Contacts of the helix formed by residues 33 - 54 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ASP* 3.3 19.4 + - - +
32E ASP* 1.3 77.0 - - - +
34E LEU* 1.3 64.3 + - - +
35E ILE 3.3 2.7 - - - -
36E GLU* 3.3 29.6 + - + +
37E TYR* 2.9 43.2 + - + +
116E GLN* 3.0 16.3 + - - +
121E ARG* 6.0 1.6 - - - +
201E ASN* 4.3 21.0 + - - +
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Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E ASP* 3.1 15.9 + - - +
33E LYS* 1.3 78.2 - - - +
35E ILE* 1.3 63.0 + - - +
37E TYR* 3.2 4.5 + - - +
38E ASP* 2.9 33.7 + - - +
109E ALA 5.0 0.2 - - - +
112E ALA* 3.8 10.5 - - + +
113E GLU* 3.8 41.1 - - + +
116E GLN* 3.6 17.1 + - + -
120E ARG* 5.5 0.9 - - - +
889E GLN* 3.5 24.5 - - + +
890E GLY* 4.6 12.8 - - - -
893E LEU* 3.7 23.3 - - + -
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Residues in contact with ILE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ASP* 4.0 9.4 - - - +
20E LEU* 3.7 32.8 - - + +
21E ARG* 3.8 42.0 - - + +
24E VAL* 4.4 9.4 - - + -
32E ASP* 4.6 4.4 + - - +
33E LYS* 3.3 0.6 - - - +
34E LEU* 1.3 77.5 - - + +
36E GLU* 1.3 62.8 + - - +
38E ASP* 3.5 5.8 + - - +
39E ALA* 3.0 23.4 + - - +
889E GLN* 5.1 7.9 - - - +
893E LEU* 3.7 35.9 - - + -
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Residues in contact with GLU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ASP* 4.8 5.4 - - - +
21E ARG* 5.3 2.6 - - - +
33E LYS* 3.3 36.1 + - + +
34E LEU 3.3 0.8 - - - -
35E ILE* 1.3 79.4 - - - +
37E TYR* 1.3 59.5 + - - +
39E ALA* 3.5 5.6 + - + +
40E LEU* 2.8 47.6 + - + +
201E ASN* 3.5 20.7 + - - -
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Residues in contact with TYR 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E LYS* 2.9 40.6 + - + -
34E LEU* 3.5 7.4 - - - +
36E GLU* 1.3 77.2 - - - +
38E ASP* 1.3 66.8 + - - +
40E LEU* 3.0 15.7 + - + +
41E LEU* 3.1 18.9 + - - +
112E ALA* 3.7 31.6 - - + -
115E VAL* 3.8 24.6 - - + +
116E GLN* 4.0 21.3 - - + -
119E HIS* 6.0 1.2 - - - +
197E LEU* 3.8 26.7 + - + -
198E THR* 5.2 3.1 - - - +
201E ASN* 3.5 40.5 - - - +
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Residues in contact with ASP 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 4.2 18.5 - - + +
34E LEU* 2.9 23.9 + - - +
35E ILE* 3.7 5.3 - - - +
37E TYR* 1.3 75.2 - - - +
39E ALA* 1.3 64.9 + - - +
41E LEU* 3.2 2.3 + - - +
42E VAL* 2.9 31.7 + - - +
108E LEU 6.2 0.2 - - - -
109E ALA* 3.6 27.5 - - - +
112E ALA* 3.3 21.5 - - - +
893E LEU* 4.0 27.3 - - - +
897E TYR* 4.7 6.8 + - - +
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Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ILE* 4.6 9.2 - - - -
17E ASP* 3.6 41.1 - - - +
20E LEU* 4.6 2.6 - - + +
35E ILE 3.0 18.1 + - - +
36E GLU* 3.8 4.7 - - + +
38E ASP* 1.3 76.8 - - - +
40E LEU* 1.3 62.2 + - - +
43E ASP* 2.9 39.6 + - - +
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Residues in contact with LEU 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E GLU* 2.8 42.2 + - + +
