Contacts of the helix formed by residues 35 - 57 (chain E) in PDB entry 1MA1
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 35 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ILE* 2.9 30.4 + - + +
34E GLN* 1.3 89.0 + - + +
36E HIS* 1.3 61.4 + - + +
38E GLN* 3.6 3.2 - - - +
39E ALA* 3.0 27.7 + - - +
178F ASN* 3.7 42.8 - - + +
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Residues in contact with HIS 36 (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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31E ILE 3.5 12.8 + - - -
32E HIS* 3.4 17.6 + - + +
35E LYS* 1.3 73.8 - - + +
37E HIS* 1.3 68.0 + - - +
38E GLN 3.0 1.1 - - - -
39E ALA* 2.8 20.8 + - - +
40E TYR* 3.2 23.5 + - + -
170E HIS* 3.2 52.2 + + + +
169F GLU* 3.9 7.0 - - - -
173F TYR* 2.8 30.4 + + - -
178F ASN* 3.6 25.9 - - + +
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Residues in contact with HIS 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 3.6 13.4 - - + +
11E PRO* 3.5 28.2 - - + +
32E HIS 3.1 8.8 + - - +
33E HIS* 3.1 18.4 + - - +
36E HIS* 1.3 77.4 - - - +
38E GLN* 1.3 62.3 + - - +
40E TYR* 3.2 17.8 + + - +
41E VAL* 3.2 9.9 + - + +
76E GLY 4.6 0.7 - - - -
77E TYR* 3.5 40.9 + + - -
80E HIS* 3.5 25.7 + + + +
81E LEU* 4.0 4.9 - - - -
84E TRP* 2.9 31.3 + + - +
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Residues in contact with GLN 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 3.4 33.4 - - - +
33E HIS 3.5 4.7 + - - +
34E GLN 3.1 28.1 - - - +
35E LYS 3.6 3.6 - - - +
36E HIS 3.0 0.2 - - - -
37E HIS* 1.3 79.8 - - - +
39E ALA* 1.3 62.2 - - - +
41E VAL* 3.2 17.6 + - - +
42E ASP* 2.9 58.8 + - - +
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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
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35E LYS 3.0 15.2 + - - +
36E HIS* 2.8 21.3 + - - +
38E GLN* 1.3 71.1 - - - +
40E TYR* 1.3 61.7 + - + +
42E ASP* 3.7 8.6 - - - +
43E GLY* 2.8 26.7 + - - -
73E HIS* 4.0 4.5 + - - +
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Residues in contact with TYR 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 HIS* 3.2 30.2 + - + +
37E HIS* 3.7 8.3 - + - +
38E GLN 3.2 0.2 - - - -
39E ALA* 1.3 79.0 - - + +
41E VAL* 1.3 61.7 + - - +
44E ALA* 2.9 33.3 + - - +
72E PHE* 3.9 17.5 - + - -
73E HIS* 3.4 38.6 - + - +
76E GLY* 3.9 8.1 - - - -
77E TYR* 3.7 9.4 - - - +
80E HIS* 3.3 37.7 - + - -
151E HIS* 3.1 23.3 + + - -
168E TRP* 3.6 10.6 - - - -
170E HIS* 3.3 22.6 - + - -
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Residues in contact with VAL 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E TYR* 3.6 19.7 - - - +
9E GLU* 3.9 5.4 - - - -
10E LEU* 3.7 26.2 - - + +
37E HIS* 3.2 15.6 + - + +
38E GLN* 3.2 19.0 + - - +
40E TYR* 1.3 76.7 - - - +
42E ASP* 1.3 65.9 + - - +
44E ALA* 3.9 1.6 - - - +
45E ASN* 3.0 49.2 + - - +
77E TYR* 3.9 23.7 - - + +
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Residues in contact with ASP 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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38E GLN* 2.9 45.7 + - - +
39E ALA* 3.9 6.7 - - - +
41E VAL* 1.3 76.2 - - - +
43E GLY* 1.3 60.3 + - - +
45E ASN* 3.8 6.7 + - - +
46E ALA* 2.8 33.5 + - - +
49E ARG* 4.9 1.6 + - - +
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Residues in contact with GLY 43 (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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39E ALA 2.8 18.3 + - - -
42E ASP* 1.3 79.5 - - - +
44E ALA* 1.3 61.3 + - - +
46E ALA* 3.4 5.9 + - - +
47E LEU* 3.2 21.1 + - - +
69E GLU* 4.8 2.1 - - - +
73E HIS* 3.6 30.2 + - - -
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Residues in contact with ALA 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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8E TYR* 3.7 28.3 - - + -
40E TYR 2.9 17.7 + - - +
41E VAL 3.9 1.1 - - - +
43E GLY* 1.3 76.3 - - - +
45E ASN* 1.3 58.0 + - - +
47E LEU* 3.4 6.4 + - - +
48E LEU* 3.0 33.1 + - - +
70E LEU* 4.4 4.2 - - + +
73E HIS* 3.6 11.6 - - + +
74E VAL* 3.9 20.0 - - + +
77E TYR* 5.6 1.3 - - + -
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Residues in contact with ASN 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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7E PHE* 3.4 17.7 - - + +
8E TYR* 2.8 53.4 + - - +
41E VAL* 3.0 30.9 + - - +
42E ASP* 3.9 6.8 + - - +
43E GLY 3.2 0.2 - - - -
44E ALA* 1.3 72.5 - - - +
46E ALA* 1.3 66.6 + - - +
47E LEU 3.0 2.0 - - - -
48E LEU* 3.1 6.8 + - - +
