Contacts of the helix formed by residues 388 - 410 (chain A) in PDB entry 2I2X
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 388 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASP* 2.9 12.4 + - + +
387A ASP* 1.3 78.2 - - + +
389A ILE* 1.3 57.4 + - - +
390A TYR* 3.3 9.4 + - - +
391A LEU* 2.8 50.1 + - + +
392A ARG* 2.9 37.1 + - - +
434A ASP 5.0 3.6 + - - -
436A MET* 4.1 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.9 37.5 - - - +
189A GLY 4.0 8.5 - - - +
190A CYS* 4.3 6.5 - - - +
193A SER* 4.0 29.0 + - - +
194A ILE* 4.0 22.9 - - + +
252A PRO* 5.3 0.5 - - - +
387A ASP 3.9 2.3 + - - +
388A ASN* 1.3 70.1 + - - +
390A TYR* 1.3 68.1 + - - +
392A ARG* 3.7 23.9 + - - +
393A ALA* 3.4 21.0 + - - +
436A MET* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.6 21.8 - - + -
190A CYS* 4.0 17.7 - - - -
388A ASN* 3.3 1.9 + - - +
389A ILE* 1.3 79.4 - - - +
391A LEU* 1.3 70.5 + - - +
393A ALA* 3.1 5.3 + - - +
394A LYS* 2.8 49.5 + - + +
432A LEU* 3.4 12.5 - - - +
433A PRO* 2.6 30.5 + - - +
434A ASP 3.6 15.9 - - - -
435A ASP 4.2 1.3 - - - -
436A MET* 3.5 44.6 - - + -
439A PHE* 3.2 44.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASP* 3.7 32.3 - - + +
388A ASN* 2.8 36.7 + - + +
390A TYR* 1.3 81.8 - - + +
392A ARG* 1.3 56.6 + - - +
394A LYS* 3.3 15.6 + - - +
395A ASN* 2.9 46.4 + - - +
434A ASP* 3.7 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.1 1.6 - - - +
6A TYR 4.5 0.6 + - - +
193A SER* 4.9 1.0 + - - -
252A PRO* 3.2 38.1 + - + +
255A LEU* 3.8 13.9 - - - +
256A VAL* 3.5 11.7 - - - +
259A GLU* 2.6 44.4 + - - -
382A ILE* 3.4 33.1 - - + +
385A ASP 3.7 6.6 + - - +
386A GLY* 3.0 30.2 + - - -
388A ASN 2.9 24.1 + - - +
389A ILE* 3.7 24.4 + - - +
391A LEU* 1.3 76.9 - - - +
393A ALA* 1.3 64.5 + - - +
395A ASN* 3.3 12.9 + - - +
396A ALA* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.7 18.4 - - + -
189A GLY* 4.0 15.5 - - - -
249A ILE* 4.2 9.5 - - + +
252A PRO* 3.7 21.5 - - + -
389A ILE 3.4 17.0 - - - +
390A TYR 3.1 4.4 + - - +
392A ARG* 1.3 79.9 - - - +
394A LYS* 1.3 66.6 + - - +
396A ALA* 3.2 4.2 + - - +
397A ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.9 21.2 - - + +
390A TYR* 2.8 50.1 + - + +
391A LEU* 3.3 14.0 + - - +
393A ALA* 1.3 76.5 - - - +
395A ASN* 1.3 65.5 + - - +
397A ALA* 3.2 5.8 + - - +
398A ILE* 3.0 44.6 + - + +
429A LEU* 3.9 20.3 + - + +
432A LEU* 4.0 12.4 + - + -
433A PRO 3.6 7.9 - - - -
434A ASP* 2.7 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A SER* 3.2 34.1 + - - +
384A LYS* 3.8 16.2 + - - +
385A ASP* 2.8 34.4 + - - +
391A LEU* 2.9 37.5 + - - +
392A ARG* 3.5 5.6 - - - +
393A ALA 3.2 0.2 - - - -
394A LYS* 1.3 76.8 + - - +
396A ALA* 1.3 51.5 + - - +
398A ILE* 3.2 7.4 + - - +
399A GLU* 2.7 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA* 3.6 26.5 - - - +
252A PRO* 4.4 3.4 - - + -
378A VAL* 3.9 11.3 - - + +
381A SER* 3.5 10.5 + - - -
382A ILE* 3.8 18.6 - - + -
392A ARG 3.2 12.8 + - - +
393A ALA 3.6 8.1 - - - +
394A LYS 3.2 0.2 - - - -
395A ASN* 1.3 75.8 - - - +
397A ALA* 1.3 54.8 + - - +
399A GLU* 3.3 1.6 + - - +
400A CYS* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 4.2 6.5 - - + +
248A ALA* 4.3 6.7 - - - +
249A ILE* 3.8 20.4 - - + +
393A ALA 3.1 12.6 + - - +
394A LYS* 3.5 8.7 - - - +
396A ALA* 1.3 77.3 - - - +
398A ILE* 1.3 59.4 + - - +
400A CYS* 3.4 8.1 - - - +
401A CYS* 3.2 27.2 + - - -
429A LEU* 3.8 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 3.0 43.7 + - + +
395A ASN* 3.9 5.8 - - - +
397A ALA* 1.3 73.3 - - - +
399A GLU* 1.3 61.8 + - - +
401A CYS* 3.2 9.5 + - - +
