Contacts of the helix formed by residues 19 - 31 (chain A) in PDB entry 1CKQ
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 GLY 19 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 3.2 6.7 + - - +
18A GLN* 1.3 77.4 + - - +
20A VAL* 1.3 63.6 + - - -
22A GLY* 3.3 11.3 + - - -
23A ILE* 3.8 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.2 2.3 + - - +
19A GLY* 1.3 67.2 - - - -
21A ILE* 1.3 64.5 + - + +
22A GLY 3.1 2.7 - - - -
23A ILE* 3.1 18.0 + - + +
24A PHE* 3.0 51.5 + - + -
45A ALA* 5.7 1.6 - - + +
48A ASN* 4.2 16.4 - - - +
49A GLU* 3.3 35.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 3.6 21.3 + - - +
18A GLN* 3.1 41.6 + - + +
20A VAL* 1.3 84.7 - - + +
22A GLY* 1.3 56.8 + - - +
24A PHE* 4.7 2.5 - - - -
25A GLY* 3.2 21.0 + - - -
45A ALA* 6.2 1.3 - - + -
49A GLU* 4.5 3.8 - - - +
252A PHE* 3.7 26.8 - - + -
253A GLU* 5.2 6.5 - - + +
256A PHE* 3.6 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 3.4 28.3 - - - +
19A GLY 3.3 9.4 + - - -
20A VAL 3.1 0.8 - - - -
21A ILE* 1.3 78.1 - - - +
23A ILE* 1.3 57.9 + - - +
25A GLY* 3.5 1.7 + - - -
26A ASP* 3.2 26.7 + - - +
249A LYS* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 4.1 9.4 - - - +
20A VAL* 3.1 22.6 + - + +
22A GLY* 1.3 75.6 - - - +
24A PHE* 1.3 70.7 + - + +
26A ASP* 3.4 7.9 + - - +
27A TYR* 3.3 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.0 48.9 + - + +
21A ILE* 4.6 0.9 - - - -
23A ILE* 1.3 80.3 - - + +
25A GLY* 1.3 63.1 + - - +
27A TYR* 3.4 6.4 + + + +
28A ALA 3.2 15.9 + - - -
41A LEU* 3.4 39.0 - - + +
44A LYS* 4.3 25.1 - - + -
45A ALA* 4.2 24.2 - - + -
48A ASN* 4.6 15.3 - - + -
252A PHE* 3.6 25.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE 3.2 16.4 + - - -
22A GLY* 3.5 2.7 + - - -
23A ILE 3.2 0.6 - - - -
24A PHE* 1.3 75.6 - - - +
26A ASP* 1.3 58.1 + - - +
28A ALA* 3.3 4.5 + - - +
29A LYS 3.1 22.2 + - - -
249A LYS* 3.2 32.7 - - - +
252A PHE* 4.0 15.0 - - - -
253A GLU* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 3.2 16.8 + - - +
23A ILE* 3.8 7.0 - - - +
24A PHE 3.3 0.2 - - - -
25A GLY* 1.3 75.4 - - - +
27A TYR* 1.3 59.9 + - - +
29A LYS* 3.7 26.4 + - - +
30A ALA* 2.9 31.4 + - - +
249A LYS* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE 3.3 10.3 + - - +
24A PHE* 3.6 12.3 - + + +
25A GLY 3.2 0.6 - - - -
26A ASP* 1.3 76.5 - - - +
28A ALA* 1.3 64.9 + - - +
30A ALA* 4.4 3.6 - - + -
31A HIS* 3.1 64.2 + + - +
33A LEU* 4.4 17.4 - - + +
41A LEU* 4.2 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE 3.2 11.3 + - - +
25A GLY* 3.5 11.4 - - - +
26A ASP 3.3 0.2 - - - -
27A TYR* 1.3 79.6 - - - +
29A LYS* 1.3 57.8 + - - +
31A HIS 3.5 0.5 + - - -
32A ASP 2.9 23.4 + - - -
33A LEU* 3.4 19.7 + - + +
38A VAL* 5.1 2.9 - - + -
41A LEU* 3.8 14.6 - - + -
248A SER* 3.3 33.2 - - - +
249A LYS* 4.5 0.2 - - - -
252A PHE* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 3.1 14.6 + - - +
26A ASP* 3.7 26.6 + - - +
28A ALA* 1.3 75.9 - - - +
30A ALA* 1.3 64.1 + - - +
31A HIS 3.3 0.7 + - - -
32A ASP* 3.4 12.2 + - - +
247A ASP* 3.8 22.7 - - - +
248A SER* 4.2 8.3 - - - -
249A LYS* 3.9 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 2.9 21.9 + - - +
27A TYR* 3.9 8.3 - - + +
28A ALA 3.4 0.2 - - - -
29A LYS* 1.3 76.7 - - - +
31A HIS* 1.3 71.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.1 62.3 + + - +
29A LYS 3.2 0.2 - - - -
30A ALA* 1.3 87.2 + - + +
32A ASP* 1.3 71.8 + - - +
33A LEU* 3.3 23.6 + - + +
----------------------------------------------------------
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