Contacts of the helix formed by residues 324 - 353 (chain A) in PDB entry 1IAX
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TRP* 3.2 18.7 + - + +
70A ASN* 3.9 22.9 + - - +
71A PRO* 5.8 0.4 - - + +
320A ALA 4.2 6.7 - - - +
321A MET 3.3 13.5 - - - +
322A LEU 3.2 2.6 - - - -
323A SER* 1.3 77.0 - - - +
325A GLU* 1.3 50.9 + - - +
326A LYS* 3.2 10.6 + - - +
327A PHE* 2.6 38.2 + - + -
328A VAL* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 4.8 20.6 + - - +
108A LYS* 3.8 26.4 + - - +
322A LEU 5.1 0.4 + - - -
323A SER 3.7 6.2 + - - +
324A ASP* 1.3 71.7 - - - +
326A LYS* 1.3 57.4 + - - +
328A VAL* 3.7 6.6 - - - +
329A ASP* 2.8 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ASP* 3.1 7.0 + - - +
325A GLU* 1.3 76.9 - - - +
327A PHE* 1.3 67.6 + - - +
329A ASP* 3.9 6.0 - - + +
330A ASN* 2.9 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.9 13.9 - - + -
63A ILE* 4.0 7.9 - - + -
66A TRP* 3.3 48.5 - + + +
280A MET* 4.7 7.4 - - + -
321A MET* 3.4 48.5 - - + -
322A LEU* 5.1 1.1 - - + -
324A ASP* 2.6 26.9 + - + +
326A LYS* 1.3 72.1 - - - +
328A VAL* 1.3 61.6 + - + +
330A ASN* 3.7 3.5 - - - +
331A PHE* 2.7 75.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.8 20.6 - - + -
108A LYS* 4.1 18.4 - - + -
280A MET* 6.1 0.2 - - - -
321A MET 4.1 2.9 - - - +
322A LEU* 3.7 40.8 - - + +
324A ASP 2.8 22.9 + - - +
325A GLU* 3.8 7.2 - - - +
327A PHE* 1.3 80.5 - - + +
329A ASP* 1.3 61.8 + - - +
331A PHE* 3.7 3.2 - - - +
332A LEU* 3.1 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS* 3.0 40.6 + - - +
325A GLU* 2.8 36.4 + - - +
326A LYS* 3.9 5.6 - - + +
328A VAL* 1.3 72.2 - - - +
330A ASN* 1.3 64.4 + - - +
332A LEU* 3.9 5.2 - - - +
333A ARG* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.4 14.3 - - - +
326A LYS* 2.9 21.4 + - + +
327A PHE* 3.9 3.6 - - - +
329A ASP* 1.3 77.0 - - - +
331A PHE* 1.3 54.1 + - - +
333A ARG* 3.5 29.9 + - - +
334A GLU* 2.7 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A CYS* 3.7 26.9 - - + -
62A LEU* 4.1 16.9 - - + +
63A ILE* 3.7 25.8 - - + -
279A ASP* 5.0 2.0 - - + -
280A MET* 3.1 56.8 - - + -
327A PHE* 2.7 49.7 + + + +
328A VAL* 3.7 4.7 - - - +
330A ASN* 1.3 74.0 - - - +
332A LEU* 1.3 67.7 + - + +
334A GLU* 3.7 1.0 - - - +
335A SER* 2.8 43.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 4.0 22.0 - - + -
108A LYS* 3.8 32.1 - - + +
109A THR* 4.5 4.3 - - - +
242A ALA* 3.7 32.2 - - + +
280A MET* 5.1 0.2 - - + -
328A VAL* 3.1 35.2 + - + +
329A ASP* 4.0 3.6 - - - +
331A PHE* 1.3 85.1 - - + +
333A ARG* 1.3 63.0 + - - +
335A SER* 3.8 5.0 - - - -
336A ALA* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASP 2.9 19.3 + - - +
330A ASN* 3.5 24.9 + - - +
332A LEU* 1.3 80.4 - - - +
334A GLU* 1.3 74.3 + - - +
336A ALA* 3.4 6.0 + - - +
337A MET* 3.2 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A CYS* 4.2 1.8 - - - -
62A LEU* 3.5 22.4 - - + +
