Contacts of the helix formed by residues 42 - 57 (chain B) in PDB entry 1A0A
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 42 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 5.7 2.9 - - - +
13A ARG* 5.9 0.8 - - - +
16A LEU* 3.2 30.7 - - + -
13B ARG* 4.3 18.6 - - - +
16B LEU* 4.7 14.8 - - + +
17B ALA* 6.5 0.9 - - + -
20B LEU* 3.1 27.4 - - + -
39B ALA* 4.4 2.0 + - - +
41B SER* 1.3 86.0 + - - +
43B ALA* 1.3 68.9 + - + +
44B THR* 3.5 2.5 - - - -
45B THR* 3.1 18.7 + - - -
46B VAL* 3.1 14.8 + - - +
5C C 4.4 22.2 - - - +
6C A 3.5 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG 5.0 2.7 - - - +
15A ARG* 3.8 8.5 - - + -
16A LEU* 2.9 45.1 - - + +
19A ALA* 3.4 3.1 - - - +
42B LYS* 1.3 74.8 - - + +
44B THR* 1.3 53.4 + - + +
46B VAL* 3.0 5.7 + - - +
47B GLU* 2.6 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 6.0 2.2 - - - -
36B VAL 5.0 0.7 - - - +
37B SER* 3.7 18.8 - - - +
38B ALA* 3.6 29.2 - - + +
39B ALA* 2.5 33.6 + - + +
42B LYS 3.1 1.5 + - - -
43B ALA* 1.3 72.9 - - + +
45B THR* 1.3 60.4 + - - +
47B GLU* 2.6 43.7 + - - +
48B ALA* 2.9 13.4 + - - +
51B ARG* 4.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.6 11.2 - - + +
23B LEU* 5.6 0.7 - - + -
24B ALA* 3.3 37.3 - - + +
27B ILE* 5.1 0.3 - - - +
32B LYS* 4.1 18.6 + - - +
40B PRO* 4.2 17.2 - - - +
41B SER 4.3 10.2 + - - +
42B LYS 3.3 11.2 - - - +
44B THR* 1.3 79.7 + - - +
46B VAL* 1.3 59.1 + - + +
48B ALA* 3.3 6.6 + - - +
49B ALA* 2.6 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.6 7.2 - - + -
19A ALA* 3.1 46.6 - - + +
20A LEU* 3.8 3.4 - - + +
23A LEU* 3.5 23.1 - - + -
20B LEU* 3.2 30.1 - - + -
23B LEU* 5.3 0.2 - - + -
42B LYS 3.1 22.4 - - - +
43B ALA 3.0 1.0 + - - +
45B THR* 1.3 76.6 - - + +
47B GLU* 1.3 63.8 + - - +
49B ALA* 3.2 9.2 - - + +
50B CYS* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.3 35.0 - - + +
18A VAL* 6.4 1.6 - - + -
19A ALA* 4.8 8.7 - - + +
22A GLU* 5.9 4.5 - - - +
43B ALA* 2.6 32.5 + - - +
44B THR* 2.6 35.4 + - - +
46B VAL* 1.3 74.1 - - - +
48B ALA* 1.3 58.1 + - - +
50B CYS* 3.2 11.3 + - - +
51B ARG* 2.8 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 3.4 9.8 - - + +
31B TRP* 5.1 3.5 - - + -
32B LYS* 3.6 36.1 - - + +
44B THR 2.9 8.2 + - - +
45B THR 3.5 3.4 - - - +
47B GLU* 1.3 71.3 - - - +
49B ALA* 1.3 61.5 + - - +
50B CYS 3.1 0.9 - - - -
51B ARG* 2.8 54.9 + - + +
52B TYR 3.1 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.2 2.2 - - + +
53A ILE* 3.6 8.2 - - - +
23B LEU* 3.8 27.6 - - + -
24B ALA 5.6 1.6 - - - +
27B ILE* 4.2 12.5 - - + +
45B THR* 2.6 26.6 + - + +
46B VAL* 3.2 20.9 - - + +