402A ASN* 3.0 40.2 + - - +
426A LYS* 5.2 4.7 - - + +
429A LEU* 3.8 31.6 - - + +
430A GLU* 4.1 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ARG* 2.7 44.9 + - + +
378A VAL* 4.4 3.8 - - + -
381A SER* 3.6 27.9 - - - +
384A LYS* 4.3 10.0 + - - -
395A ASN 2.7 21.5 + - - +
396A ALA* 3.7 3.1 - - - +
398A ILE* 1.3 70.5 - - - +
400A CYS* 1.3 59.7 + - - +
402A ASN* 3.2 14.1 + - - +
403A ILE* 2.8 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 3.8 50.9 - - - -
245A ILE* 4.1 8.7 - - - -
248A ALA* 3.5 15.5 - - + -
369A MET* 4.0 9.6 - - + -
378A VAL* 4.6 3.1 - - + +
396A ALA 2.8 18.5 + - - +
397A ALA* 3.4 6.7 - - - +
398A ILE 3.2 0.2 - - - -
399A GLU* 1.3 75.8 - - - +
401A CYS* 1.3 57.3 + - - +
403A ILE* 3.1 12.1 + - - +
404A ILE* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 3.9 17.9 - - - -
397A ALA 3.2 17.2 + - - -
398A ILE* 3.2 8.7 + - - +
400A CYS* 1.3 79.0 - - - +
402A ASN* 1.3 57.0 + - - +
404A ILE* 3.5 1.6 + - - +
405A GLU* 3.0 35.4 + - - +
422A LEU* 3.9 28.3 - - + +
426A LYS* 3.9 44.4 - - + -
429A LEU* 4.0 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ARG* 3.7 16.7 - - - +
398A ILE* 3.0 30.0 + - - +
399A GLU* 3.2 22.1 + - - +
401A CYS* 1.3 74.5 - - - +
403A ILE* 1.3 58.3 + - - +
405A GLU* 3.3 9.8 + - - +
406A GLU* 2.9 37.2 + - - +
426A LYS* 3.6 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A TYR* 3.5 27.6 - - + -
369A MET* 4.5 9.0 - - + -
374A ASN* 3.6 29.6 - - + +
377A ARG* 3.5 44.6 - - + +
378A VAL* 3.6 29.8 - - + -
399A GLU* 2.8 20.1 + - + +
400A CYS* 3.1 7.8 + - - +
402A ASN* 1.3 75.7 - - - +
404A ILE* 1.3 57.7 + - + +
406A GLU* 3.2 5.1 + - - +
407A GLY 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A THR* 4.3 3.6 - - + -
244A VAL* 4.1 17.7 - - + -
365A PRO* 3.5 39.0 - - + +
368A TYR* 4.2 12.8 - - + -
369A MET* 4.1 17.0 - - + -
400A CYS* 2.9 23.1 + - - +
403A ILE* 1.3 74.6 - - + +
405A GLU* 1.3 51.6 + - - +
407A GLY* 3.2 1.7 + - - -
408A ALA* 2.6 32.9 + - - +
412A LEU* 4.0 11.2 - - + +
414A LEU* 3.9 19.3 - - + -
422A LEU* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A CYS 3.0 20.2 + - - +
402A ASN* 3.5 10.8 - - - +
404A ILE* 1.3 74.0 - - - +
406A GLU* 1.3 66.5 + - + +
408A ALA* 3.2 7.5 + - + +
409A ALA* 3.0 23.4 + - - +
422A LEU* 4.0 18.3 - - + +
423A ALA* 5.1 6.4 - - - +
426A LYS* 3.1 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A TYR* 4.6 3.1 - - - +
377A ARG* 2.7 47.1 + - - -
402A ASN* 2.9 20.1 + - - +
403A ILE* 3.7 4.0 - - - +
405A GLU* 1.3 73.0 - - + +
407A GLY* 1.3 65.9 + - - +
409A ALA* 3.1 8.5 + - - +
410A GLY* 3.1 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TYR* 6.1 0.2 - - - -
368A TYR* 3.4 35.3 + - - -
403A ILE 2.9 10.3 + - - -
404A ILE 3.4 4.3 - - - -
406A GLU* 1.3 75.5 - - - +
408A ALA* 1.3 57.2 + - - +
410A GLY* 2.8 19.9 + - - -
411A LYS 3.4 0.5 + - - -
412A LEU* 3.3 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ILE 2.6 19.3 + - - +
405A GLU* 3.2 8.5 + - + +
407A GLY* 1.3 72.3 - - - +
409A ALA* 1.3 59.5 + - - +
410A GLY 3.5 4.0 + - - +
412A LEU* 3.4 20.5 - - - +
414A LEU* 3.9 29.4 - - + -
419A THR* 5.7 2.7 - - + +
422A LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLU 3.0 12.4 + - - +
406A GLU* 3.1 10.5 + - - +
408A ALA* 1.3 75.4 - - - +
410A GLY* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU 3.1 8.3 + - - -
407A GLY* 2.8 10.6 + - - -
408A ALA 3.7 5.9 - - - +
409A ALA* 1.3 82.5 - - - +
411A LYS* 1.3 65.7 + - - +
412A LEU 4.5 0.3 - - - +
----------------------------------------------------------
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