Contacts of the helix formed by residues 43 - 65 (chain Y) in PDB entry 1KKC
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 43 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186X ASN* 2.9 44.2 - - + +
39Y LEU* 2.9 28.0 + - + +
42Y LYS* 1.3 90.4 - - + +
44Y HIS* 1.3 61.0 + - - +
45Y HIS 3.5 0.2 - - - -
46Y GLN* 3.4 2.1 + - - +
47Y THR* 2.9 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177X GLU* 3.9 5.4 - - - -
180X TYR* 6.1 0.4 - - - -
181X TYR* 2.6 35.6 + + - -
186X ASN* 3.7 22.9 - - + +
39Y LEU 3.0 22.6 + - - -
40Y HIS* 3.4 25.8 - - + +
43Y LYS* 1.3 75.8 - - - +
45Y HIS* 1.3 64.8 + - - +
47Y THR* 3.0 16.8 + - - -
48Y TYR* 3.2 26.9 + - + -
178Y HIS* 3.5 41.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 45 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Y LEU* 3.6 8.1 - - + +
19Y PRO* 3.5 27.3 - - + +
40Y HIS* 3.0 16.3 + - - +
41Y HIS* 3.4 14.6 + - - +
43Y LYS 3.5 0.2 - - - -
44Y HIS* 1.3 72.0 - - - +
46Y GLN* 1.3 63.2 + - - +
48Y TYR* 3.1 11.2 + - + +
49Y VAL* 3.0 25.5 + - + +
84Y GLY 4.5 0.9 - - - -
85Y HIS* 3.0 35.3 + + - -
88Y HIS* 3.5 15.8 - - + +
89Y SER* 3.5 17.8 + - - -
92Y TRP* 2.8 29.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Y THR* 5.8 0.2 - - - +
18Y LEU* 3.4 34.6 - - + +
41Y HIS 3.3 5.3 + - - +
42Y LYS 3.0 28.1 - - - +
43Y LYS 3.6 2.0 - - - +
44Y HIS 3.2 0.4 - - - -
45Y HIS* 1.3 78.6 - - - +
47Y THR* 1.3 58.7 + - - +
49Y VAL* 3.2 14.8 + - - +
50Y ASN* 2.9 67.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Y LYS* 2.9 22.6 + - - +
44Y HIS* 3.0 12.2 + - - -
46Y GLN* 1.3 77.6 - - - +
48Y TYR* 1.3 65.3 + - + +
50Y ASN* 3.3 9.0 + - + +
51Y GLY* 2.8 25.3 + - - -
81Y ASN* 3.5 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Y HIS* 3.2 28.4 + - + -
45Y HIS* 3.1 9.8 + - - +
47Y THR* 1.3 82.8 - - + +
49Y VAL* 1.3 53.3 - - - +
51Y GLY 3.2 0.2 + - - -
52Y LEU* 2.7 38.7 + - - +
80Y PHE* 3.8 27.3 - + - -
81Y ASN* 3.3 34.5 + - - +
84Y GLY* 3.9 9.9 - - - -
85Y HIS* 4.0 9.0 - - - +
88Y HIS* 3.2 38.8 - + - -
161Y GLN* 3.0 21.8 + - + -
176Y TRP* 3.7 18.2 - - - -
178Y HIS* 3.9 7.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Y TYR* 3.3 36.3 - - + +
17Y THR* 3.8 7.9 - - - -
18Y LEU* 4.1 18.2 - - - +
45Y HIS* 3.0 25.2 + - + +
46Y GLN* 3.5 17.7 - - - +
48Y TYR* 1.3 76.1 - - - +
50Y ASN* 1.3 65.5 + - - +
52Y LEU* 3.3 8.3 + - - +
53Y ASN* 3.1 24.6 + - - +
85Y HIS* 3.9 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Y GLN* 2.9 49.9 + - - +
47Y THR* 3.6 8.4 - - + +
49Y VAL* 1.3 80.7 - - - +
51Y GLY* 1.3 62.7 + - - +
53Y ASN* 3.4 7.7 + - - +
54Y ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Y THR 2.8 11.6 + - - -
48Y TYR 3.5 0.2 - - - -
50Y ASN* 1.3 74.0 - - - +
52Y LEU* 1.3 59.3 + - - +
54Y ALA* 3.8 6.0 - - - +
55Y ALA* 2.8 31.5 + - - +
77Y ALA* 5.2 0.3 - - - +
81Y ASN* 3.4 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL* 4.2 12.1 - - + -
71B LEU* 5.7 1.8 - - + -
16Y TYR* 3.5 33.7 - - + -
48Y TYR 2.7 21.4 + - - +
49Y VAL* 3.5 4.7 - - - +
50Y ASN 3.2 0.2 - - - -
51Y GLY* 1.3 73.6 - - - +
53Y ASN* 1.3 62.6 + - - +
55Y ALA* 3.3 2.9 + - - +
56Y LEU* 3.1 40.6 + - + +
78Y ILE* 4.5 10.3 - - + +
81Y ASN* 3.4 10.9 - - + +
82Y GLY* 3.7 22.4 - - - +
85Y HIS* 3.6 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Y GLN 4.9 0.2 - - - +
