Contacts of the helix formed by residues 18 - 37 (chain R) in PDB entry 1KYO
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 SER 18 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R TYR* 3.5 22.9 + - - -
15R ILE 3.2 3.6 + - - +
16R LEU 3.2 1.9 - - - -
17R LYS* 1.3 78.4 - - - +
19R PRO* 1.3 63.5 - - - +
20R VAL* 3.5 14.0 + - - +
21R LEU* 3.7 23.1 + - - +
22R SER* 2.9 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 19 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R LEU 5.4 0.2 - - - +
17R LYS 3.6 8.2 - - - +
18R SER* 1.3 85.8 - - - +
20R VAL* 1.3 67.8 + - + +
22R SER* 3.9 4.9 - - - -
23R LYS* 2.9 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R SER* 3.2 8.7 - - - +
19R PRO* 1.3 84.7 - - + +
21R LEU* 1.3 74.6 + - + +
23R LYS* 3.6 6.1 + - - +
24R LEU* 3.6 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R TYR* 5.3 14.1 - - + +
15R ILE* 3.8 32.5 - - + +
18R SER* 3.5 19.1 + - - +
20R VAL* 1.3 86.0 - - + +
22R SER* 1.3 66.5 + - - +
24R LEU* 3.2 14.9 + - + -
25R CYS* 3.0 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R ILE* 3.3 7.6 + - - -
16R LEU* 3.7 18.8 + - - +
18R SER 2.9 21.1 + - - -
19R PRO* 3.9 7.6 - - - -
21R LEU* 1.3 78.7 - - - +
23R LYS* 1.3 64.7 + - - +
24R LEU 3.1 0.5 + - - -
26R VAL* 3.2 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R PRO* 2.9 24.4 + - + +
20R VAL* 4.0 5.8 - - - +
21R LEU 3.4 0.6 - - - -
22R SER* 1.3 76.8 - - - +
24R LEU* 1.3 56.7 + - + +
25R CYS 3.5 0.2 - - - -
27R PRO* 3.5 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R VAL* 3.6 15.2 + - + +
21R LEU* 3.2 20.1 + - + +
22R SER 3.1 0.8 - - - -
23R LYS* 1.3 80.3 - - - +
25R CYS* 1.3 62.3 + - - +
27R PRO* 4.3 1.8 - - - -
28R VAL* 3.7 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 25 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377N LEU* 5.2 4.0 - - + +
380N ILE* 3.7 20.4 - - + +
15R ILE* 3.9 24.0 - - + -
21R LEU* 3.0 29.5 + - - +
22R SER 3.2 0.2 + - - -
24R LEU* 1.3 85.3 - - - +
26R VAL* 1.3 68.4 + - - +
27R PRO* 3.2 3.4 - - - -
28R VAL* 2.9 12.7 + - - +
29R ALA* 2.8 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380N ILE* 4.1 18.8 - - + +
381N GLY 5.4 0.2 - - - -
15R ILE* 5.7 0.2 - - + -
16R LEU* 3.9 27.1 - - + -
22R SER* 3.2 25.1 - - - +
25R CYS* 1.3 74.4 - - + +
27R PRO* 1.4 62.4 - - + +
29R ALA* 3.0 8.8 + - + +
30R ASN* 2.8 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R SER 3.9 1.6 - - - +
23R LYS* 3.5 26.7 - - - +
24R LEU 4.3 1.1 - - - -
25R CYS 3.3 6.3 - - - +
26R VAL* 1.4 94.8 - - + +
28R VAL* 1.3 62.5 + - + +
30R ASN* 3.4 11.0 + - - +
31R GLN* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377N LEU* 4.8 17.9 - - + -
24R LEU 3.7 22.2 - - - +
25R CYS* 2.9 7.7 + - - +
27R PRO* 1.3 77.8 - - + +
29R ALA* 1.3 58.0 + - - +
31R GLN* 3.3 7.1 + - + +
