Contacts of the helix formed by residues 27 - 50 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 3.2 24.0 + - + +
25B ILE 3.1 4.1 - - - -
26B SER* 1.3 78.0 + - - +
28B THR* 1.3 60.7 + - - +
29B VAL* 3.7 3.3 + - - +
30B GLY* 3.1 23.9 + - - -
31B VAL* 3.2 16.3 + - - +
80B ARG* 5.3 0.5 + - - -
83B TRP* 3.0 33.8 + - - -
84B ILE* 4.4 12.1 - - - +
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Residues in contact with THR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE 4.5 7.6 + - - -
26B SER 3.3 8.3 + - - -
27B ASP* 1.3 72.5 + - - +
29B VAL* 1.3 63.3 + - - +
31B VAL* 3.3 9.2 + - + +
32B SER* 3.1 22.4 + - - -
218B SER* 5.9 1.1 - - - -
222B LEU* 4.1 24.9 - - + -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 3.2 1.4 + - - +
28B THR* 1.3 74.8 - - - +
30B GLY* 1.3 64.8 + - - +
31B VAL 3.2 0.2 + - - -
32B SER* 3.4 2.4 + - - -
33B PHE* 2.9 43.7 + - + -
83B TRP* 3.4 36.1 - - + +
218B SER* 3.6 43.1 - - - +
221B ASN* 3.8 14.8 - - + -
222B LEU* 4.1 14.8 - - + -
225B ASN* 5.0 2.5 - - - +
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 5.1 0.2 - - - -
27B ASP* 3.1 29.9 + - - -
29B VAL* 1.3 75.4 - - - +
31B VAL* 1.3 55.6 + - - +
33B PHE* 3.5 2.3 + - - +
34B TRP* 3.1 11.4 + - - +
80B ARG* 2.7 41.8 + - - -
83B TRP* 3.6 10.8 - - - +
84B ILE* 4.2 0.9 - - - -
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.7 14.4 - - + -
24B ASP 4.1 13.5 - - - +
25B ILE* 4.5 23.1 - - + +
27B ASP 3.2 13.2 + - - +
28B THR* 3.6 11.0 - - + +
29B VAL 3.2 0.4 - - - -
30B GLY* 1.3 74.5 - - - +
32B SER* 1.3 68.0 + - - +
34B TRP* 2.9 10.7 + - + +
35B LEU* 2.9 32.0 + - + +
92C VAL* 5.3 3.4 - - + -
96C ILE* 4.0 26.2 - - + -
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Residues in contact with SER 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 3.1 17.4 + - - -
29B VAL 3.5 2.7 - - - -
31B VAL* 1.3 77.2 - - - +
33B PHE* 1.3 63.6 + - - +
35B LEU* 3.3 9.6 + - - +
36B VAL* 3.0 26.5 + - - +
222B LEU* 3.8 20.6 + - - +
225B ASN* 2.7 36.7 + - - +
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 2.9 44.2 + - + -
30B GLY* 3.6 8.5 - - - +
32B SER* 1.3 75.9 - - - +
34B TRP* 1.3 59.3 + - - +
36B VAL* 3.5 2.7 - - - +
37B THR* 2.7 34.5 + - - -
76B TYR* 3.7 20.0 - + - -
79B MET* 3.6 26.7 - - + -
80B ARG* 3.6 31.0 - - + -
83B TRP* 4.0 22.4 - + + -
90B PRO* 4.3 6.5 - - + -
94B ARG* 3.6 22.4 - - - -
221B ASN* 4.1 5.8 - - - -
225B ASN* 3.4 21.5 - - - +
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Residues in contact with TRP 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.0 14.7 - - + +
30B GLY 3.1 13.4 + - - +
31B VAL* 2.9 13.1 + - + +
33B PHE* 1.3 74.8 - - - +
35B LEU* 1.3 65.9 + - + +
37B THR* 3.2 6.8 + - - -
38B ALA* 3.0 21.5 + - + +
80B ARG* 3.6 36.0 - - - +
