Contacts of the helix formed by residues 322 - 341 (chain A) in PDB entry 1AX4
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 GLU 322 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TYR* 4.7 14.4 - - + -
235A LYS* 3.0 45.7 + - - +
245A THR* 5.1 1.4 - - - -
246A ILE* 3.8 25.8 + - + +
320A THR 3.3 4.2 + - - -
321A GLU* 1.4 71.5 - - - +
323A GLU* 1.3 66.0 + - + +
325A LEU* 3.2 4.0 + - - +
326A HIS* 2.9 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 3.7 21.3 - - + +
321A GLU* 4.0 20.3 - - - +
322A GLU* 1.3 87.2 + - + +
324A TYR* 1.3 60.8 + - - +
326A HIS* 3.6 7.2 + - - +
327A TYR* 3.2 22.3 + - - +
16C LYS* 4.8 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 3.9 14.2 - - + +
9A PHE* 5.0 3.1 - + + -
229A GLU* 5.0 0.7 + - - -
267A ASP 5.3 1.1 - - - -
269A LEU* 4.0 8.3 - - + -
318A GLU 3.9 16.6 - - - +
319A GLY* 4.2 12.8 - - - -
321A GLU* 3.1 20.3 + - + +
323A GLU* 1.3 81.1 + - - +
325A LEU* 1.3 85.1 + - + +
327A TYR* 3.2 10.5 + + - +
328A ARG* 2.8 49.5 + - + +
419A ARG* 3.2 36.5 + - + +
420A ARG* 3.7 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A CYS* 3.9 33.4 - - + +
229A GLU* 4.2 15.0 - - + +
232A TYR* 3.9 13.5 - - + -
246A ILE* 4.0 22.4 - - + -
267A ASP* 5.6 0.9 - - - -
319A GLY 3.6 25.4 - - - +
320A THR 3.9 12.3 - - - +
321A GLU 2.9 18.2 + - - +
322A GLU 3.6 4.0 - - - +
324A TYR* 1.3 92.6 - - + +
326A HIS* 1.3 58.0 + - - +
328A ARG* 4.2 3.6 - - + -
329A ILE* 2.9 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 4.8 9.7 + - - -
5A ILE* 3.6 35.5 - - + +
232A TYR* 2.8 37.9 + - + -
322A GLU* 2.9 20.7 + - + +
323A GLU* 3.8 8.1 - - - +
325A LEU* 1.3 75.5 - - - +
327A TYR* 1.3 57.4 + - - +
329A ILE* 4.5 0.2 - - - +
330A GLY* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.7 37.0 - - + +
6A VAL 3.8 2.2 - - - +
7A GLU* 3.1 47.4 + - + +
8A PRO* 3.7 19.1 - - + -
9A PHE* 3.7 24.0 - + - -
323A GLU 3.2 11.0 + - - +
324A TYR* 3.2 13.6 + + - +
326A HIS* 1.3 77.2 - - - +
328A ARG* 1.3 80.8 + - + +
330A GLY 3.7 0.5 - - - -
331A GLN* 2.9 44.6 + - + +
420A ARG* 4.8 12.6 - - + -
422A TYR 3.6 18.0 + - - -
424A ASN* 4.8 1.8 - - - -
11C ILE* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP* 3.9 0.2 + - - -
229A GLU* 2.7 28.9 + - - -
324A TYR* 2.8 47.8 + - + +
325A LEU* 3.7 6.5 - - + +
327A TYR* 1.3 86.6 - - + +
329A ILE* 1.3 66.5 + - - +
331A GLN* 3.2 17.7 + - - +
332A VAL* 3.3 16.7 + - - +
352A GLY 3.2 16.6 + - - -
353A HIS* 3.3 19.1 - - - +
417A ILE* 2.8 43.2 + - - +
418A ALA 3.7 11.5 + - - -
419A ARG* 3.3 27.2 - - + +
420A ARG 5.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 4.2 20.2 - - + +
232A TYR* 3.2 50.9 - - + +
233A PHE* 3.8 28.9 - - + -
325A LEU* 2.9 22.1 + - + +
326A HIS 4.5 0.4 - - - +
328A ARG* 1.3 80.8 - - - +
330A GLY* 1.3 64.8 + - - +
332A VAL* 3.2 4.8 + - - +
333A LYS* 3.1 24.6 + - + +
350A THR* 5.2 0.6 + - - +
351A GLY 4.8 4.1 - - - +
352A GLY* 4.0 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS 4.4 4.7 - - - +
5A ILE* 3.8 23.0 + - - +
326A HIS 2.9 21.0 + - - -
327A TYR 3.7 0.7 - - - -
329A ILE* 1.3 77.1 - - - +
331A GLN* 1.3 56.9 + - - +
333A LYS* 3.6 11.1 - - - +
334A TYR* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 5.4 1.3 - - - +
327A TYR* 2.9 37.4 + - + +
328A ARG* 3.2 9.3 + - - +
330A GLY* 1.3 78.8 - - - +
332A VAL* 1.3 62.4 + - - +
334A TYR* 3.4 5.1 + - - +
335A LEU* 3.0 21.8 + - - +
417A ILE* 3.7 20.2 - - + +
418A ALA 4.9 2.3 - - - +
420A ARG 5.7 2.4 + - - -
421A VAL 5.9 0.3 + - - -
