Contacts of the helix formed by residues 378 - 392 (chain B) 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 THR 378 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 4.2 0.5 - - - +
376B GLU* 3.6 17.7 + - + +
377B SER* 1.3 78.3 - - - +
379B PHE* 1.3 59.1 + - - +
380B ASP* 3.0 16.0 - - + +
381B SER* 3.1 18.0 + - - -
382B GLU 2.9 21.3 + - - -
408B PRO* 3.5 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B THR* 1.3 74.2 - - - +
380B ASP* 1.3 58.5 + - - +
382B GLU* 3.2 30.5 - - - +
383B MET* 2.8 33.6 + - + +
401B SER* 3.5 27.8 - - - -
405B CYS 2.7 30.3 - - - -
406B GLN* 3.6 22.9 - - - -
407B GLU 3.6 2.0 - - - -
408B PRO* 3.5 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B THR* 3.0 11.4 - - + -
379B PHE* 1.3 76.4 - - - +
381B SER* 1.3 66.4 + - - +
382B GLU 3.0 1.6 - - - -
383B MET* 3.3 8.1 + - - +
384B SER* 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 3.3 22.0 - - - +
375B ARG* 3.4 27.4 + - - +
376B GLU* 3.6 11.9 + - - -
378B THR* 3.1 30.4 + - - -
380B ASP* 1.3 80.6 + - - +
382B GLU* 1.3 62.3 + - - +
384B SER* 3.4 6.8 + - - -
385B LEU* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 3.6 10.5 - - + +
378B THR 2.9 10.3 + - - +
379B PHE* 3.2 27.7 - - - +
380B ASP 3.0 0.2 - - - -
381B SER* 1.3 74.2 - - - +
383B MET* 1.3 61.5 + - - +
385B LEU* 3.2 6.1 + - - +
386B TRP* 3.0 24.9 + - - +
399B PRO* 3.6 5.8 - - + +
400B GLY* 3.5 13.2 + - - -
401B SER* 3.0 36.5 + - - -
407B GLU 4.4 1.0 - - - +
408B PRO* 3.1 29.5 - - + +
409B GLY 3.1 9.8 + - - +
410B TRP 4.6 1.6 - - - -
411B PHE* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PRO* 4.9 9.0 - - + +
27B TYR* 3.5 41.3 - - + +
379B PHE* 2.8 24.5 + - + +
380B ASP* 3.3 9.6 + - - +
382B GLU* 1.3 73.7 - - - +
384B SER* 1.3 57.1 + - - +
386B TRP* 3.2 31.6 - - + +
387B ARG* 2.9 35.2 + - + +
399B PRO* 4.3 9.6 - - - -
401B SER* 3.8 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ASP* 3.1 12.9 + - - -
381B SER* 3.5 11.7 - - - -
382B GLU 3.1 0.2 - - - -
383B MET* 1.3 74.4 - - - +
385B LEU* 1.3 67.2 + - - +
386B TRP 3.0 1.3 - - - -
387B ARG* 3.1 17.3 + - - +
388B VAL* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 3.8 28.0 - - + +
373B LEU* 4.2 16.8 - - + +
374B LEU* 4.2 13.2 - - + -
375B ARG* 5.8 3.6 - - - +
381B SER 3.2 9.5 + - - +
382B GLU 3.2 8.2 + - - +
384B SER* 1.3 78.1 - - - +
386B TRP* 1.3 63.7 + - - +
388B VAL* 3.0 18.5 + - + +
389B ILE* 3.0 21.3 + - + +
411B PHE* 3.5 29.6 - - + -
433B PHE* 3.5 35.0 - - + -
437B GLU* 4.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PRO 4.1 5.4 - - - -
27B TYR* 3.5 23.1 - + - -
29B ASP* 3.5 22.0 - - + -
30B GLY* 3.5 30.5 - - - -
382B GLU 3.0 12.7 + - - +
383B MET* 3.2 42.4 - - + +
385B LEU* 1.3 75.1 - - - +
387B ARG* 1.3 71.8 + - - +
388B VAL 3.0 0.9 + - - -
389B ILE* 3.1 4.2 + - + +
390B ILE* 3.0 41.9 + - + +
396B ASN* 4.7 0.7 - - - -
397B VAL* 3.0 33.7 + - + +
399B PRO* 3.4 25.7 - - + +
411B PHE* 3.5 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 2.7 29.7 + - - -
383B MET* 2.9 22.8 + - + +
384B SER* 3.1 11.6 + - - +
386B TRP* 1.3 77.3 - - + +
388B VAL* 1.3 58.1 + - + +
390B ILE* 3.4 13.9 - - - +
391B ASN* 2.6 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B SER* 3.1 15.2 + - - +
385B LEU* 3.0 12.0 + - + +
386B TRP 3.0 0.8 - - - -
387B ARG* 1.3 77.4 - - + +
389B ILE* 1.3 60.2 + - - +
390B ILE 3.2 0.2 - - - -
392B ASP* 2.7 53.2 + - + +
393B VAL 2.9 7.3 + - - -
433B PHE* 3.4 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B MET* 5.1 2.7 - - + -
370B LEU* 3.7 30.7 - - + -
385B LEU* 3.0 22.4 + - + +
386B TRP 3.1 5.8 + - - +
388B VAL* 1.3 76.5 - - - +
390B ILE* 1.3 52.9 + - - +
393B VAL* 3.2 15.5 - - + +
394B LYS 2.7 26.3 + - - -
395B LEU* 2.8 39.2 + - + +
397B VAL* 4.0 19.7 - - + -
411B PHE* 4.4 15.9 - - + -
433B PHE* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 3.9 9.6 - - + +
30B GLY* 3.8 31.9 - - - +
33B ALA* 4.3 9.6 - - + +
48B VAL* 4.1 12.2 - - + +
386B TRP* 3.0 56.3 + - + +
387B ARG* 3.4 14.4 - - - +
389B ILE* 1.3 80.8 - - + +
391B ASN* 1.3 72.4 + - - +
394B LYS* 3.6 13.7 - - - +
395B LEU 3.1 21.1 - - - +
396B ASN* 4.1 10.8 - - - -
397B VAL 4.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 5.0 6.8 - - - +
387B ARG* 2.6 63.1 + - - +
390B ILE* 1.3 87.4 - - - +
392B ASP* 1.3 70.0 + - - +
394B LYS* 3.3 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B VAL* 2.7 46.8 + - + +
391B ASN* 1.3 85.4 - - - +
393B VAL* 1.3 62.3 + - + +
394B LYS* 3.2 6.5 - - - +
433B PHE* 6.3 0.2 - - + -
----------------------------------------------------------
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