74C TRP* 6.0 1.8 - - + -
75C HIS* 2.9 33.5 + + - -
78C TYR* 3.7 37.9 - + - -
93C PHE* 3.5 30.5 - + - -
96C ILE* 3.4 26.0 - - + +
100C LEU* 4.8 0.9 - - + -
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 2.9 33.1 + - + +
32B SER* 3.7 8.1 - - - +
34B TRP* 1.3 76.1 - - - +
36B VAL* 1.3 57.8 + - - +
38B ALA* 3.2 5.6 + - - +
39B GLY* 2.9 24.4 + - - -
229B PHE* 4.8 6.1 - - + -
96C ILE* 3.7 35.9 - - + +
99C LEU* 3.8 27.4 - - + -
100C LEU* 3.7 30.7 - - + +
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B SER 3.0 19.4 + - - +
33B PHE* 3.5 3.6 - - - +
35B LEU* 1.3 73.9 - - - +
37B THR* 1.3 66.1 + - - +
39B GLY 4.2 0.9 - - - +
40B MET* 2.7 45.9 + - + +
76B TYR* 2.9 49.1 - - + +
225B ASN* 4.2 21.8 - - + +
229B PHE* 4.2 28.0 - - + +
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE 2.7 24.9 + - - -
34B TRP* 3.3 12.6 - - - -
36B VAL* 1.3 77.9 - - - +
38B ALA* 1.3 57.1 + - - +
40B MET* 3.4 2.4 + - - +
41B LEU* 3.1 22.2 + - - +
73B PHE* 3.4 35.1 - - + +
76B TYR* 3.5 27.4 + - + +
77B LEU* 3.9 23.9 - - + +
80B ARG* 4.7 4.0 - - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TRP* 3.0 13.2 + - + +
35B LEU 3.5 7.6 - - - +
36B VAL 3.1 0.2 - - - -
37B THR* 1.3 73.0 - - - +
39B GLY* 1.3 67.1 + - - +
41B LEU* 3.2 10.5 + - - +
42B ALA* 2.9 25.7 + - - +
73B PHE* 5.8 0.2 - - - -
71C ILE* 5.1 10.2 - - + +
75C HIS* 4.7 7.4 - - + -
100C LEU* 3.7 28.9 - - + -
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU 2.9 15.1 + - - -
36B VAL 3.1 3.6 + - - -
38B ALA* 1.3 76.3 - - - +
40B MET* 1.3 56.4 + - - +
42B ALA* 3.3 6.2 + - - +
43B ALA* 2.8 32.2 + - - +
229B PHE* 4.5 8.5 - - - -
233B ILE* 3.8 19.3 - - - +
100C LEU* 4.8 4.1 - - - +
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Residues in contact with MET 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 2.7 42.0 + - + +
37B THR* 3.7 5.2 - - - +
39B GLY* 1.3 70.4 - - - +
41B LEU* 1.3 64.9 + - - +
44B THR* 2.8 31.8 + - - -
69B THR* 3.1 54.4 - - + +
72B ALA* 3.8 18.4 - - + -
73B PHE* 3.7 16.8 - - - +
76B TYR* 4.6 7.0 - - + -
228B ASP 4.6 3.8 - - - +
232B LYS* 4.1 17.7 - - + -
233B ILE* 3.7 19.5 - - + -
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B THR 3.1 13.9 + - - +
38B ALA* 3.4 11.4 - - - +
40B MET* 1.3 74.9 - - - +
42B ALA* 1.3 62.8 + - - +
44B THR* 3.4 7.9 + - + -
45B VAL* 3.1 37.6 + - + +
73B PHE* 3.9 40.2 - - + -
71C ILE* 6.4 2.9 - - + -
74C TRP* 4.1 33.2 - - + +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA 2.9 20.1 + - - +
39B GLY* 3.6 7.0 - - - +
41B LEU* 1.3 73.0 - - - +
43B ALA* 1.3 58.5 + - - +
45B VAL* 3.3 6.1 + - - +
46B PHE* 2.9 29.4 + - - +
67C LEU* 3.7 22.4 - - + +
71C ILE* 4.0 25.6 - - + -
104C LEU* 5.9 1.6 - - + -
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLY 2.8 21.3 + - - +
