Contacts of the helix formed by residues 42 - 65 (chain B) in PDB entry 6CKX
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B GLN* 3.9 0.7 - - - -
40B GLY 3.5 4.7 + - - +
41B LEU* 1.3 75.0 - - - +
43B PRO* 1.3 77.1 - - + +
44B ALA* 4.1 11.6 + - - +
45B THR* 2.8 39.3 + - - -
46B GLU* 3.0 10.0 + - - +
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Residues in contact with PRO 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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32B ALA* 6.4 3.4 - - + -
37B GLN* 3.4 29.3 - - - +
42B ASP* 1.3 91.9 - - + +
44B ALA* 1.3 56.4 + - - +
46B GLU* 3.7 2.5 - - + +
47B ALA* 2.8 31.0 + - - +
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Residues in contact with ALA 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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42B ASP* 3.2 11.4 - - - +
43B PRO* 1.3 79.5 - - - +
45B THR* 1.3 58.6 - - - +
47B ALA* 3.1 7.1 + - - +
48B ARG* 2.9 29.6 + - - +
51B ARG* 5.1 0.7 + - - -
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Residues in contact with THR 45 (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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41B LEU* 4.1 14.8 - - + -
42B ASP* 2.8 25.4 + - - -
44B ALA* 1.3 78.6 - - - +
46B GLU* 1.3 55.9 + - - +
48B ARG* 3.4 19.9 + - - +
49B TYR* 2.8 63.7 + - + +
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Residues in contact with GLU 46 (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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34B THR* 2.9 34.9 + - - +
36B SER* 3.8 14.1 + - - -
37B GLN* 2.9 26.5 + - - +
41B LEU* 4.0 13.2 - - + +
42B ASP 3.0 7.9 + - - +
43B PRO* 3.8 6.3 - - + +
44B ALA 3.2 0.2 - - - -
45B THR* 1.3 77.1 - - - +
47B ALA* 1.3 58.9 + - - +
49B TYR* 3.2 4.4 + - - +
50B ARG* 2.9 60.6 + - - +
82B TYR 4.2 0.9 - - - +
87B PHE* 3.7 17.6 - - + -
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Residues in contact with ALA 47 (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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43B PRO 2.8 17.0 + - - +
44B ALA* 3.6 5.6 - - - +
46B GLU* 1.3 77.8 - - - +
48B ARG* 1.3 59.9 + - - +
50B ARG* 3.3 11.5 + - - +
51B ARG* 3.1 39.9 + - + +
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Residues in contact with ARG 48 (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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44B ALA 2.9 16.5 + - - +
45B THR* 3.7 26.3 + - - +
47B ALA* 1.3 74.7 - - - +
49B TYR* 1.3 87.2 + - - +
51B ARG* 3.2 31.3 + - - +
52B GLU* 2.9 58.5 + - + +
92B ARG* 4.3 4.4 - - - +
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Residues in contact with TYR 49 (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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41B LEU* 3.9 21.2 - - + +
45B THR* 2.8 43.6 + - + +
46B GLU 3.7 4.5 - - - +
48B ARG* 1.3 98.2 + - - +
50B ARG* 1.3 56.2 + - - +
52B GLU* 4.0 3.4 - - - -
53B GLY* 3.0 24.6 + - - -
78B PHE* 4.1 2.9 - - - -
87B PHE* 3.7 39.5 - + + -
92B ARG* 3.4 51.1 + - - +
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Residues in contact with ARG 50 (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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31B LEU 5.5 0.4 + - - -
34B THR* 4.1 3.4 - - - +
46B GLU* 2.9 45.3 + - - +
47B ALA* 3.5 13.0 - - - +
48B ARG 3.2 0.2 - - - -
49B TYR* 1.3 74.1 - - - +
51B ARG* 1.3 60.9 + - - +
53B GLY 3.4 0.3 + - - -
54B ALA* 3.0 30.1 + - - +
