Contacts of the helix formed by residues 19 - 34 (chain D) in PDB entry 2AAZ
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 19 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ASP 3.1 8.6 + - - +
18D HIS* 1.3 74.1 + - - +
20D GLU* 1.3 62.7 + - - +
21D TYR 3.1 0.2 - - - -
22D GLN* 3.0 40.2 + - - +
23D TYR 4.3 0.2 + - - -
55D ARG 3.9 8.7 - - - +
56D PHE* 3.4 28.9 - - + +
57D SER* 2.9 45.0 + - - +
62D THR* 5.7 0.5 - - - +
277D PHE* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D HIS* 2.9 21.3 + - + +
19D GLU* 1.3 76.8 - - - +
21D TYR* 1.3 62.3 + - - +
22D GLN 3.0 0.2 - - - -
23D TYR* 3.0 18.3 + - + +
24D LEU* 3.1 15.3 + - + +
56D PHE* 4.9 2.5 - - - -
66D LEU* 3.6 24.5 - - + +
67D THR* 2.9 36.0 + - - -
68D THR* 2.6 43.8 + - - +
274D PRO* 3.8 11.7 - - + +
277D PHE* 3.7 14.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ARG* 3.5 66.2 - - + +
14D SER 4.8 0.7 + - - -
15D ASN 3.2 27.6 + - - -
16D PRO 4.0 13.2 - - - +
18D HIS* 3.0 29.4 + - + +
20D GLU* 1.3 77.8 - - - +
22D GLN* 1.3 54.8 + - - +
24D LEU* 4.0 18.2 - - + -
25D ASP* 2.7 41.8 + - - +
272D ARG 5.1 2.0 - - - -
273D GLU* 3.8 15.2 - - - +
274D PRO* 3.4 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D HIS 4.5 0.4 + - - +
19D GLU* 3.0 27.3 + - - +
20D GLU 3.0 0.4 - - - -
21D TYR* 1.3 78.9 - - - +
23D TYR* 1.3 61.9 + - - +
25D ASP* 4.0 3.8 - - - +
26D LEU* 3.1 18.0 + - - +
53D SER 4.2 4.8 + - - -
54D PHE* 3.3 37.6 - - + +
55D ARG* 2.9 50.1 + - - +
56D PHE* 3.6 10.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU* 3.0 11.9 + - + +
22D GLN* 1.3 81.3 - - - +
24D LEU* 1.3 75.1 + - + +
26D LEU* 3.4 3.6 + - - +
27D ILE* 3.2 49.2 + - + +
54D PHE* 3.7 17.7 - + + -
56D PHE* 5.4 2.5 - - + -
66D LEU* 3.7 40.4 - - + -
68D THR* 5.0 0.4 - - - -
69D LYS* 5.0 0.2 + - - -
220D LEU* 2.6 36.1 + - + +
221D GLY* 3.7 6.9 + - - -
224D VAL* 3.9 26.5 - - + -
225D PRO* 3.5 10.3 - - + +
228D ILE* 4.6 3.6 - - + -
266D LEU* 4.4 3.5 - - - +
269D GLN* 3.8 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU* 3.1 13.6 + - + +
21D TYR* 4.0 20.6 - - + +
23D TYR* 1.3 91.5 - - + +
25D ASP* 1.3 65.3 + - - +
27D ILE* 3.3 3.1 + - + -
28D ARG* 3.0 28.4 + - - +
68D THR* 3.8 39.5 - - + +
269D GLN* 4.3 14.6 - - + +
270D LEU* 3.4 35.3 - - + +
272D ARG 4.0 9.6 - - - +
274D PRO* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ARG* 2.7 43.6 + - - -
21D TYR* 2.7 30.5 + - - +
22D GLN* 4.0 4.2 - - - +
24D LEU* 1.3 72.0 - - - +
26D LEU* 1.3 57.7 + - - +
28D ARG* 3.2 13.2 + - - +
29D ARG* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLN 3.1 19.0 + - - +
