Contacts of the helix formed by residues 27 - 50 (chain C) in PDB entry 4KNF
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 ASP 27 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP* 3.0 28.2 + - + +
25C ILE 4.2 0.4 - - - -
26C SER* 1.3 74.5 + - - +
28C THR* 1.3 56.9 + - - +
29C VAL 4.1 1.2 + - - -
30C GLY* 2.8 22.3 + - - -
31C VAL* 2.9 14.8 + - - +
83C TRP* 2.8 31.0 + - - -
84C ILE* 3.6 27.2 - - - +
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Residues in contact with THR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 3.2 21.8 - - + +
26C SER* 2.7 16.6 + - - +
27C ASP* 1.3 68.9 - - - +
29C VAL* 1.3 63.4 + - - +
31C VAL* 3.3 9.2 + - + +
32C SER* 3.0 26.0 + - - -
218C SER* 5.9 1.2 - - - -
222C LEU* 3.8 18.4 - - - +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 4.4 0.4 - - - +
28C THR* 1.3 75.5 + - - +
30C GLY* 1.3 65.7 + - - +
32C SER* 3.2 2.5 + - - -
33C PHE* 2.9 45.7 + - + -
83C TRP* 3.3 33.9 - - + +
218C SER* 3.5 47.8 - - - +
221C ASN* 4.0 12.6 - - + -
222C LEU* 3.8 17.7 - - + -
225C ASN* 5.2 1.3 - - - +
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Residues in contact with GLY 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 5.4 0.2 - - - -
27C ASP* 2.8 32.6 + - - -
29C VAL* 1.3 77.6 - - - +
31C VAL* 1.3 59.6 + - - -
33C PHE* 3.6 4.1 + - - +
34C TRP 3.2 9.9 + - - -
80C ARG* 2.7 31.8 + - - -
83C TRP* 3.6 10.4 - - - +
84C ILE* 4.5 2.2 - - - -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 5.1 13.2 - - + -
24C ASP 3.9 15.7 - - - +
25C ILE* 4.2 24.5 - - + +
27C ASP 2.9 18.1 + - - +
28C THR* 3.3 10.3 + - + +
29C VAL 3.2 0.4 - - - -
30C GLY* 1.3 74.1 - - - +
32C SER* 1.3 60.8 + - - +
34C TRP* 3.0 7.6 + - + +
35C LEU* 2.9 37.6 + - + +
80C ARG* 4.7 0.4 - - - +
92D VAL* 5.2 0.7 - - + -
96D ILE* 3.6 31.0 - - + -
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C THR 3.0 15.0 + - - -
29C VAL 3.4 8.1 - - - -
31C VAL* 1.3 76.9 - - - +
33C PHE* 1.3 62.4 + - - +
34C TRP 3.3 0.2 + - - -
35C LEU* 3.3 10.5 + - - +
36C VAL* 3.0 28.5 + - - +
222C LEU* 3.6 22.1 + - - +
225C ASN* 3.2 27.4 + - - +
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Residues in contact with PHE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 2.9 44.1 + - + +
30C GLY 3.7 1.3 - - - +
32C SER* 1.3 76.7 - - - +
34C TRP* 1.3 57.6 + - - +
37C THR* 2.6 35.1 + - - -
76C TYR* 3.7 21.4 - + + -
79C MET* 3.8 20.0 - - + -
80C ARG* 3.6 27.6 - - + -
83C TRP* 3.9 28.7 - + + -
90C PRO* 4.2 15.3 - - + -
94C ARG* 3.6 19.3 - - - -
221C ASN* 4.0 9.6 - - + -
225C ASN* 3.3 25.5 - - - +
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Residues in contact with TRP 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.1 11.9 - - + -
30C GLY 3.2 11.0 + - - +
31C VAL* 3.0 13.1 + - + +
33C PHE* 1.3 81.9 - - - +
35C LEU* 1.3 67.5 + - + +
37C THR* 3.3 5.9 + - - -
38C ALA* 3.2 19.9 + - + +
80C ARG* 3.6 39.9 - - - +
74D TRP* 5.9 2.2 - - + -
