Contacts of the helix formed by residues 34 - 44 (chain 2) in PDB entry 1JJ2
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 LYS 34 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24330 A 3.6 27.8 - - - +
24340 A 3.7 29.9 + - - +
24510 G 3.4 35.8 + - - +
24520 G 4.0 15.7 + - - +
302 GLN* 6.0 2.0 - - - +
312 THR* 3.5 21.1 - - - +
322 GLY 4.9 1.3 - - - +
332 MET* 1.3 84.0 - - - +
352 TRP* 1.3 67.0 + - - +
362 ILE* 3.2 4.7 - - + +
372 ASP* 2.9 26.0 + - - +
382 ARG* 3.2 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 35 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2170 C 5.0 1.2 + - - -
2180 C 3.4 22.1 + - - -
2190 G 4.8 0.4 - - - -
2200 C 3.6 23.8 - + - -
3950 A 3.9 13.4 + - - -
3960 U 3.7 9.4 - - - -
24310 C 5.8 0.4 - - - -
24320 C 4.4 8.3 - - - -
24510 G 3.8 2.4 + - - -
24520 G 3.1 33.7 + - - +
342 LYS* 1.3 71.2 - - - +
362 ILE* 1.3 89.1 + - + +
382 ARG* 3.0 33.4 + - - +
392 GLN* 2.9 55.2 + - + -
422 ARG* 3.8 11.3 - - - +
512 LYS* 5.9 0.2 - - - -
48K LYS* 3.3 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24320 C 3.5 46.4 - - - +
24330 A 4.0 14.3 + - - +
24520 G 4.9 0.2 + - - -
302 GLN* 5.9 0.4 - - - +
342 LYS* 4.3 2.6 - - + +
352 TRP* 1.3 97.8 - - + +
372 ASP* 1.3 78.3 + - - +
392 GLN* 3.2 25.6 + - - +
402 ARG* 3.0 23.0 + - - +
512 LYS* 3.8 21.8 - - - +
522 PHE* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24330 A 6.0 0.2 - - - +
302 GLN* 4.3 14.2 + - - -
322 GLY* 3.2 37.7 + - - +
332 MET 3.2 1.0 + - - -
342 LYS* 2.9 37.0 + - - +
362 ILE* 1.3 87.4 - - - +
382 ARG* 1.3 61.8 + - + +
402 ARG* 3.4 7.6 + - - +
412 GLU* 3.3 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3960 U 2.4 98.4 + - - +
24510 G 2.6 39.8 + - - +
24520 G 5.1 0.2 - - - -
322 GLY 5.9 0.2 - - - +
332 MET* 4.0 14.4 + - - +
342 LYS 3.5 8.7 - - - +
352 TRP* 3.0 32.4 + - - +
372 ASP* 1.3 74.4 - - + +
392 GLN* 1.3 59.6 + - - +
412 GLU* 3.5 11.8 + - - +
422 ARG* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2180 C 2.9 35.0 + - - +
2190 G 3.1 27.0 + - - -
2200 C 4.2 0.2 - - - -
352 TRP* 2.9 44.1 + - + +
362 ILE* 3.2 20.9 + - - +
382 ARG* 1.3 74.3 - - - +
402 ARG* 1.3 60.1 + - - +
422 ARG* 3.4 14.8 - - - +
432 ASN* 2.9 42.4 + - - +
512 LYS* 4.5 2.1 + - - -
522 PHE* 3.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 ILE 3.0 13.6 + - - +
372 ASP* 3.6 11.9 - - - +
382 ARG 3.3 0.2 - - - -
392 GLN* 1.3 77.7 - - - +
412 GLU* 1.3 64.9 + - + +
432 ASN 4.0 0.3 - - - -
442 SER* 2.8 36.0 + - - +
522 PHE* 3.6 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19220 A 5.5 0.2 - - - +
19230 G 4.5 14.4 + - - +
322 GLY 4.9 7.4 - - - +
372 ASP* 3.3 19.5 + - - +
382 ARG* 3.8 10.0 - - - +
402 ARG* 1.3 82.9 - - + +
422 ARG* 1.3 64.8 + - - +
442 SER* 3.7 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2170 C 5.7 0.4 + - - -
2180 C 4.7 6.1 + - - -
3900 G 5.7 0.9 + - - -
3910 U 5.4 3.6 - - - +
3950 A 3.3 48.7 + - - +
3960 U 3.0 45.4 + - - -
83690 NA 3.7 14.6 - - - -
352 TRP* 3.8 8.9 - - - +
382 ARG* 2.9 28.1 + - - +
392 GLN* 3.4 28.5 - - - +
412 GLU* 1.3 79.3 - - - +
432 ASN* 1.3 72.3 + - - +
442 SER 3.6 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 43 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700 U 4.9 11.7 + - - +
2180 C 3.2 39.6 + - - -
2190 G 5.0 1.6 + - - -
392 GLN* 2.9 32.3 + - - +
422 ARG* 1.3 86.9 + - - +
442 SER* 1.3 63.2 + - - +
452 GLY 3.5 2.4 + - - -
492 ASP* 4.5 6.6 - - - +
522 PHE* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3890 G 4.5 12.3 + - - +
3900 G 4.5 3.0 + - - -
402 ARG* 2.8 28.1 + - - +
412 GLU* 3.7 10.7 + - - +
422 ARG 3.4 3.8 - - - +
432 ASN* 1.3 77.3 - - - +
452 GLY* 1.3 58.0 + - - +
492 ASP* 3.4 30.7 + - - +
522 PHE* 4.1 10.6 - - - +
----------------------------------------------------------
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