78B PHE* 3.8 12.3 - - + -
79B HIS* 3.2 53.0 + - + +
82B TYR* 3.4 26.8 + - - +
83B MET* 3.7 15.7 - - - -
87B PHE* 4.2 9.6 - - + -
194B CYS 4.1 6.9 - - - +
195B THR* 6.2 0.2 - - - +
196B THR* 3.8 25.7 - - - +
199B LEU* 4.0 9.3 - - - +
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Residues in contact with ARG 51 (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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44B ALA 5.1 0.6 + - - -
47B ALA* 3.1 37.6 + - - +
48B ARG* 3.6 35.6 + - - +
50B ARG* 1.3 72.9 - - - +
52B GLU* 1.3 61.6 + - + +
54B ALA* 3.3 0.5 + - - +
55B ARG* 2.9 63.3 + - - +
194B CYS* 3.9 26.0 - - + +
257B LEU* 4.2 22.7 - - + -
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Residues in contact with GLU 52 (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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48B ARG* 2.9 50.7 + - + +
49B TYR* 4.0 6.4 - - - +
51B ARG* 1.3 76.5 - - + +
53B GLY* 1.3 58.0 + - - +
55B ARG* 3.8 5.5 - - - +
56B PHE* 2.8 31.1 + - - +
92B ARG* 2.8 33.5 + - - +
93B TYR* 3.7 20.1 - - + +
128B GLN* 6.1 0.2 - - - -
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Residues in contact with GLY 53 (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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49B TYR 3.0 12.2 + - - -
52B GLU* 1.3 78.1 - - - +
54B ALA* 1.3 56.8 + - - +
56B PHE* 3.2 8.8 + - - +
57B ILE* 2.9 32.2 + - - +
78B PHE* 3.7 29.7 - - - -
92B ARG* 4.7 4.9 - - - +
93B TYR* 4.7 7.4 - - - -
96B GLY* 5.1 0.2 - - - -
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Residues in contact with ALA 54 (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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50B ARG 3.0 16.6 + - - +
51B ARG 3.9 2.5 - - - +
53B GLY* 1.3 71.2 - - - +
55B ARG* 1.3 67.3 + - - +
57B ILE* 3.1 8.1 + - - +
58B PHE* 2.9 22.1 + - - +
75B ILE* 3.7 26.0 - - + +
78B PHE* 4.3 3.1 - - + -
79B HIS* 4.4 3.6 - - + +
193B LEU 3.7 24.5 - - - +
194B CYS* 4.0 10.5 - - - -
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Residues in contact with ARG 55 (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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51B ARG* 2.9 54.5 + - - +
52B GLU* 4.0 4.5 - - - +
54B ALA* 1.3 76.1 - - - +
56B PHE* 1.3 53.3 + - - +
58B PHE* 3.1 9.2 + - + +
59B ASP* 2.7 49.8 + - - +
194B CYS* 3.4 31.5 - - - -
257B LEU* 4.4 15.6 + - - +
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Residues in contact with PHE 56 (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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52B GLU 2.8 20.2 + - - +
53B GLY 3.3 6.1 - - - +
54B ALA 3.1 0.2 - - - -
55B ARG* 1.3 75.4 - - - +
57B ILE* 1.3 66.2 + - - +
59B ASP* 3.2 6.3 + - + +
60B VAL* 2.9 49.5 + - + +
92B ARG 5.1 0.2 - - - -
93B TYR* 3.2 52.3 - + + -
96B GLY* 4.5 6.5 - - - -
97B ALA* 4.0 12.8 - - + -
120B ALA* 3.7 28.5 - - + -
123B LEU* 4.7 8.7 - - + -
124B LEU* 3.6 33.9 - - + -
132B PHE* 4.6 0.9 - + - -
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Residues in contact with ILE 57 (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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53B GLY 2.9 17.7 + - - +
54B ALA* 3.4 6.5 - - - +
56B PHE* 1.3 75.8 - - - +
58B PHE* 1.3 64.4 + - - +
60B VAL* 4.0 3.7 - - - +
61B GLY* 3.0 22.3 + - - -
71B LEU* 3.9 13.9 - - - +
74B GLY 3.8 12.8 - - - +
75B ILE* 3.7 24.0 - - + +
78B PHE* 3.7 31.0 - - + -
96B GLY* 3.6 34.5 - - - +
99B CYS* 4.5 0.2 - - + -
