Contacts of the helix formed by residues 40 - 55 (chain A) in PDB entry 3S1K
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 GLN 40 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 3.2 30.5 + - + +
39A SER* 1.3 84.0 + - - +
41A SER* 1.3 64.3 + - - +
42A ALA 3.3 2.5 - - - -
43A ASN* 3.2 33.3 + - + +
44A LEU* 3.1 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A HIS* 3.8 9.0 - - - -
12A TYR* 3.6 43.1 - - - +
16A ILE* 4.7 0.2 - - - +
34A LEU* 4.1 15.0 - - - +
37A ASP 4.2 0.2 + - - -
38A PRO* 2.2 36.1 + - - +
39A SER 3.2 2.4 - - - -
40A GLN* 1.3 77.1 - - - +
42A ALA* 1.3 62.9 + - - +
44A LEU* 3.6 10.7 + - - +
45A LEU* 3.2 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.5 33.2 - - + +
39A SER 4.8 2.0 + - - +
40A GLN 3.2 1.0 + - - -
41A SER* 1.3 77.5 - - - +
43A ASN* 1.3 69.4 + - - +
45A LEU* 3.2 12.7 + - - +
46A ALA* 3.2 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER 5.4 1.0 + - - -
40A GLN* 3.2 41.3 + - + +
42A ALA* 1.3 80.9 - - - +
44A LEU* 1.3 65.5 + - + +
46A ALA* 3.1 8.6 + - - +
47A GLU* 3.1 23.9 + - - +
50A LYS* 5.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.8 13.9 - - + +
30A PHE* 3.8 21.2 - - + +
33A SER* 4.0 22.9 - - - +
34A LEU* 3.7 35.0 - - + +
40A GLN* 3.1 38.5 + - + +
41A SER* 3.8 4.9 - - - +
43A ASN* 1.3 76.9 - - + +
45A LEU* 1.3 62.0 + - - +
47A GLU* 3.7 11.8 + - - +
48A ALA* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.6 28.0 - - + -
15A GLU* 3.4 44.2 - - + +
16A ILE* 3.7 28.0 - - + +
19A LEU* 4.7 6.5 - - + -
41A SER 3.2 12.5 + - - +
42A ALA 3.2 10.9 + - - +
43A ASN 3.1 0.6 - - - -
44A LEU* 1.3 76.0 - - - +
46A ALA* 1.3 65.3 + - - +
48A ALA* 3.4 1.9 + - - +
49A LYS* 3.0 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 3.2 7.8 + - - +
43A ASN* 3.1 11.9 + - - +
45A LEU* 1.3 79.5 - - - +
47A GLU* 1.3 58.2 + - - +
49A LYS* 2.8 16.3 + - - +
50A LYS* 2.8 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.0 20.4 - - + -
43A ASN 3.1 12.8 + - - +
44A LEU* 4.1 12.8 - - - +
46A ALA* 1.3 78.5 - - - +
48A ALA* 1.3 57.1 + - - +
50A LYS* 3.4 25.7 + - + +
51A LEU* 3.0 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.4 5.8 - - + -
19A LEU* 3.6 22.3 - - + +
22A LEU* 3.9 4.6 - - + +
30A PHE* 3.6 34.0 - - + -
44A LEU 3.2 17.1 + - - +
45A LEU 3.8 2.7 - - - +
46A ALA 3.1 0.4 - - - -
47A GLU* 1.3 75.0 - - - +
49A LYS* 1.3 56.8 + - - +
51A LEU* 3.6 3.1 - - - +
52A ASN* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 4.2 16.0 + - - -
19A LEU* 4.2 17.9 - - + +
45A LEU* 3.0 31.9 + - + +
46A ALA* 2.8 17.7 + - - +
48A ALA* 1.3 73.8 - - - +
50A LYS* 1.3 62.7 + - + +
52A ASN* 3.3 5.2 + - - +
53A ASP* 2.6 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN 5.0 1.0 + - - -
46A ALA* 2.8 23.0 + - + +
47A GLU* 3.5 38.7 - - + +
49A LYS* 1.3 76.4 - - + +
51A LEU* 1.3 62.9 + - - +
53A ASP* 3.6 2.5 + - - +
54A ALA* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.8 8.5 - - + -
26A GLN* 3.2 40.6 - - + +
30A PHE* 3.7 28.3 - - + -
47A GLU* 3.0 18.1 + - + +
48A ALA* 3.6 4.7 - - - +
50A LYS* 1.3 77.7 - - - +
52A ASN* 1.3 61.6 + - - +
54A ALA* 3.4 6.6 + - + +
55A GLN* 3.1 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.3 32.8 - - + +
20A PRO* 3.4 16.0 - - - +
21A ASN* 2.8 67.0 + - - +
22A LEU* 3.6 12.8 + - + +
48A ALA 2.7 22.4 + - - +
49A LYS 3.3 5.4 + - - +
51A LEU* 1.3 74.2 - - - +
53A ASP* 1.3 69.5 + - - +
55A GLN* 3.5 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.9 0.2 - - - +
21A ASN* 4.8 1.6 + - - +
49A LYS* 2.6 30.7 + - - +
50A LYS* 4.4 1.8 - - - +
52A ASN* 1.3 82.8 + - - +
54A ALA* 1.3 58.8 + - - +
55A GLN 2.9 5.2 - - - -
56A ALA* 3.0 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS 3.1 19.8 + - - +
51A LEU* 3.4 9.2 + - + +
53A ASP* 1.3 76.8 - - - +
55A GLN* 1.3 60.1 + - + +
56A ALA 3.3 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 2.8 37.5 + - - +
22A LEU* 3.7 4.2 - - - +
23A ASN* 4.8 2.0 + - - +
26A GLN* 2.4 42.0 + - - +
51A LEU* 3.1 26.0 + - + +
52A ASN 3.5 7.6 - - - +
53A ASP 2.9 0.8 - - - -
54A ALA* 1.3 82.0 - - + +
56A ALA* 1.3 63.4 + - - +
57A PRO* 3.3 8.8 - - - +
----------------------------------------------------------
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