330A ASN* 2.7 37.8 + - - +
331A PHE 3.7 0.2 - - - +
333A ARG* 1.3 86.5 + - - +
335A SER* 1.3 66.7 + - - +
337A MET* 3.1 25.7 + - - +
338A ARG* 2.7 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 4.3 7.3 + - - -
59A CYS* 3.5 21.3 - - - +
242A ALA 4.2 12.4 + - - -
279A ASP* 6.1 0.2 - - - +
331A PHE* 2.8 33.5 + - - -
332A LEU* 3.8 7.4 - - - -
334A GLU* 1.3 72.9 - - - +
336A ALA* 1.3 58.2 + - - +
338A ARG* 4.0 0.3 - - - +
339A LEU* 2.9 56.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 6.3 0.4 - - - +
244A VAL 3.7 23.3 - - - +
245A PHE* 3.3 17.5 - - - +
332A LEU 3.2 10.9 + - - +
333A ARG* 3.7 10.1 - - - +
334A GLU 3.2 0.2 - - - -
335A SER* 1.3 79.9 - - - +
337A MET* 1.3 58.0 + - + +
339A LEU* 4.7 2.2 - - - -
340A GLY* 3.0 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG* 3.2 57.1 + - + +
334A GLU* 3.1 28.5 + - - +
336A ALA* 1.3 76.8 - - + +
338A ARG* 1.3 56.4 + - + +
340A GLY* 3.2 1.1 + - - -
341A LYS* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 2.9 38.1 + - + +
59A CYS* 3.9 7.5 - - - -
61A ASP* 2.5 38.4 + - - -
62A LEU* 3.5 27.3 - - - +
334A GLU* 2.7 47.1 + - - +
335A SER 4.0 2.7 - - - +
337A MET* 1.3 73.7 - - + +
339A LEU* 1.3 67.0 - - - +
341A LYS* 3.3 12.6 + - - +
342A ARG* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 3.7 17.3 - - - +
58A LEU* 3.7 23.1 - - + -
243A THR* 4.4 18.2 - - - -
245A PHE* 4.0 19.4 - - + -
335A SER* 2.9 41.5 + - - +
338A ARG* 1.3 77.5 - - - +
340A GLY* 1.3 56.4 + - - +
342A ARG* 4.1 0.6 - - - +
343A HIS* 2.9 32.6 + - - +
363A GLY 3.8 8.7 - - - +
364A LEU* 3.5 28.3 - - + -
415A PHE* 5.0 5.6 - - + -
416A ALA* 3.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.6 19.5 - - - +
336A ALA 3.0 17.9 + - - -
337A MET* 3.5 4.5 - - - -
338A ARG 3.1 0.2 - - - -
339A LEU* 1.3 76.5 - - - +
341A LYS* 1.3 62.8 + - - +
344A LYS* 3.0 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A MET 2.7 19.5 + - - +
338A ARG* 3.9 11.2 - - - +
340A GLY* 1.3 73.1 - - - +
342A ARG* 1.3 66.2 + - - +
344A LYS* 4.0 2.6 - - - +
345A HIS* 3.0 36.7 + - + +
420A ASP* 3.2 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 2.8 37.2 - - + +
338A ARG 3.0 17.5 + - - +
339A LEU* 4.1 2.2 - - - +
341A LYS* 1.3 81.1 - - - +
343A HIS* 1.3 61.1 + - - +
345A HIS* 3.2 7.8 + - - +
346A PHE* 2.7 29.3 + - - +
415A PHE* 2.8 41.1 + - + +
418A MET 2.4 30.6 + - - +
419A ASP* 3.6 3.0 + - - +
420A ASP* 2.6 49.1 + - - +
423A VAL* 3.7 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.4 21.7 - + + -
339A LEU 2.9 20.7 + - - +
340A GLY 4.2 1.6 - - - +
342A ARG* 1.3 77.4 - - - +
344A LYS* 1.3 71.5 + - + +
346A PHE* 3.6 2.4 - - - +
347A THR* 2.9 58.2 + - + -
357A CYS* 6.3 0.2 - - - +
359A LYS* 6.3 0.2 - - - -
360A ASN* 3.2 56.0 + - - -
366A CYS* 4.7 2.1 - - + +
415A PHE* 3.6 31.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.6 32.1 + - - -
246A ASP* 2.8 28.8 + - - +
