Contacts of the helix formed by residues 19 - 34 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASP 3.1 8.8 + - - +
18B HIS* 1.3 73.9 + - - +
20B GLU* 1.3 62.3 + - - +
21B TYR 3.1 0.2 - - - -
22B GLN* 3.0 39.7 + - - +
23B TYR 4.2 0.2 + - - -
55B ARG 3.9 8.4 - - - +
56B PHE* 3.4 28.8 - - + +
57B SER* 2.9 46.6 + - - +
62B THR* 5.6 0.5 - - - +
277B PHE* 3.6 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS* 2.9 21.6 + - + +
19B GLU* 1.3 77.0 - - - +
21B TYR* 1.3 62.2 + - - +
22B GLN 3.1 0.2 - - - -
23B TYR* 3.1 18.0 + - + +
24B LEU* 3.1 16.1 + - + +
56B PHE* 4.9 2.7 - - - -
66B LEU* 3.6 24.3 - - + +
67B THR* 2.8 35.4 + - - -
68B THR* 2.5 44.9 + - - +
274B PRO* 3.8 11.6 - - + +
277B PHE* 3.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.4 66.3 - - + +
14B SER 4.8 0.2 + - - -
15B ASN 3.1 28.2 + - - -
16B PRO 3.9 12.6 - - - +
18B HIS* 3.0 29.4 + - + +
20B GLU* 1.3 77.9 - - - +
22B GLN* 1.3 54.2 + - - +
24B LEU* 4.0 17.9 - - + -
25B ASP* 2.7 41.6 + - - +
272B ARG 5.2 1.8 - - - -
273B GLU* 3.9 14.6 - - - +
274B PRO* 3.4 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS 4.5 0.4 + - - +
19B GLU* 3.0 27.2 + - - +
20B GLU 3.1 0.4 - - - -
21B TYR* 1.3 78.7 - - - +
23B TYR* 1.3 61.8 + - - +
25B ASP* 4.0 4.4 - - - +
26B LEU* 3.1 17.5 + - - +
53B SER 4.2 4.9 + - - -
54B PHE* 3.4 37.4 - - + +
55B ARG* 2.9 50.3 + - - +
56B PHE* 3.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 3.1 11.9 + - + +
22B GLN* 1.3 78.8 - - - +
24B LEU* 1.3 78.8 + - + +
26B LEU* 3.4 2.9 + - - +
27B ILE* 3.2 48.3 + - + +
54B PHE* 3.7 17.7 - + + -
56B PHE* 5.4 2.5 - - + -
66B LEU* 3.7 40.6 - - + -
68B THR* 5.0 0.4 - - - -
69B LYS* 5.0 0.3 + - - -
220B LEU* 2.6 36.6 + - + +
221B GLY* 3.7 6.8 + - - -
224B VAL* 3.9 26.7 - - + -
225B PRO* 3.6 10.0 - - + +
228B ILE* 4.6 3.8 - - + -
266B LEU* 4.3 4.0 - - - +
269B GLN* 3.9 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 3.1 11.5 + - + +
21B TYR* 4.0 28.3 - - + +
23B TYR* 1.3 89.7 - - + +
25B ASP* 1.3 65.8 + - - +
27B ILE* 3.4 2.6 + - + -
28B ARG* 3.1 26.4 + - - +
68B THR* 3.8 39.0 - - + +
269B GLN* 4.3 15.7 - - + +
270B LEU* 3.4 36.6 - - + +
272B ARG 4.0 11.4 - - - +
274B PRO* 4.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 2.8 42.6 + - - -
21B TYR* 2.7 30.3 + - - +
22B GLN* 4.0 4.4 - - - +
24B LEU* 1.3 72.6 - - - +
26B LEU* 1.3 56.7 + - - +
28B ARG* 3.2 14.4 + - - +
29B ARG* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLN 3.1 18.8 + - - +
23B TYR 3.8 2.7 - - - +
24B LEU 3.3 0.2 - - - -
25B ASP* 1.3 76.7 - - - +
27B ILE* 1.3 58.2 + - - +
29B ARG* 3.2 11.7 + - - +
30B ILE* 2.8 54.8 + - + +
48B LEU* 4.6 8.1 - - + -
51B PRO* 3.9 31.0 - - + -
52B PRO* 5.5 0.4 - - + +
54B PHE* 3.5 28.9 - - + -
220B LEU* 3.7 15.0 - - + -
253B MET* 3.8 18.2 - - - -
256B ALA* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 3.2 53.6 + - + +
24B LEU* 3.6 10.3 - - + +
25B ASP 3.3 0.2 - - - -
26B LEU* 1.3 76.2 - - - +
28B ARG* 1.3 64.4 + - - +
30B ILE* 3.3 7.6 + - - +
31B ILE* 3.0 43.8 + - + +
220B LEU* 3.7 22.9 - - + -
258B VAL* 4.5 2.5 - - + -
266B LEU* 3.9 33.4 - - + -
269B GLN* 5.8 0.4 - - - -
270B LEU* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.8 12.1 - - - +
24B LEU* 3.1 20.7 + - - +
25B ASP* 3.3 31.4 + - - +
27B ILE* 1.3 76.7 - - - +
29B ARG* 1.3 58.9 + - - +
31B ILE* 3.4 4.3 + - - +
32B ASN* 2.9 49.9 + - - +
270B LEU* 3.6 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP 2.9 17.3 + - - +
26B LEU* 3.5 12.8 - - - +
28B ARG* 1.3 77.9 - - - +
30B ILE* 1.3 56.6 + - - +
32B ASN* 3.2 5.5 + - - -
33B VAL* 2.8 52.5 + - + +
48B LEU* 3.6 25.0 - - + +
51B PRO* 4.1 13.1 - - - +
52B PRO* 3.7 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 2.8 38.2 + - + +
27B ILE 3.7 4.0 - - - +
29B ARG* 1.3 71.6 - - - +
31B ILE* 1.3 59.5 + - - +
34B GLY* 2.7 30.8 + - - +
46B VAL* 3.1 48.6 - - + +
47B ALA* 4.1 4.3 - - - -
48B LEU* 3.9 21.1 - - + -
220B LEU* 3.7 31.9 - - + -
256B ALA* 3.8 15.7 - - + +
258B VAL* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 3.0 39.0 + - + +
28B ARG* 3.7 4.7 - - - +
30B ILE* 1.3 77.7 - - - +
32B ASN* 1.3 71.7 + - - +
34B GLY 4.5 1.2 + - - +
46B VAL* 4.6 10.2 - - - +
258B VAL* 4.7 14.8 - - + -
263B VAL* 4.2 44.0 - - + +
266B LEU* 4.8 2.9 - - + -
267B LYS* 4.6 13.7 - - + -
270B LEU* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 2.9 38.3 + - - +
29B ARG* 3.7 5.0 - - - +
31B ILE* 1.3 88.7 + - - +
33B VAL* 1.3 68.6 + - + +
34B GLY 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ARG* 2.8 47.3 + - + +
32B ASN* 1.3 83.3 - - + +
34B GLY* 1.3 64.7 + - - +
35B GLU* 3.8 0.7 + - - +
48B LEU* 4.0 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ARG 3.6 2.4 + - - -
30B ILE 2.7 28.7 + - - -
31B ILE 5.3 0.5 - - - +
32B ASN 3.7 1.5 - - - +
33B VAL* 1.3 78.9 - - - +
35B GLU* 1.3 60.7 + - - -
36B VAL* 3.9 3.5 + - - +
46B VAL* 3.4 14.9 - - - +
47B ALA 3.5 11.0 - - - -
48B 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