +
----------------------------------------------------------
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