Contacts of the helix formed by residues 33 - 54 (chain B) in PDB entry 6V3O
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 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASP* 3.7 26.5 + - - +
32B ASP* 1.3 75.3 - - - +
34B LEU* 1.3 64.6 + - - +
35B ILE 3.3 2.9 - - - -
36B GLU* 3.1 27.2 + - - +
37B TYR* 2.9 55.9 + - + +
116B GLN* 2.9 9.8 + - - +
201B ASN* 4.8 16.6 - - - +
203B LYS* 5.9 8.5 - - - +
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 3.1 15.5 + - - +
33B LYS* 1.3 77.0 - - - +
35B ILE* 1.3 58.7 + - + +
37B TYR* 3.2 7.4 + - + +
38B ASP* 2.9 37.2 + - - +
109B ALA 4.9 0.2 - - - +
112B ALA* 3.8 9.6 - - + +
113B GLU* 3.7 46.4 - - + +
116B GLN* 3.5 17.3 + - + -
120B ARG* 5.9 0.9 - - - +
889B GLN* 3.6 24.7 - - + +
890B GLY* 4.7 7.9 - - - -
893B LEU* 3.7 24.9 - - + -
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Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASP* 3.9 10.3 - - - +
20B LEU* 3.8 37.3 - - + +
21B ARG* 3.6 49.1 - - - +
24B VAL* 4.3 20.0 - - + +
26B GLY 5.8 1.1 - - - +
32B ASP* 4.7 2.1 + - - +
33B LYS 3.3 0.4 - - - -
34B LEU* 1.3 76.9 - - + +
36B GLU* 1.3 59.1 + - - +
38B ASP* 3.7 6.5 - - - +
39B ALA* 3.0 28.2 + - - +
889B GLN* 5.5 4.3 - - - +
893B LEU* 4.3 21.8 - - + -
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Residues in contact with GLU 36 (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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17B ASP* 4.6 9.9 - - - +
21B ARG* 3.4 25.5 + - - +
32B ASP 5.7 1.1 - - - +
33B LYS* 3.1 30.8 + - + +
35B ILE* 1.3 75.2 - - + +
37B TYR* 1.3 61.6 + - + +
39B ALA* 3.9 2.1 - - - +
40B LEU* 2.9 38.8 + - + +
201B ASN* 5.6 3.1 + - - -
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Residues in contact with TYR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 2.9 49.3 + - + +
34B LEU* 3.2 11.2 + - - +
36B GLU* 1.3 76.4 - - + +
38B ASP* 1.3 65.7 + - - +
40B LEU* 3.0 20.7 + - + +
41B LEU* 3.0 17.9 + - - +
112B ALA* 3.7 30.5 - - + -
115B VAL* 3.9 21.9 - - + +
116B GLN* 4.3 14.8 - - + -
197B LEU* 3.6 23.4 + - + -
198B THR* 5.6 2.1 - - - -
201B ASN* 3.1 39.0 + - - +
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.4 3.6 - - + -
20B LEU* 3.6 23.0 - - + +
34B LEU* 2.9 27.4 + - - +
35B ILE 3.7 0.7 - - - +
37B TYR* 1.3 72.7 - - - +
39B ALA* 1.3 62.9 + - - +
41B LEU* 4.0 2.8 - - - +
42B VAL* 3.1 31.7 + - + +
108B LEU 6.2 0.2 - - - -
109B ALA* 3.7 26.8 - - - +
112B ALA* 3.3 21.9 - - - +
893B LEU* 3.9 29.2 - - - +
897B TYR* 4.8 4.4 + - - +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 4.5 0.2 - - - +
16B ILE* 3.8 14.3 - - + +
17B ASP* 3.7 36.6 - - + +
20B LEU* 4.3 0.8 - - + +
35B ILE 3.0 17.4 + - - +
36B GLU 3.9 3.1 - - - +
38B ASP* 1.3 76.2 - - - +
40B LEU* 1.3 64.3 + - - +
43B ASP* 2.9 41.7 + - - +
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Residues in contact with LEU 40 (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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36B GLU* 2.9 30.1 + - + +
37B TYR* 3.0 13.4 + - + +
39B ALA* 1.3 78.3 - - - +
41B LEU* 1.3 62.0 + - - +
43B ASP* 4.9 0.7 - - - -
44B ARG* 3.2 68.3 + - - +
197B LEU* 4.3 20.9 - - + -