37E TYR* 3.0 8.0 + - + +
39E ALA* 1.3 76.5 - - - +
41E LEU* 1.3 61.8 + - - +
43E ASP* 4.2 0.8 - - - +
44E ARG* 3.1 65.1 + - - +
197E LEU* 3.8 24.9 - - + -
200E LEU* 4.7 13.5 - - + -
201E ASN* 4.5 11.2 - - - +
217E LEU* 5.0 2.5 - - + -
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E TYR 3.1 17.4 + - - +
38E ASP* 4.1 2.7 - - - +
40E LEU* 1.3 73.3 - - - +
42E VAL* 1.3 62.5 + - + +
44E ARG* 3.4 3.1 + - - +
45E PHE* 2.9 27.4 + - - +
108E LEU* 3.8 34.6 - - + +
111E LEU* 5.3 1.1 - - + -
112E ALA* 3.8 18.4 - - + +
193E ILE* 3.8 19.1 - - + -
197E LEU* 3.8 32.1 - - + -
217E LEU* 3.7 32.8 - - + -
221E ILE* 4.0 11.1 - - + +
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Residues in contact with VAL 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 3.7 20.6 - - + -
38E ASP* 2.9 24.8 + - + +
39E ALA 4.5 0.2 - - - +
41E LEU* 1.3 73.5 - - - +
43E ASP* 1.3 67.7 + - - +
45E PHE* 3.1 6.6 + - - +
46E LEU* 2.9 41.1 + - + +
105E MET* 3.9 44.0 - - + +
108E LEU* 4.7 6.7 - - + -
109E ALA* 5.3 2.2 - - + +
897E TYR* 3.7 20.2 - - + +
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Residues in contact with ASP 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E HIS 4.8 0.5 - - - +
15E SER* 2.4 33.8 + - - -
16E ILE* 3.1 30.1 + - - +
17E ASP* 4.6 0.5 - - - +
39E ALA* 2.9 27.8 + - - +
40E LEU* 4.2 3.1 - - - +
42E VAL* 1.3 77.4 - - - +
44E ARG* 1.3 66.5 + - + +
46E LEU* 3.6 6.8 + - - +
47E ASN* 3.2 31.8 + - - +
58E ARG* 4.4 5.2 + - - +
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Residues in contact with ARG 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU* 3.1 47.5 + - - +
41E LEU 3.4 3.5 + - - +
42E VAL 3.2 0.2 - - - -
43E ASP* 1.3 79.8 - - + +
45E PHE* 1.3 65.1 + - - +
47E ASN* 3.3 12.1 + - - +
48E ILE* 3.0 30.2 + - + +
200E LEU* 5.3 3.9 - - - +
214E ASP* 2.5 45.3 + - - -
217E LEU* 3.9 24.2 - - - +
218E GLN* 4.4 19.6 - - + +
221E ILE* 4.4 9.2 - - + -
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Residues in contact with PHE 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU 2.9 15.3 + - - +
42E VAL* 3.1 8.5 + - - +
44E ARG* 1.3 76.2 - - - +
46E LEU* 1.3 64.1 + - + +
48E ILE* 3.1 9.2 + - + +
49E LEU* 2.8 40.1 + - + +
101E SER* 3.8 37.0 - - - -
104E HIS* 4.0 10.5 - - + -
105E MET* 3.6 31.0 - - + -
108E LEU* 3.8 18.8 - - + -
221E ILE* 4.0 23.5 - - + +
225E PHE* 3.7 38.8 - + + -
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Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 4.0 22.2 - - + -
42E VAL* 2.9 39.2 + - + +
43E ASP* 4.0 4.5 - - - +
45E PHE* 1.3 82.3 - - + +
47E ASN* 1.3 57.8 + - - +
49E LEU* 3.6 7.8 - - + +
50E GLN* 2.9 23.7 + - - +
58E ARG* 3.2 42.9 - - + +
61E VAL* 3.5 31.9 - - + -
62E GLN* 4.0 17.5 - - + +
105E MET* 4.7 10.5 - - + -
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Residues in contact with ASN 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ASP* 3.2 17.9 + - - +
44E ARG* 3.6 14.6 - - - +
45E PHE 3.2 0.6 - - - -
46E LEU* 1.3 74.8 - - - +