422A TYR* 3.0 28.1 + - - +
423A THR 3.4 15.2 + - - -
424A ASN* 3.3 28.7 + - - +
427A MET* 3.5 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 3.6 20.4 - - - +
329A ILE 3.2 7.7 + - - +
331A GLN* 1.3 77.9 - - - +
333A LYS* 1.3 53.1 + - - +
335A LEU* 3.3 5.5 + - - +
336A GLY* 2.8 28.4 + - - -
350A THR* 4.1 5.5 - - - +
351A GLY 3.6 21.3 - - - +
352A GLY 3.7 17.0 - - - +
353A HIS 4.1 11.4 - - - -
354A ALA* 3.7 27.4 - - - +
355A VAL* 3.4 10.7 - - + +
417A ILE* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 6.2 5.4 - - - +
329A ILE* 3.1 19.8 + - + +
330A GLY* 3.6 10.1 - - - +
332A VAL* 1.3 73.7 - - - +
334A TYR* 1.4 55.0 + - - +
336A GLY* 3.0 2.2 + - - +
337A ASP* 2.6 72.6 + - - +
348A TYR* 5.5 5.7 + - - -
350A THR* 3.4 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 3.7 27.4 - - + -
3A LYS 3.6 27.1 - - - +
4A ARG* 3.4 32.4 + - + -
5A ILE 5.8 0.4 - - - +
330A GLY 2.9 15.2 + - - +
331A GLN* 3.4 11.9 - - - +
333A LYS* 1.4 75.0 - - - +
335A LEU* 1.4 64.4 + - - +
337A ASP* 3.8 4.6 - - - +
338A ARG* 3.0 46.0 + - + +
424A ASN* 3.8 22.9 - - - +
427A MET* 4.0 16.4 - - + -
428A ASP* 2.3 39.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLN 3.0 11.3 + - - +
332A VAL* 3.5 7.4 - - - +
334A TYR* 1.4 83.6 - - - +
336A GLY* 1.3 64.8 + - - +
338A ARG* 3.4 4.0 + - - +
339A LEU* 3.2 31.2 + - + +
355A VAL* 4.0 16.8 - - + -
415A LEU* 4.1 17.0 - - + -
417A ILE* 4.0 27.6 - - + -
427A MET* 3.7 37.0 - - + +
430A ILE* 4.1 13.5 - - + -
431A ALA* 4.1 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL 2.8 19.2 + - - -
333A LYS 3.5 2.2 - - - -
335A LEU* 1.3 73.9 - - - +
337A ASP* 1.3 57.6 + - - +
339A LEU* 3.1 4.6 + - - +
340A ARG* 2.9 30.1 + - - +
346A ILE* 3.7 12.0 - - - +
350A THR* 3.9 18.4 - - - -
355A VAL* 3.7 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 3.6 28.6 - - + -
3A LYS 4.9 2.1 + - - -
333A LYS* 2.6 59.1 + - - +
334A TYR* 3.9 1.3 - - - +
336A GLY* 1.3 67.5 - - - +
338A ARG* 1.3 66.1 + - - +
340A ARG* 4.4 8.2 + - - +
341A GLU* 2.9 39.9 + - - +
348A TYR* 4.5 16.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
2A ALA* 4.1 9.2 - - + +
334A TYR* 3.0 58.6 + - + +
335A LEU* 3.7 5.6 - - - +
336A GLY 3.3 0.2 - - - -
337A ASP* 1.3 75.3 - - - +
339A LEU* 1.3 63.9 + - - +
341A GLU* 4.1 6.5 - - - +
342A ALA* 3.3 21.7 + - - +
427A MET 6.2 0.2 - - - -
428A ASP* 2.9 37.8 + - - +
431A ALA* 3.8 16.9 - - + +
432A ASP* 3.2 28.3 + - - -
435A ILE* 3.5 23.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
335A LEU* 3.2 16.4 + - + +
336A GLY 3.1 7.1 + - - +
338A ARG* 1.3 77.5 - - - +
340A ARG* 1.3 57.4 + - - +
342A ALA* 3.0 15.7 + - - +
343A GLY 3.3 0.2 + - - -
344A ILE* 2.9 38.8 + - + +
346A ILE* 4.1 4.9 - - + -
355A VAL* 4.0 12.6 - - + -
357A VAL* 3.8 19.1 - - + -
415A LEU* 3.8 28.7 - - + -
431A ALA* 3.9 33.0 - - + +
434A LEU* 4.0 20.0 - - + -
435A ILE* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLU 5.0 4.8 + - - -
336A GLY 2.9 17.4 + - - +
337A ASP* 4.0 8.5 + - - +
339A LEU* 1.3 71.8 - - - +
341A GLU* 1.3 56.3 + - + +
343A GLY* 2.7 25.8 + - - -
344A ILE 3.6 12.3 + - - +
345A PRO* 6.2 0.4 - - + -
346A ILE* 4.2 13.9 - - + +
348A TYR* 3.5 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 2.6 43.4 + - - +
337A ASP* 2.9 32.8 + - + +
338A ARG* 4.2 6.1 - - - +
340A ARG* 1.3 70.3 - - + +
342A ALA* 1.3 58.5 + - - +
343A GLY 3.5 0.9 + - - -
----------------------------------------------------------
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