200B LEU* 5.1 13.2 - - + -
201B ASN* 4.6 13.9 - - - +
217B LEU* 5.4 0.9 - - + -
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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 TYR 3.0 15.0 + - - +
38B ASP* 4.2 2.7 - - - +
40B LEU* 1.3 76.9 - - - +
42B VAL* 1.3 59.7 + - + +
44B ARG* 3.3 5.5 + - - +
45B PHE* 2.9 25.8 + - - +
108B LEU* 3.7 42.9 - - + +
111B LEU* 5.2 1.1 - - + -
112B ALA* 3.8 20.0 - - + +
193B ILE* 3.9 27.4 - - + -
197B LEU* 3.6 31.2 - - + -
217B LEU* 4.0 15.3 - - + -
221B ILE* 3.8 11.4 - - + +
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Residues in contact with VAL 42 (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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16B ILE* 3.8 17.9 - - + -
38B ASP* 3.1 18.5 + - + +
41B LEU* 1.3 75.9 - - + +
43B ASP* 1.3 62.4 + - - +
45B PHE* 3.5 5.1 - - - +
46B LEU* 2.8 37.6 + - + +
105B MET* 3.6 57.4 - - + +
108B LEU* 4.4 10.5 - - + -
109B ALA* 5.2 2.5 - - - +
897B TYR* 4.1 16.6 - - - +
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Residues in contact with ASP 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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14B HIS 4.9 0.7 - - - +
15B SER* 3.1 29.3 + - - -
16B ILE* 3.1 30.9 + - - +
39B ALA* 2.9 31.9 + - - +
40B LEU* 4.1 2.4 - - - +
42B VAL* 1.3 76.7 - - - +
44B ARG* 1.3 68.2 + - - +
46B LEU* 3.4 7.2 + - - +
47B ASN* 3.2 31.7 + - - +
58B ARG* 5.1 3.8 + - - +
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Residues in contact with ARG 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 LEU* 3.2 52.8 + - - +
41B LEU 3.6 4.5 - - - +
42B VAL 3.2 0.6 - - - -
43B ASP* 1.3 81.0 - - - +
45B PHE* 1.3 66.6 + - - +
47B ASN* 3.4 11.2 + - + +
48B ILE* 3.1 29.3 + - + +
200B LEU* 5.3 2.6 - - - +
214B ASP* 3.0 40.5 + - - -
217B LEU* 3.7 28.1 - - - +
218B GLN* 3.9 22.7 - - + +
221B ILE* 4.2 10.1 - - + -
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Residues in contact with PHE 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 2.9 15.3 + - - +
42B VAL* 3.1 7.4 + - - +
44B ARG* 1.3 77.4 - - - +
46B LEU* 1.3 65.4 + - + +
48B ILE* 3.0 8.0 + - + +
49B LEU* 2.8 42.6 + - + +
101B SER* 3.8 46.0 - - - -
104B HIS* 3.8 12.8 - - + -
105B MET* 3.8 18.4 - - + -
108B LEU* 3.8 19.7 - - + -
221B ILE* 4.0 24.0 - - + +
225B PHE* 3.7 36.1 - + + -
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Residues in contact with LEU 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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16B ILE* 3.8 26.2 - - + -
42B VAL* 2.8 30.4 + - + +
43B ASP* 3.9 4.3 - - - +
45B PHE* 1.3 75.3 - - + +
47B ASN* 1.3 58.0 + - - +
49B LEU* 3.2 10.2 + - + +
50B GLN 2.8 23.6 + - - -
58B ARG* 3.2 48.3 - - + +
61B VAL* 4.0 25.8 - - + -
62B GLN* 3.7 24.9 - - + +
105B MET* 4.1 11.4 - - + -
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Residues in contact with ASN 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 ASP* 3.2 18.8 + - - +
44B ARG* 3.7 11.9 - - - +
45B PHE 3.2 0.2 - - - -
46B LEU* 1.3 72.9 - - - +
48B ILE* 1.3 65.7 + - + +
50B GLN* 3.2 3.9 + - - +
51B ASP* 2.9 37.3 + - - +
58B ARG* 2.6 35.6 + - - +