40B MET 3.8 0.4 - - - +
42B ALA* 1.3 69.4 - - - +
44B THR* 1.3 61.2 + - - +
46B PHE* 3.1 8.9 + - - +
47B PHE* 2.8 47.7 + - + -
69B THR* 3.7 21.5 - - + -
233B ILE* 3.9 22.4 - - + -
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Residues in contact with THR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET 2.8 24.4 + - - -
41B LEU* 3.5 9.3 - - + -
43B ALA* 1.3 72.4 - - - +
45B VAL* 1.3 66.2 + - + +
47B PHE* 4.0 1.0 - - - +
48B PHE* 3.1 43.5 + - + -
66B GLY* 3.4 18.8 - - - +
69B THR* 2.7 26.1 + - - -
70B GLY* 3.0 17.9 + - - -
73B PHE* 4.9 0.9 - - - +
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.1 24.4 + - + +
42B ALA* 3.3 7.8 + - - +
44B THR* 1.3 82.0 - - + +
46B PHE* 1.3 59.7 + - - +
48B PHE* 3.2 3.9 + - - +
49B VAL* 2.9 43.9 + - + +
48C PHE* 3.6 34.5 - - + -
67C LEU* 3.6 9.2 - - + -
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA 2.9 14.6 + - - +
43B ALA* 3.4 11.9 - - - +
45B VAL* 1.3 75.8 - - - +
47B PHE* 1.3 72.8 + + - +
49B VAL* 4.1 0.2 - - - +
50B GLU* 3.0 43.5 + - + +
237B LEU* 3.6 26.9 - - + -
240B TRP* 3.7 49.1 - + - -
60C THR* 4.4 12.8 - - + -
63C THR* 3.7 27.1 - - + -
64C VAL* 4.6 10.1 - - + -
67C LEU* 3.8 17.3 - - + -
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Residues in contact with PHE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ALA* 2.8 35.8 + - + +
46B PHE* 1.3 92.8 - + - +
48B PHE* 1.3 64.1 + - - +
50B GLU* 3.6 1.8 + - - -
51B ARG* 3.4 20.5 + - - +
62B LEU* 3.7 41.4 - - + +
65B SER* 3.8 23.1 - - - -
66B GLY* 3.8 7.4 - - - +
69B THR* 3.7 24.5 - - + -
232B LYS 4.4 2.9 - - - -
233B ILE* 3.8 8.1 - - + -
236B GLY* 3.4 42.6 - - - -
237B LEU* 3.6 11.7 - - + -
240B TRP* 4.6 0.9 - - + -
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.6 31.4 - - + -
49A VAL* 4.0 26.5 - - + -
44B THR* 3.1 40.9 + - + +
45B VAL* 3.8 4.3 - - - +
47B PHE* 1.3 77.1 - - - +
49B VAL* 1.3 64.5 + - + +
51B ARG* 3.3 26.2 + - - +
63B THR* 3.9 23.1 - - + -
66B GLY* 3.6 32.8 - - - -
67B LEU* 3.8 7.0 - - + -
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 2.9 33.7 + - + +
46B PHE 4.1 2.0 - - - +
48B PHE* 1.3 77.4 - - + +
50B GLU* 1.3 58.3 + - - +
51B ARG 3.1 5.7 + - - -
52B ASP* 3.2 21.3 + - - +
48C PHE* 4.2 15.0 - - + +
51C ARG* 3.3 44.4 + - - +
63C THR* 3.6 11.2 - - + +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 3.0 34.4 + - + +
47B PHE 4.0 4.0 - - - +
48B PHE 3.3 0.2 - - - -
49B VAL* 1.3 72.9 - - - +
51B ARG* 1.3 59.1 + - - +
52B ASP* 3.0 7.4 - - - -
53B GLN* 3.0 30.8 + - - +
54B VAL* 3.9 10.0 - - - +
62B LEU* 4.3 2.0 - - - -
240B TRP* 2.9 38.7 + - + +
51C ARG* 3.0 16.5 + - - -
60C THR* 2.7 32.0 + - - -
63C THR* 2.9 26.7 + - + +
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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