Contacts of the helix formed by residues 19 - 34 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP 3.1 7.2 + - - +
18A HIS* 1.3 74.8 + - - +
20A GLU* 1.3 61.4 + - - +
22A GLN* 3.1 40.2 + - - +
55A ARG 3.9 8.4 - - - +
56A PHE* 3.4 28.5 - - + +
57A SER* 2.9 44.7 + - - +
62A THR* 5.6 0.5 - - - +
277A PHE* 3.6 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 2.9 21.0 + - + +
19A GLU* 1.3 75.9 - - - +
21A TYR* 1.3 62.6 + - - +
22A GLN 3.0 0.4 - - - -
23A TYR* 3.0 17.6 + - + +
24A LEU* 3.1 15.8 + - + +
56A PHE* 4.9 2.9 - - - -
66A LEU* 3.6 21.7 - - + +
67A THR* 2.8 37.1 + - - -
68A THR* 2.6 43.6 + - - +
274A PRO* 3.8 11.8 - - + +
277A PHE* 3.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 3.4 67.1 - - + +
14A SER 4.9 0.7 + - - -
15A ASN* 3.1 28.3 + - + -
16A PRO 3.7 12.1 - - - +
18A HIS* 3.1 29.7 + - + +
20A GLU* 1.3 78.2 - - - +
22A GLN* 1.3 54.1 + - - +
24A LEU* 3.8 19.1 - - + -
25A ASP* 2.7 42.6 + - - +
272A ARG 5.1 1.8 - - - -
273A GLU* 3.8 15.1 - - - +
274A PRO* 3.4 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS 4.6 0.6 + - - +
19A GLU* 3.1 28.4 + - - +
20A GLU 3.0 0.4 - - - -
21A TYR* 1.3 78.5 - - - +
23A TYR* 1.3 63.7 + - - +
25A ASP* 4.0 4.1 - - - +
26A LEU* 3.1 19.2 + - - +
53A SER 4.2 4.6 + - - -
54A PHE* 3.4 35.2 - - + +
55A ARG* 2.9 49.7 + - - +
56A PHE* 3.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 4.2 0.2 + - - -
20A GLU* 3.0 11.7 + - + +
22A GLN* 1.3 80.1 - - - +
24A LEU* 1.3 76.6 + - + +
26A LEU* 3.4 2.9 + - - +
27A ILE* 3.2 48.3 + - + +
54A PHE* 3.7 17.9 - + + -
56A PHE* 5.5 2.2 - - + -
66A LEU* 3.7 39.5 - - + -
68A THR* 5.0 1.3 - - - -
69A LYS* 5.0 0.3 + - - -
220A LEU* 2.5 36.9 + - + +
221A GLY* 3.7 6.8 + - - -
224A VAL* 3.9 26.2 - - + -
225A PRO* 3.5 9.6 - - + +
228A ILE* 4.7 3.6 - - + -
266A LEU* 4.3 4.0 - - - +
269A GLN* 3.9 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 3.1 13.2 + - + +
21A TYR* 4.0 27.4 - - + +
23A TYR* 1.3 88.5 - - + +
25A ASP* 1.3 64.1 + - - +
27A ILE* 3.4 2.6 + - + +
28A ARG* 3.0 27.7 + - - +
68A THR* 3.8 38.4 - - + +
269A GLN* 4.3 14.4 - - + +
270A LEU* 3.4 35.9 - - + +
272A ARG 4.0 9.0 - - - +
274A PRO* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 2.9 41.8 + - - -
21A TYR* 2.7 31.6 + - - +
22A GLN* 4.0 4.2 - - - +
24A LEU* 1.3 73.0 - - - +
26A LEU* 1.3 55.8 + - - +
28A ARG* 3.2 15.0 + - - +
29A ARG* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 3.1 19.2 + - - +
23A TYR 3.8 2.7 - - - +
24A LEU 3.3 0.2 - - - -
25A ASP* 1.3 77.3 - - - +
27A ILE* 1.3 57.5 + - - +
29A ARG* 3.2 11.0 + - - +
30A ILE* 2.8 55.2 + - + +
48A LEU* 4.6 8.3 - - + -
51A PRO* 3.9 31.9 - - + -
52A PRO* 5.4 0.7 - - + +
54A PHE* 3.4 29.2 - - + -
220A LEU* 3.7 15.0 - - + -
253A MET* 3.8 17.9 - - - -
256A ALA* 4.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 3.2 53.4 + - + +
24A LEU* 3.7 9.0 - - + +
26A LEU* 1.3 77.0 - - - +
28A ARG* 1.3 63.1 + - - +
30A ILE* 3.3 8.0 + - - +
31A ILE* 3.0 43.3 + - + +
220A LEU* 3.7 23.1 - - + -
258A VAL* 4.4 2.9 - - + -
266A LEU* 3.9 34.5 - - + -
269A GLN* 5.7 0.4 - - - +
270A LEU* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 3.8 12.9 - - - +
24A LEU* 3.0 20.9 + - - +
25A ASP* 3.4 30.4 + - - +
27A ILE* 1.3 78.1 - - - +
29A ARG* 1.3 56.3 + - - +
31A ILE* 3.4 3.3 + - - +
32A ASN* 2.9 50.9 + - - +
270A LEU* 3.6 52.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP 2.9 16.8 + - - +
26A LEU* 3.5 11.5 - - - +
28A ARG* 1.3 74.9 - - - +
30A ILE* 1.3 60.9 + - - +
32A ASN* 3.1 5.5 + - - -
33A VAL* 2.8 52.4 + - + +
48A LEU* 3.6 25.3 - - + +
51A PRO* 4.2 12.5 - - - +
52A PRO* 3.7 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 2.8 34.4 + - + +
27A ILE 3.7 3.8 - - - +
29A ARG* 1.3 74.8 - - - +
31A ILE* 1.3 58.9 + - - +
34A GLY* 2.8 30.7 + - - +
46A VAL* 3.1 48.2 - - + +
47A ALA* 4.1 5.2 - - - -
48A LEU* 3.9 22.4 - - + -
220A LEU* 3.6 32.5 - - + -
256A ALA* 3.8 14.8 - - + +
258A VAL* 3.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.0 35.0 + - + +
28A ARG* 3.8 4.5 - - - +
30A ILE* 1.3 77.1 - - - +
32A ASN* 1.3 71.1 + - - +
34A GLY 4.6 0.9 + - - +
46A VAL* 4.6 10.7 - - + +
258A VAL* 4.6 15.0 - - + -
263A VAL* 4.2 44.0 - - + +
266A LEU* 4.8 2.5 - - + -
267A LYS* 4.6 12.3 - - + -
270A LEU* 4.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 2.9 37.3 + - - +
29A ARG* 3.1 6.1 + - - +
31A ILE* 1.3 88.2 - - - +
33A VAL* 1.3 70.3 + - + +
34A GLY 5.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 2.8 43.9 + - + +
32A ASN* 1.3 82.7 - - + +
34A GLY* 1.3 68.1 + - - +
35A GLU* 3.8 0.5 + - - +
48A LEU* 4.0 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG 3.6 2.2 + - - -
30A ILE 2.8 28.5 + - - -
31A ILE 4.5 0.5 - - - +
32A ASN 3.7 1.5 - - - +
33A VAL* 1.3 77.9 - - - +
35A GLU* 1.3 59.8 + - - -
36A VAL* 3.9 3.6 + - - +
46A VAL* 3.4 14.1 - - - +
47A ALA 3.5 10.3 - - - -
48A LEU* 3.9 10.1 - - - -
----------------------------------------------------------
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