48B ALA* 1.3 74.8 - - - +
50B CYS* 1.3 55.9 + - - +
52B TYR* 4.3 2.3 + - - +
53B ILE* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.7 6.3 - - - -
22A GLU* 2.9 21.1 - - + +
23A LEU* 2.6 58.8 - - - -
26A LEU* 5.3 3.4 - - + +
46B VAL 2.9 8.9 + - - +
47B GLU* 3.6 10.1 - - - +
49B ALA* 1.3 77.4 - - - +
51B ARG* 1.3 52.6 + - + +
53B ILE* 3.1 13.9 - - + +
54B ARG* 2.7 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 3.2 40.6 + - + -
32B LYS* 5.7 0.2 - - - +
35B ASN* 5.0 18.2 - - - +
36B VAL* 6.2 1.2 - - - +
44B THR 5.1 0.8 + - - -
47B GLU* 2.8 62.8 + - - +
48B ALA* 2.8 32.2 + - - +
50B CYS* 1.3 72.8 - - + +
52B TYR* 1.3 52.0 + - - +
53B ILE 2.6 6.2 + - - -
54B ARG* 2.3 36.5 + - + +
55B HIS 2.7 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.3 22.4 - - + -
57A GLN* 3.2 28.2 + - + +
27B ILE* 3.9 10.8 - - + -
28B PRO* 3.1 48.4 - - + +
29B ALA* 3.2 32.5 - - + -
31B TRP* 3.6 13.9 - + - -
48B ALA 3.1 5.0 + - - +
49B ALA 4.3 3.6 + - - +
51B ARG* 1.3 75.0 - - - +
53B ILE* 1.3 62.0 + - - +
55B HIS* 3.7 5.5 - + + +
56B LEU* 2.8 60.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 16.2 - - + +
26A LEU* 3.9 19.1 - - + +
49A ALA* 5.1 2.0 - - + -
52A TYR* 4.1 6.3 - - + -
53A ILE* 3.1 32.3 - - + -
56A LEU* 4.0 17.9 - - + -
49B ALA 2.9 20.4 - - - +
50B CYS* 3.1 19.3 - - + +
51B ARG 2.6 4.4 + - - -
52B TYR* 1.3 72.9 - - - +
54B ARG* 1.3 52.1 + - - +
56B LEU* 2.4 29.9 + - - +
57B GLN* 2.5 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 5.8 6.1 - - - +
25A SER* 5.1 2.8 + - - -
26A LEU* 3.1 52.4 - - + +
31B TRP* 5.9 0.2 - - + -
50B CYS* 2.7 17.4 + - - +
51B ARG* 2.3 31.2 + - + +
53B ILE* 1.3 67.8 - - - +
55B HIS* 1.3 61.2 + - - +
57B GLN* 3.6 12.5 + - - +
58B GLN* 4.3 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 4.6 13.6 - - + -
51B ARG 2.7 12.8 + - - +
52B TYR* 3.7 13.0 - + + +
54B ARG* 1.3 71.0 - - - +
56B LEU* 1.3 100.6 + - + +
58B GLN* 2.7 73.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 6.0 0.9 - - + -
56A LEU* 4.4 32.2 - - + +
57A GLN* 5.1 4.7 - - + +
52B TYR* 2.8 61.9 + - + +
53B ILE* 2.4 20.1 + - + +
55B HIS* 1.3 93.3 - - + +
57B GLN* 1.3 65.7 + - - +
58B GLN* 2.9 11.8 + - - +
59B ASN* 4.5 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 2.9 37.6 - - + +
52A TYR* 2.5 39.6 + - - +
56A LEU* 3.3 30.5 - - - +
53B ILE* 2.5 21.5 + - - +
54B ARG* 3.6 6.7 + - - +
55B HIS 3.0 1.8 + - - -
56B LEU* 1.3 76.6 + - - +
58B GLN* 1.4 56.2 + - - +
59B ASN* 3.1 18.3 + - - +
----------------------------------------------------------
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