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Residues in contact with ILE 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 ARG 3.1 18.4 + - - +
45B PHE* 3.0 8.6 + - + +
47B ASN* 1.3 75.8 - - + +
49B LEU* 1.3 63.0 + - - +
51B ASP* 3.4 8.1 + - - +
52B LEU* 3.1 34.0 + - + +
218B GLN* 3.4 39.9 - - + +
221B ILE* 3.7 25.4 - - + -
222B GLN* 3.8 36.3 - - + +
225B PHE* 5.0 6.3 - - + -
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Residues in contact with LEU 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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45B PHE* 2.8 29.3 + - + +
46B LEU* 3.3 15.5 - - + +
47B ASN 3.2 0.2 - - - -
48B ILE* 1.3 77.6 - - - +
50B GLN* 1.3 57.0 + - - +
52B LEU* 3.3 2.1 + - - +
53B HIS* 2.9 36.2 + - + +
54B GLY 3.8 1.0 + - - +
57B LEU* 3.9 21.1 - - + -
58B ARG* 4.1 16.4 - - - -
61B VAL* 4.1 23.3 - - + -
97B LEU* 5.2 0.7 - - + -
101B SER* 3.8 25.8 - - - +
225B PHE* 3.9 26.9 - - + -
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Residues in contact with GLN 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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12B LYS 3.5 16.4 + - - +
46B LEU 2.8 19.0 + - - +
47B ASN* 3.2 6.9 + - - +
49B LEU* 1.3 74.2 - - - +
51B ASP* 1.3 64.7 + - - +
54B GLY* 2.8 32.2 + - - -
55B PRO* 3.8 34.5 - - + +
58B ARG* 3.2 35.8 + - + +
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASN* 2.9 24.8 + - - +
48B ILE* 4.0 7.4 - - - +
50B GLN* 1.3 85.4 + - - +
52B LEU* 1.3 65.3 + - + +
928B GLU* 5.0 1.9 - - - +
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Residues in contact with LEU 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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427A GLY* 3.6 25.6 - - - +
428A ASP* 4.4 3.6 - - - +
48B ILE* 3.1 33.7 + - + +
49B LEU* 4.1 0.7 - - - +
51B ASP* 1.3 84.0 - - + +
53B HIS* 1.3 70.3 + - + +
54B GLY 3.9 0.2 - - - -
222B GLN* 3.9 11.7 - - + +
225B PHE* 3.9 19.5 - - + -
226B ARG* 3.8 34.3 - - - +
927B LYS* 5.4 0.2 - - - +
928B GLU* 3.0 46.2 - - - +
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Residues in contact with HIS 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 LEU* 2.9 23.1 + - + +
52B LEU* 1.3 92.7 + - + +
54B GLY* 1.3 62.6 + - - +
57B LEU* 3.5 22.3 - - + +
97B LEU* 3.6 30.7 - - + +
225B PHE* 4.3 7.2 - + - -
226B ARG* 3.9 20.0 + - - -
925B LEU 4.4 1.7 - - - +
926B SER* 3.2 26.0 + - - +
927B LYS* 3.3 29.7 + - - +
928B GLU* 4.3 16.5 + - + +
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Residues in contact with GLY 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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49B LEU 4.5 0.2 - - - +
50B GLN* 2.8 23.5 + - - -
51B ASP 5.1 0.2 + - - -
52B LEU 3.9 0.6 - - - -
53B HIS* 1.3 80.1 - - - +
55B PRO* 1.3 76.0 - - - +
56B SER 3.4 2.2 - - - -
57B LEU* 3.4 4.1 + - - +
58B ARG 3.3 15.9 + - - -
925B LEU 5.9 0.2 - - - -
927B LYS* 4.7 13.0 - - - -
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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) + - + + + + + -
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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