75D HIS* 2.8 36.9 + + - -
78D TYR* 3.7 38.4 - + - -
93D PHE* 3.5 30.7 - + - -
96D ILE* 3.5 21.4 - - + +
100D LEU* 4.9 1.6 - - + -
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 2.9 32.6 + - + +
32C SER* 3.6 8.5 - - - +
34C TRP* 1.3 77.2 - - - +
36C VAL* 1.3 59.7 + - + +
38C ALA* 3.3 6.1 + - - +
39C GLY* 2.9 23.6 + - - -
229C PHE* 5.8 1.7 - - - -
96D ILE* 3.8 32.3 - - + +
99D LEU* 4.3 23.3 - - + -
100D LEU* 3.9 26.2 - - + +
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C SER* 3.0 21.0 + - - +
35C LEU* 1.3 76.9 - - + +
37C THR* 1.3 53.6 + - - +
39C GLY* 3.0 3.9 + - - +
40C MET* 2.6 48.5 + - + +
76C TYR* 3.3 36.1 - - + +
225C ASN* 3.5 29.8 - - + +
228C ASP* 5.0 0.4 - - + -
229C PHE* 4.4 26.5 - - + +
233C ILE* 4.7 0.3 - - - +
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE 2.6 21.5 + - - -
34C TRP* 3.4 10.6 - - - -
36C VAL* 1.3 77.1 - - - +
38C ALA* 1.3 56.8 + - - +
40C MET* 3.3 3.1 + - - +
41C LEU* 3.0 22.9 + - - +
73C PHE* 3.5 35.7 - - + +
76C TYR* 3.4 25.5 + - + +
77C LEU* 3.8 23.5 - - + -
80C ARG* 5.2 3.7 - - - +
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TRP* 3.2 11.5 + - - +
35C LEU 3.5 8.5 - - - +
37C THR* 1.3 75.9 - - - +
39C GLY* 1.3 59.7 + - - +
41C LEU* 3.3 9.0 + - - +
42C ALA* 2.9 32.1 + - - +
71D ILE* 4.8 10.7 - - + +
75D HIS* 4.7 9.9 - - + -
100D LEU* 4.0 27.1 - - + -
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Residues in contact with GLY 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU 2.9 14.3 + - - -
36C VAL* 3.0 5.1 + - - -
38C ALA* 1.3 75.2 - - - +
40C MET* 1.3 63.5 + - - +
42C ALA* 4.0 4.5 - - - +
43C ALA* 3.0 26.9 + - - +
229C PHE* 5.1 6.5 - - - -
233C ILE* 3.4 18.1 - - - +
100D LEU* 4.6 6.6 - - - +
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Residues in contact with MET 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 2.6 37.0 + - + +
37C THR* 3.7 6.5 - - - +
38C ALA 3.2 0.2 - - - -
39C GLY* 1.3 75.7 - - - +
41C LEU* 1.3 53.0 + - - +
43C ALA* 3.7 1.7 - - - +
44C THR* 2.4 39.7 + - - -
69C THR* 2.9 55.0 - - + +
72C ALA* 3.0 30.3 - - + -
73C PHE* 3.9 13.0 - - - +
76C TYR* 4.9 3.1 - - + -
228C ASP* 4.7 5.8 - - - +
232C LYS* 4.0 15.5 - - + -
233C ILE* 3.9 20.9 - - - -
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C THR 3.0 17.2 + - - +
38C ALA* 3.3 8.3 + - - +
40C MET* 1.3 77.9 - - - +
42C ALA* 1.3 61.9 + - - +
44C THR* 3.3 10.1 - - + -
45C VAL* 3.2 33.2 + - + +
73C PHE* 3.6 39.7 - - + -
71D ILE* 6.2 3.8 - - + -
74D TRP* 4.2 33.9 - - + +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA 2.9 17.4 + - - +
39C GLY* 4.0 4.9 - - - +
41C LEU* 1.3 75.1 - - - +
43C ALA* 1.3 67.1 + - - +
45C VAL* 3.0 6.2 + - - +
46C PHE* 2.9 22.9 + - - +
67D LEU* 3.6 22.1 - - + +
71D ILE* 3.8 27.1 - - + +
104D LEU* 5.7 1.8 - - + -
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLY 3.0 18.9 + - - +
40C MET 3.7 2.7 - - - +
42C ALA* 1.3 75.8 - - - +
