Contacts of the helix formed by residues 18 - 31 (chain B) in PDB entry 2A3Z
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 ASN 18 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR 3.5 8.3 + - - +
15B LYS 3.2 13.2 + - - +
17B SER* 1.3 77.9 - - - +
19B ALA* 1.3 54.5 + - - +
20B THR* 3.1 16.5 + - - -
21B LEU* 3.1 20.8 + - + +
22B ALA* 2.8 35.0 + - - +
1D NAG 1.4 70.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER 3.5 6.8 + - - +
18B ASN* 1.3 71.8 + - - +
20B THR* 1.3 58.1 + - - +
22B ALA* 3.8 7.0 - - - +
23B SER* 3.0 28.9 + - - -
54B TYR* 4.6 12.4 + - - +
1D NAG 5.8 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASN* 3.1 9.2 + - - -
19B ALA* 1.3 74.9 - - - +
21B LEU* 1.3 65.1 + - + +
23B SER* 2.3 26.8 + - - +
24B TYR* 3.2 33.1 + - + +
245B MET* 3.8 24.5 - - + -
1D NAG 4.7 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 3.8 31.9 - - + +
18B ASN* 3.1 33.4 + - + +
20B THR* 1.3 78.7 - - - +
22B ALA* 1.3 63.7 + - - +
24B TYR* 3.2 6.3 + - + +
25B ILE* 3.0 30.4 + - + +
245B MET* 4.1 16.2 - - - -
248B ALA* 3.7 45.8 - - + +
249B ILE* 4.0 13.4 - - + +
1D NAG 3.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS 4.1 1.6 + - - -
16B MET* 3.8 43.2 - - + +
18B ASN 2.8 21.7 + - - +
19B ALA 3.8 4.9 - - - +
21B LEU* 1.3 71.4 - - - +
23B SER* 1.3 53.8 + - - +
25B ILE* 3.2 3.1 + - - +
26B VAL* 2.8 40.7 + - - +
54B TYR* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA 3.0 15.4 + - - -
20B THR* 2.3 34.1 + - - +
22B ALA* 1.3 76.4 - - - +
24B TYR* 1.3 62.4 + - - +
26B VAL* 3.4 6.8 + - - +
27B ARG* 3.0 27.0 + - - +
54B TYR* 5.7 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 3.2 39.1 + - + +
21B LEU* 3.2 4.0 + - - +
23B SER* 1.3 82.8 + - - +
25B ILE* 1.3 61.6 + - - +
27B ARG* 3.2 10.0 + - - +
28B ILE* 2.9 36.5 + - + +
239B TYR* 3.8 29.6 + + + -
241B LEU* 3.2 32.6 - - + +
245B MET* 4.1 15.4 - - + +
249B ILE* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 5.3 1.6 - - + -
8B ILE* 4.1 29.6 - - + -
11B PHE* 4.4 9.9 - - + -
15B LYS* 3.7 37.2 - - + -
16B MET* 4.4 11.7 - - - -
21B LEU* 3.0 23.7 + - + +
22B ALA* 3.7 4.5 - - - +
24B TYR* 1.3 75.2 - - - +
26B VAL* 1.3 64.1 + - - +
28B ILE* 3.4 8.3 + - - +
29B VAL* 3.1 27.5 + - + +
51B LEU* 4.2 19.1 - - + -
249B ILE* 4.3 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B MET* 5.1 0.4 - - + -
22B ALA 2.8 25.0 + - - +
23B SER* 3.9 6.1 - - - +
24B TYR 3.2 0.2 - - - -
25B ILE* 1.3 69.4 - - - +
27B ARG* 1.3 68.6 + - - +
29B VAL* 3.2 3.4 + - - +
30B ARG* 3.0 66.0 + - - +
51B LEU* 3.7 22.4 - - + -
54B TYR* 3.6 36.8 - - + -
55B LEU* 4.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER 3.0 17.9 + - - +
24B TYR* 3.2 13.0 + - - +
26B VAL* 1.3 80.6 - - - +
28B ILE* 1.3 63.3 + - - +
30B ARG* 3.4 11.9 + - - +
31B ARG* 3.7 12.5 + - + +
239B TYR* 3.5 39.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.8 31.0 - - + -
24B TYR* 2.9 23.0 + - + +
25B ILE* 3.7 4.9 - - - +
27B ARG* 1.3 76.9 - - - +
29B VAL* 1.3 63.6 + - + +
31B ARG* 3.2 19.5 + - - +
32B TYR* 3.3 17.6 - - + -
233B PHE* 4.3 7.6 - - + -
235B PHE* 4.0 28.9 - - + -
239B TYR* 3.7 22.7 - - + +
249B ILE* 4.3 11.7 - - + -
254B PRO* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 5.6 3.1 - - + -
8B ILE* 5.5 1.3 - - + -
25B ILE* 3.1 30.3 + - + +
26B VAL* 3.2 4.0 + - - +
28B ILE* 1.3 80.0 - - + +
30B ARG* 1.3 63.7 - - - +
31B ARG 3.0 1.4 + - - -
32B TYR* 3.1 21.0 + - - +
35B VAL* 4.0 15.8 - - + +
37B ILE* 4.2 24.7 - - + -
51B LEU* 4.6 3.1 - - + -
55B LEU* 3.8 33.0 - - + -
63B TYR* 3.0 17.4 + - + -
83B LEU* 3.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 3.0 42.5 + - - +
27B ARG* 3.4 7.1 + - - +
28B ILE 3.3 0.6 - - - -
29B VAL* 1.3 75.0 - - - +
31B ARG* 1.3 61.2 + - - +
32B TYR 3.1 1.1 + - - -
54B TYR 3.2 25.3 + - - -
55B LEU* 3.5 31.3 + - + +
57B GLN* 3.7 13.7 - - - +
62B THR* 5.1 4.3 - - - -
63B TYR* 3.2 16.2 - - + -
85B ARG* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 3.8 30.3 - - + +
27B ARG* 3.7 9.1 + - + +
28B ILE* 3.3 17.5 - - - +
29B VAL 3.0 0.6 + - - -
30B ARG* 1.3 77.3 - - - +
32B TYR* 1.3 84.3 + - + +
33B ASP* 5.4 0.5 - - - +
233B PHE* 3.4 50.0 - - - -
239B TYR* 4.0 9.7 + - - +
256B GLU* 3.0 26.5 + - - -
----------------------------------------------------------
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