100B LEU* 4.1 23.3 - - + +
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Residues in contact with PHE 58 (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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54B ALA 2.9 12.7 + - - +
55B ARG* 3.4 13.0 - - + +
57B ILE* 1.3 78.1 - - - +
59B ASP* 1.3 66.2 + - - +
62B THR* 2.9 49.5 + - + -
68B TYR* 6.6 0.2 - - + -
71B LEU* 4.0 25.4 - - + +
75B ILE* 4.3 16.8 - - + -
161B TYR* 4.7 5.4 - - - -
190B ASN* 3.7 44.0 - - + -
193B LEU* 5.1 4.9 - - + -
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Residues in contact with ASP 59 (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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55B ARG* 2.7 31.5 + - - +
56B PHE* 3.8 6.0 + - + +
58B PHE* 1.3 83.2 - - - +
60B VAL* 1.3 56.9 + - - +
62B THR* 3.8 4.9 - - - -
63B ARG* 3.0 29.5 + - - +
123B LEU* 3.7 25.3 - - + +
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Residues in contact with VAL 60 (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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56B PHE* 2.9 56.8 + - + +
57B ILE* 4.0 1.8 - - - +
59B ASP* 1.3 70.3 - - - +
61B GLY* 1.3 58.6 + - - +
63B ARG 3.2 2.4 + - - -
64B LEU* 3.0 36.4 + - + +
97B ALA* 6.3 1.1 - - + -
100B LEU* 3.6 21.8 - - + -
116B ILE* 4.4 12.8 - - + +
119B THR* 3.6 20.1 - - + +
120B ALA* 4.1 8.3 - - + +
123B LEU* 3.7 16.2 - - + -
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Residues in contact with GLY 61 (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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57B ILE 3.0 7.7 + - - -
60B VAL* 1.3 75.9 - - - +
62B THR* 1.3 64.8 + - - +
64B LEU* 3.0 8.9 + - - -
66B LEU* 2.9 32.2 + - - +
71B LEU* 3.4 27.1 - - - -
100B LEU* 3.6 13.2 - - - +
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Residues in contact with THR 62 (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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58B PHE* 2.9 46.5 + - + -
59B ASP* 3.8 5.4 - - - -
61B GLY* 1.3 74.2 - - - +
63B ARG* 1.3 63.8 + - - +
65B GLY* 3.1 12.8 + - - -
66B LEU 4.5 6.5 - - - -
71B LEU* 3.7 8.3 - - - +
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Residues in contact with ARG 63 (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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59B ASP 3.0 18.3 + - - +
60B VAL 3.2 4.9 + - - +
62B THR* 1.3 78.2 - - - +
64B LEU* 1.3 59.9 + - - +
65B GLY 3.3 1.2 + - - -
119B THR* 3.7 22.6 - - + +
122B SER* 3.4 25.2 + - - -
123B LEU* 3.5 28.5 - - - +
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Residues in contact with LEU 64 (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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60B VAL* 3.0 36.4 + - + +
61B GLY 3.0 7.1 + - - +
63B ARG* 1.3 75.9 - - - +
65B GLY* 1.3 60.1 + - - +
66B LEU* 3.5 10.9 + - + -
100B LEU* 4.6 6.1 - - + -
111B LYS* 3.6 36.6 + - + -
115B ASP* 3.8 22.2 - - + +
116B ILE* 3.8 24.0 - - + -
119B THR* 3.2 22.7 - - - +
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Residues in contact with GLY 65 (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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61B GLY 3.1 2.4 + - - -
62B THR 3.1 12.7 + - - -
63B ARG 3.2 2.0 + - - -
64B LEU* 1.3 77.9 - - - +
66B LEU* 1.3 63.0 + - - +
67B HIS* 3.1 31.7 + - - -
111B LYS* 5.5 0.4 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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