23D TYR 3.8 4.3 - - - +
24D LEU 3.3 0.2 - - - -
25D ASP* 1.3 75.6 - - - +
27D ILE* 1.3 58.4 + - - +
29D ARG* 3.2 11.9 + - - +
30D ILE* 2.9 56.3 + - + +
48D LEU* 4.6 8.1 - - + -
51D PRO* 3.9 31.0 - - + -
52D PRO* 5.4 0.9 - - + +
54D PHE* 3.5 26.0 - - + -
220D LEU* 3.7 15.9 - - + -
253D MET* 3.8 18.8 - - - -
256D ALA* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TYR* 3.2 53.2 + - + +
24D LEU* 3.6 9.6 - - + +
25D ASP 3.3 0.2 - - - -
26D LEU* 1.3 76.2 - - - +
28D ARG* 1.3 64.1 + - - +
30D ILE* 3.3 7.8 + - - +
31D ILE* 3.0 44.2 + - + +
220D LEU* 3.7 23.1 - - + -
258D VAL* 4.5 2.7 - - + -
266D LEU* 3.9 34.3 - - + -
269D GLN* 5.8 0.2 - - - -
270D LEU* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ARG* 3.5 14.7 - - - +
24D LEU* 3.0 23.9 + - - +
25D ASP* 3.3 32.4 + - - +
27D ILE* 1.3 77.2 - - - +
29D ARG* 1.3 58.3 + - - +
31D ILE* 3.4 4.3 + - - +
32D ASN* 2.9 51.1 + - - +
270D LEU* 3.8 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ASP 2.9 17.2 + - - +
26D LEU* 3.5 12.4 - - - +
28D ARG* 1.3 78.4 - - - +
30D ILE* 1.3 56.7 + - - +
32D ASN* 4.4 5.2 - - - -
33D VAL* 2.8 50.5 + - + +
48D LEU* 3.6 27.1 - - + +
51D PRO* 4.1 12.9 - - - +
52D PRO* 3.7 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 2.9 38.2 + - + +
27D ILE 3.7 3.8 - - - +
29D ARG* 1.3 71.6 - - - +
31D ILE* 1.3 59.6 + - - +
34D GLY* 2.7 30.8 + - - +
46D VAL* 3.0 48.1 - - + +
47D ALA* 4.1 4.3 - - - -
48D LEU* 3.9 21.3 - - + -
220D LEU* 3.7 31.9 - - + -
256D ALA* 3.8 15.5 - - + +
258D VAL* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.0 39.6 + - + +
28D ARG* 3.7 4.5 - - - +
30D ILE* 1.3 77.5 - - - +
32D ASN* 1.3 71.9 + - - +
34D GLY 4.5 1.2 + - - +
46D VAL* 4.5 10.2 - - - +
258D VAL* 4.6 14.4 - - + -
263D VAL* 4.3 44.2 - - + +
266D LEU* 4.7 3.4 - - + -
267D LYS* 4.6 13.5 - - + -
270D LEU* 4.4 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ARG* 2.9 40.0 + - - +
29D ARG* 3.7 5.4 - - - +
31D ILE* 1.3 89.2 + - - +
33D VAL* 1.3 68.3 + - + +
34D GLY 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ARG* 2.8 44.8 + - + +
32D ASN* 1.3 83.8 - - + +
34D GLY* 1.3 68.1 + - - +
35D GLU* 3.8 0.5 + - - +
48D LEU* 4.0 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ARG 3.6 2.4 + - - -
30D ILE 2.7 28.9 + - - -
31D ILE 5.3 0.5 - - - +
32D ASN 3.7 1.5 - - - +
33D VAL* 1.3 78.5 - - - +
35D GLU* 1.3 61.3 + - - -
36D VAL* 3.9 3.6 + - - +
46D VAL* 3.4 14.7 - - - +
47D ALA 3.5 11.0 - - - -
48D LEU* 3.8 9.9 - - - -
----------------------------------------------------------
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