44C THR* 1.3 54.8 + - - +
46C PHE* 3.0 9.8 + - - +
47C PHE* 2.7 56.3 + - + -
69C THR* 3.9 8.5 - - + -
233C ILE* 3.7 26.0 - - + -
237C LEU* 5.9 1.6 - - + -
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Residues in contact with THR 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C MET 2.4 22.8 + - - -
41C LEU* 3.3 13.9 - - + -
43C ALA* 1.3 77.2 - - - +
45C VAL* 1.3 62.2 + - + +
47C PHE* 3.7 1.0 + - - +
48C PHE* 3.1 45.2 + - + -
66C GLY* 3.4 20.2 - - - +
69C THR* 2.8 26.5 + - - -
70C GLY* 3.8 11.8 - - - -
73C PHE* 4.9 0.7 - - - +
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 3.2 24.0 + - + +
42C ALA* 3.0 8.0 + - - +
44C THR* 1.3 78.1 - - + +
46C PHE* 1.3 60.1 + - - +
48C PHE* 3.4 4.2 + - - +
49C VAL* 2.9 40.3 + - + +
48D PHE* 3.6 35.2 - - + -
67D LEU* 3.8 9.2 - - + -
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Residues in contact with PHE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA 2.9 12.5 + - - +
43C ALA* 3.3 10.8 - - - +
45C VAL* 1.3 78.3 - - - +
47C PHE* 1.3 71.7 + + - +
50C GLU* 3.0 40.6 + - + +
237C LEU* 3.6 30.3 - - + -
240C TRP* 3.4 52.3 - + - -
60D THR* 4.0 15.5 - - + -
63D THR* 3.6 26.5 - - + -
64D VAL* 4.8 8.1 - - + -
67D LEU* 3.9 17.9 - - + +
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Residues in contact with PHE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA* 2.7 37.5 + - + +
46C PHE* 1.3 81.3 - + - +
48C PHE* 1.3 64.7 + - - +
50C GLU* 4.0 1.9 - - - -
51C ARG* 3.5 20.8 + - - +
62C LEU* 3.7 39.8 - - + +
65C SER* 3.8 10.8 - - - -
66C GLY* 3.8 20.6 - - - +
69C THR* 3.6 24.0 - - + -
232C LYS 4.4 0.4 - - - -
233C ILE 3.7 7.9 - - - -
236C GLY* 3.3 46.4 - - - -
237C LEU* 3.5 24.7 - - + -
240C TRP* 4.5 1.8 - + + -
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Residues in contact with PHE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B VAL* 3.6 29.6 - - + -
49B VAL* 4.2 15.5 - - + -
44C THR* 3.1 33.0 + - + +
45C VAL* 4.0 4.0 - - - +
47C PHE* 1.3 80.2 - - - +
49C VAL* 1.3 64.7 + - + +
51C ARG* 3.4 31.4 + - - +
62C LEU 4.9 0.4 - - - -
63C THR* 3.6 42.4 - - + -
66C GLY* 3.7 20.4 - - - -
67C LEU* 3.7 9.0 - - + -
70C GLY* 5.9 0.4 - - - -
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 2.9 40.1 + - + +
46C PHE 4.3 1.3 - - - +
48C PHE* 1.3 75.6 - - + +
50C GLU* 1.3 59.5 + - - +
51C ARG* 3.1 5.6 + - - +
52C ASP* 3.1 18.4 + - - +
48D PHE* 4.2 14.6 - - + +
51D ARG* 3.1 41.7 + - - +
63D THR* 3.9 9.6 - - + +
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 3.0 37.9 + - + +
47C PHE 4.3 1.8 - - - +
49C VAL* 1.3 71.7 - - - +
51C ARG* 1.3 55.5 + - - +
52C ASP* 2.9 8.7 - - - -
53C GLN* 2.8 38.2 + - - +
54C VAL* 4.2 0.7 - - - +
62C LEU* 3.7 10.2 - - - +
240C TRP* 3.3 32.2 + - + +
51D ARG* 2.7 16.1 + - - -
60D THR* 2.7 32.5 + - - -
63D THR* 2.6 27.9 + - + +
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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