15Y GLN* 3.1 40.5 - - - +
16Y TYR* 2.8 57.6 + - - -
49Y VAL* 3.1 22.1 + - - +
50Y ASN* 3.8 9.6 - - - +
52Y LEU* 1.3 76.4 - - - +
54Y ALA* 1.3 62.7 + - - +
56Y LEU* 3.6 5.9 + - - +
57Y GLU* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Y ASN 3.1 17.9 + - - +
51Y GLY* 3.8 7.4 - - - +
52Y LEU 3.3 0.2 - - - -
53Y ASN* 1.3 75.8 - - - +
55Y ALA* 1.3 63.3 + - - +
57Y GLU* 3.3 7.5 + - - +
58Y ALA* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Y GLY 2.8 19.2 + - - +
52Y LEU* 3.6 4.9 - - - +
53Y ASN 3.3 0.2 - - - -
54Y ALA* 1.3 77.4 - - - +
56Y LEU* 1.3 58.0 + - - +
58Y ALA* 3.2 2.1 + - - -
59Y GLN* 2.9 25.3 + - - +
74Y VAL* 3.2 17.2 - - + +
77Y ALA* 3.8 24.7 - - + +
78Y ILE* 3.7 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 4.9 7.2 - - + -
71B LEU* 3.6 38.8 - - + -
16Y TYR* 3.5 33.7 - - + -
52Y LEU* 3.1 30.7 + - + +
53Y ASN* 4.1 4.7 - - - +
55Y ALA* 1.3 78.7 - - - +
57Y GLU* 1.3 58.2 + - - +
59Y GLN* 3.3 17.0 + - - +
60Y LYS* 3.1 26.0 + - - +
78Y ILE* 4.4 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Y ASN 3.1 18.0 + - - +
54Y ALA* 3.6 7.6 - - - +
55Y ALA 3.1 0.2 - - - -
56Y LEU* 1.3 76.9 - - - +
58Y ALA* 1.3 64.1 + - - +
60Y LYS* 3.3 16.1 + - - +
61Y LYS* 3.1 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Y ALA 3.1 13.9 + - - +
55Y ALA* 3.6 7.9 - - - +
57Y GLU* 1.3 77.7 - - - +
59Y GLN* 1.3 57.6 + - - +
61Y LYS* 3.4 8.7 + - - +
62Y ALA* 3.0 31.4 + - - +
70Y LYS* 4.5 18.3 - - - +
74Y VAL* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 59 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.6 5.9 - - - +
59B GLN* 3.0 46.6 + - - +
60B LYS* 5.5 1.0 + - - -
55Y ALA 2.9 16.6 + - - +
56Y LEU* 3.3 17.1 + - - +
58Y ALA* 1.3 74.6 - - - +
60Y LYS* 1.3 78.3 + - - +
62Y ALA* 4.5 0.4 - - - -
63Y ALA* 3.0 28.6 + - - +
71Y LEU* 3.1 26.5 - - + +
74Y VAL* 3.7 20.8 - - + +
75Y GLN* 4.2 0.4 - - - +
78Y ILE* 4.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Y LEU 3.1 14.1 + - - +
57Y GLU* 3.5 18.8 - - - +
58Y ALA 3.2 0.4 - - - -
59Y GLN* 1.3 86.4 - - - +
61Y LYS* 1.3 60.9 + - + +
63Y ALA* 3.2 5.7 + - + +
64Y GLU* 2.9 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Y GLU* 3.1 43.7 + - + +
58Y ALA* 3.8 7.0 - - - +
60Y LYS* 1.3 77.0 - - - +
62Y ALA* 1.3 58.4 + - - +
64Y GLU* 3.2 15.9 + - - +
65Y ALA* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Y ALA 3.0 19.2 + - - +
59Y GLN* 4.4 0.9 - - - -
61Y LYS* 1.3 76.9 - - - +
63Y ALA* 1.3 57.8 + - - +
65Y ALA* 3.3 3.1 + - - -
66Y THR 3.0 6.6 + - - -
67Y ASP* 2.8 34.9 + - - +
70Y LYS* 3.4 36.6 - - + -
71Y LEU* 3.8 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 4.8 0.7 + - - -
56B LEU* 5.3 5.6 - - + -
59Y GLN* 3.0 27.1 + - - +
60Y LYS* 3.4 7.9 - - - +
62Y ALA* 1.3 74.5 - - - +
64Y GLU* 1.3 61.7 + - + +
66Y THR* 2.9 22.2 + - - -
71Y LEU* 3.4 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Y LYS* 2.9 46.7 + - + +
61Y LYS* 3.2 15.8 + - - +
63Y ALA* 1.3 77.4 - - + +
65Y ALA* 1.3 59.1 + - - +
66Y THR* 3.1 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Y LYS 2.9 16.4 + - - +
62Y ALA* 3.8 5.8 - - - +
63Y ALA 3.1 0.4 - - - -
64Y GLU* 1.3 74.9 - - - +
66Y THR* 1.3 72.6 + - - +
67Y ASP* 3.1 11.4 + - + +
----------------------------------------------------------
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