32R PHE* 2.8 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377N LEU* 3.8 18.6 - - + +
380N ILE* 3.6 24.7 - - + -
381N GLY* 3.5 21.5 - - - +
25R CYS 2.8 9.1 + - - +
26R VAL* 3.1 10.1 - - - +
28R VAL* 1.3 77.1 - - - +
30R ASN* 1.3 61.8 + - - +
32R PHE* 3.1 4.2 + - - +
33R ILE* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381N GLY* 3.1 28.1 + - - -
26R VAL* 2.8 41.2 + - - +
27R PRO* 3.7 9.0 - - - +
29R ALA* 1.3 71.9 - - - +
31R GLN* 1.3 57.2 + - - +
33R ILE* 3.5 8.9 + - - +
34R ASN* 2.6 39.8 + - - +
39R LYS* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R PRO 3.1 18.9 + - - +
28R VAL* 3.4 9.4 - - + +
30R ASN* 1.3 76.2 - - - +
32R PHE* 1.3 65.2 + - - +
34R ASN* 3.0 28.1 + - - +
35R LEU* 3.1 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 32 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318N PHE 4.4 3.8 - - - -
319N LYS* 4.4 0.2 - - - -
320N VAL* 3.6 34.7 - - + +
321N LEU* 3.9 13.5 - - + -
374N GLU* 3.6 33.0 - - + -
377N LEU* 3.7 36.1 - - + -
378N PHE* 3.6 43.7 - + - -
28R VAL* 2.8 22.1 + - + +
29R ALA 3.1 3.3 + - - +
31R GLN* 1.3 73.0 - - - +
33R ILE* 1.3 71.8 + - + +
35R LEU* 3.4 10.9 + - - +
36R ALA* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377N LEU 4.4 2.9 - - - +
378N PHE* 4.0 20.6 - - + +
381N GLY* 3.6 39.0 - - - +
382N ARG* 4.4 4.9 - - + -
29R ALA 3.0 15.0 + - - +
30R ASN* 3.6 7.4 - - - +
32R PHE* 1.3 86.4 - - + +
34R ASN* 1.3 64.5 + - - +
36R ALA* 3.2 19.5 + - - +
37R GLY* 3.5 4.9 + - - -
38R TYR* 3.3 32.5 - - + +
39R LYS* 3.3 26.9 + - - +
99R ASP* 4.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 34 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R ASN* 2.6 30.4 + - - +
31R GLN* 3.0 20.0 + - - +
33R ILE* 1.3 76.3 - - - +
35R LEU* 1.3 62.7 + - + +
36R ALA 3.5 0.2 + - - -
37R GLY* 3.6 8.5 + - - -
39R LYS* 4.0 21.5 + - - +
40R LYS* 3.6 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320N VAL* 3.4 35.4 - - + +
323N LYS* 5.4 3.6 + - - -
31R GLN* 3.1 38.2 + - + +
32R PHE* 3.7 5.2 - - - +
33R ILE 3.2 0.2 - - - -
34R ASN* 1.3 77.2 - - + +
36R ALA* 1.3 64.8 + - - +
37R GLY* 4.4 0.5 - - - -
58S TYR* 4.3 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317N THR 3.9 6.9 - - - +
318N PHE* 3.1 48.1 - - - +
320N VAL* 4.0 4.2 - - + +
323N LYS* 5.0 3.1 + - - +
378N PHE* 4.5 4.3 - - + -
32R PHE* 3.1 13.2 + - + +
33R ILE* 3.2 13.4 + - - +
35R LEU* 1.3 79.1 - - - +
37R GLY* 1.3 59.3 + - - +
38R TYR* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318N PHE* 4.5 3.9 - - - -
33R ILE 3.5 6.8 + - - -
34R ASN 3.6 10.3 + - - -
35R LEU 3.3 2.5 - - - -
36R ALA* 1.3 78.3 - - - +
38R TYR* 1.3 59.1 + - - +
39R LYS* 3.0 5.2 - - - -
40R LYS* 2.8 42.1 + - - +
41R LEU* 3.7 4.9 + - - +
87R LEU* 5.3 1.7 - - - +
----------------------------------------------------------
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