48E ILE* 1.3 59.7 + - + +
50E GLN* 3.4 4.5 + - - +
51E ASP* 2.9 29.7 + - - +
58E ARG* 3.2 28.2 + - - +
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Residues in contact with ILE 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ARG 3.0 20.5 + - - +
45E PHE* 3.4 8.7 - - + +
47E ASN* 1.3 75.3 - - + +
49E LEU* 1.3 58.1 + - - +
51E ASP* 3.2 8.1 + - + +
52E LEU* 3.0 39.2 + - + +
218E GLN* 3.3 39.5 - - + +
221E ILE* 3.6 26.0 - - + -
222E GLN* 3.7 39.7 - - + +
225E PHE* 4.9 6.7 - - + -
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Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E PHE* 2.8 28.0 + - + +
46E LEU* 3.6 11.4 - - + +
48E ILE* 1.3 78.1 - - - +
50E GLN* 1.3 57.5 + - - +
52E LEU* 3.1 4.7 + - - -
53E HIS* 2.8 50.8 + - + +
54E GLY 4.4 0.4 - - - +
57E LEU* 3.5 28.9 - - + -
58E ARG* 3.9 10.8 - - - +
61E VAL* 3.6 30.7 - - + -
97E LEU* 4.6 1.6 - - + -
101E SER* 4.3 17.3 - - - +
225E PHE* 4.6 10.8 - - + -
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Residues in contact with GLN 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LYS* 3.2 32.4 + - - +
46E LEU 2.9 15.0 + - - +
47E ASN* 3.8 5.6 - - - +
49E LEU* 1.3 77.2 - - - +
51E ASP* 1.3 60.2 + - - +
54E GLY* 3.0 30.4 + - - -
55E PRO* 3.9 25.3 - - + +
58E ARG* 2.5 41.4 + - + +
927E LYS* 4.5 4.0 + - - -
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Residues in contact with ASP 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E ASN 2.9 18.1 + - - +
48E ILE* 3.2 10.0 + - - +
50E GLN* 1.3 77.7 - - - +
52E LEU* 1.3 67.9 + - - +
54E GLY 4.8 0.2 - - - -
222E GLN* 5.0 7.1 + - - +
927E LYS* 4.9 8.1 + - - +
427F GLY 5.4 1.6 - - - +
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Residues in contact with LEU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ILE* 3.0 34.1 + - + +
49E LEU* 3.9 0.7 - - - +
51E ASP* 1.3 89.4 - - - +
53E HIS* 1.3 79.2 + - + +
54E GLY 3.9 0.2 - - - -
222E GLN* 3.9 11.9 - - + +
225E PHE* 4.0 14.6 - - + -
226E ARG* 3.8 39.9 - - - +
927E LYS* 4.1 13.9 - - - +
928E GLU 5.1 1.7 + - - -
427F GLY* 3.3 31.4 - - - +
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Residues in contact with HIS 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU* 2.8 37.6 + - + +
52E LEU* 1.3 91.9 + - + +
54E GLY* 1.3 60.5 + - - +
57E LEU* 4.2 12.4 - - + +
97E LEU* 3.7 29.3 - - + +
225E PHE* 4.2 11.2 - + - -
226E ARG* 4.7 12.9 + - - -
925E LEU 3.8 3.6 - - - +
926E SER* 3.1 32.6 + - - +
927E LYS* 2.8 30.8 + - - +
928E GLU 4.4 12.1 - - - -
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Residues in contact with GLY 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU 4.4 0.3 - - - +
50E GLN* 3.0 25.7 + - - -
52E LEU 3.9 0.6 - - - -
53E HIS* 1.3 80.6 - - - +
55E PRO* 1.3 76.5 - - - +
56E SER 3.4 2.9 + - - -
57E LEU* 3.6 2.2 + - - +
58E ARG 3.3 15.6 + - - -
925E LEU 5.4 0.9 - - - -
927E LYS* 3.7 15.5 - - - +
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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