340A GLY* 3.0 27.8 + - - +
341A LYS* 4.0 3.1 - - - +
343A HIS* 1.3 90.6 + - + +
345A HIS* 1.3 58.5 + - - +
347A THR* 3.0 4.5 + - - -
348A ASN* 2.6 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LYS* 3.0 24.3 + - + +
342A ARG* 3.6 8.1 - - - +
344A LYS* 1.3 78.4 - - - +
346A PHE* 1.3 63.3 + - - +
348A ASN* 3.4 7.8 + - + +
349A GLY* 3.1 20.2 + - - -
420A ASP* 5.0 14.5 + - + -
423A VAL* 4.9 9.5 - - + +
424A ASP* 2.8 38.4 + - - -
427A LEU* 4.4 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MET* 3.9 15.5 - - + -
342A ARG 2.7 21.1 + - - +
343A HIS 3.6 3.4 - - - +
345A HIS* 1.3 76.2 + - - +
347A THR* 1.3 62.7 + - - +
349A GLY 3.4 1.2 + - - -
350A LEU* 3.2 54.2 + - + +
366A CYS* 3.8 17.3 - - - -
368A MET* 5.3 0.2 - - - -
413A VAL* 3.9 24.2 - - + -
415A PHE* 3.5 34.1 - + + -
423A VAL* 3.6 22.7 - - + -
427A LEU* 3.4 33.6 - - + +
430A ILE* 4.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A HIS* 2.9 41.7 + - + -
344A LYS* 3.7 3.6 - - - -
346A PHE* 1.3 79.3 - - - +
348A ASN* 1.3 69.5 + - - +
350A LEU* 3.1 9.2 + - + +
351A GLU* 3.0 33.9 + - + +
355A ILE 4.7 1.3 - - - +
356A LYS* 5.9 0.9 - - - -
357A CYS* 4.7 25.6 - - + +
366A CYS* 5.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LYS* 2.6 39.1 + - - +
345A HIS* 3.9 7.6 - - + +
347A THR* 1.3 75.1 - - - +
349A GLY* 1.3 59.3 + - - +
351A GLU* 3.8 17.0 - - - +
352A VAL* 2.9 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A HIS* 3.1 14.7 + - - -
346A PHE 3.8 3.4 - - - -
347A THR 3.1 0.8 - - - -
348A ASN* 1.3 76.9 - - - +
350A LEU* 1.3 57.1 + - - +
351A GLU 3.1 0.2 - - - -
352A VAL* 3.0 31.0 + - - +
353A VAL* 3.6 8.1 + - - +
427A LEU* 4.1 20.2 - - - -
431A ARG* 5.5 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PHE* 3.2 42.9 + - + +
347A THR* 3.1 8.6 + - - +
349A GLY* 1.3 75.1 - - - +
351A GLU* 1.3 52.5 + - - +
353A VAL* 3.1 11.2 - - - +
355A ILE* 2.5 57.2 + - + +
357A CYS* 3.6 25.4 - - - -
368A MET* 4.0 13.5 - - - -
427A LEU* 4.0 6.7 - - + +
430A ILE* 3.8 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A THR* 3.0 25.9 + - - +
348A ASN* 3.8 18.4 - - - +
349A GLY 3.1 0.2 - - - -
350A LEU* 1.3 73.6 - - - +
352A VAL* 1.3 68.1 + - - +
353A VAL 2.9 2.0 - - - -
354A GLY* 2.8 15.6 + - - +
355A ILE 3.5 4.9 - - - +
356A LYS* 3.9 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN* 2.9 24.7 + - + +
349A GLY* 3.0 18.1 + - - +
351A GLU* 1.3 77.2 - - - +
353A VAL* 1.3 62.4 + - + +
354A GLY 3.8 0.2 + - - -
431A ARG* 5.1 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLY 4.1 5.8 - - - +
350A LEU* 3.1 24.5 - - - +
351A GLU 2.9 0.6 - - - -
352A VAL* 1.3 85.0 - - + +
354A GLY* 1.3 53.9 + - - +
355A ILE* 3.3 21.7 + - + +
430A ILE* 4.9 5.6 - - + -
431A ARG* 3.2 43.5 - - + +
434A VAL* 3.8 28.3 - - + +
----------------------------------------------------------
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