49E ARG* 2.9 46.1 + - - +
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Residues in contact with ALA 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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42E ASP 2.8 18.7 + - - +
43E GLY* 3.4 6.0 + - - +
45E ASN* 1.3 76.5 - - - +
47E LEU* 1.3 56.7 + - - +
49E ARG* 3.5 23.5 + - - +
50E LYS* 3.0 26.6 + - - +
69E GLU* 6.2 0.2 - - - +
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Residues in contact with LEU 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 GLY 3.2 13.1 + - - +
44E ALA* 3.7 5.2 - - - +
45E ASN 3.0 0.6 - - - -
46E ALA* 1.3 78.5 - - - +
48E LEU* 1.3 65.5 + - - +
50E LYS* 3.2 25.8 + - + +
51E LEU* 3.0 30.0 + - + +
66E ALA* 3.2 43.5 - - + +
69E GLU* 3.9 22.9 - - + +
70E LEU* 3.2 37.7 - - + +
73E HIS* 5.5 0.9 - - - +
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Residues in contact with LEU 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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140C THR* 4.7 0.2 - - + -
142C ARG* 3.9 36.4 + - - +
144C PHE* 3.8 28.3 - - + -
6E LYS 4.4 2.9 - - - +
7E PHE* 4.1 11.7 - - + -
8E TYR* 4.0 26.7 - - + -
44E ALA 3.0 19.8 + - - +
45E ASN* 3.5 14.1 - - - +
47E LEU* 1.3 76.7 - - - +
49E ARG* 1.3 56.6 + - - +
51E LEU* 3.2 11.8 + - + +
52E ASP* 2.9 33.6 + - - +
70E LEU* 4.4 12.6 - - + -
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Residues in contact with ARG 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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7E PHE* 3.7 27.0 - - + -
42E ASP 4.9 1.6 + - - -
45E ASN* 2.9 35.0 + - - +
46E ALA* 3.5 29.7 - - - +
48E LEU* 1.3 74.1 - - - +
50E LYS* 1.3 60.5 + - - +
52E ASP* 3.2 8.1 + - - +
53E GLU* 2.8 40.5 + - - +
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Residues in contact with LYS 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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46E ALA 3.0 14.3 + - - +
47E LEU* 3.3 28.5 - - + +
49E ARG* 1.3 78.3 - - - +
51E LEU* 1.3 63.7 + - + +
53E GLU* 3.3 10.7 + - - +
54E ALA* 3.1 22.5 + - - +
61E VAL* 4.8 20.6 - - + +
62E ASP* 5.9 4.0 - - - +
66E ALA* 5.4 6.3 - - - +
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Residues in contact with LEU 51 (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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118C GLU* 5.4 4.7 - - - +
47E LEU* 3.0 30.3 + - + +
48E LEU* 3.7 11.2 - - + +
50E LYS* 1.3 75.7 - - + +
52E ASP* 1.3 65.0 + - - +
54E ALA* 3.4 4.9 + - - +
55E ARG* 3.1 60.2 + - - +
61E VAL* 4.1 24.5 - - + -
63E ILE* 5.5 1.8 - - + -
66E ALA* 4.1 22.9 - - + -
67E LEU* 4.7 19.3 - - + -
70E LEU* 5.1 9.0 - - + -
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Residues in contact with ASP 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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108C ASP 4.8 0.5 - - - +
142C ARG* 2.7 35.2 + - - -
5E LYS* 3.5 31.2 + - + +
7E PHE* 4.5 6.1 - - - -
48E LEU 2.9 17.5 + - - +
49E ARG* 3.5 11.1 - - - +
51E LEU* 1.3 73.4 - - - +
53E GLU* 1.3 65.7 + - - +
55E ARG* 3.1 17.5 + - - +
56E GLU* 2.9 41.1 + - - +
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Residues in contact with GLU 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 ARG* 2.8 28.6 + - - +
50E LYS* 3.6 8.8 - - - +
52E ASP* 1.3 73.2 - - - +
54E ALA* 1.3 61.7 + - - +
56E GLU* 3.2 16.3 + - - +
57E SER* 3.0 27.3 + - - -
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Residues in contact with ALA 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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114C ARG* 3.8 7.3 + - - +
50E LYS 3.1 11.9 + - - +
51E LEU* 3.8 4.5 - - - +
52E ASP 3.2 0.4 - - - -
53E GLU* 1.3 77.3 - - - +
55E ARG* 1.3 57.6 - - - +
57E SER* 3.8 0.2 - - - -
58E ASP* 2.9 6.2 + - - -
59E THR* 2.8 51.3 + - - +
61E VAL* 3.2 35.4 - - + -
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Residues in contact with ARG 55 (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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108C ASP* 2.8 35.7 + - - +
109C PHE* 3.5 37.1 - - - +
110C GLY* 5.7 2.3 - - - -
114C ARG* 3.6 16.7 - - - +
118C GLU* 3.0 42.5 + - - +
142C ARG* 5.2 3.8 - - - +
143C LEU 5.6 3.6 + - - -
145C ILE* 6.0 0.4 - - - +
5E LYS* 6.2 0.2 - - - +
51E LEU* 3.1 44.5 + - - +
52E ASP* 3.1 21.2 + - - +
54E ALA* 1.3 76.3 - - - +
56E GLU* 1.3 65.8 + - + +
58E ASP* 3.2 12.9 + - - +
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Residues in contact with GLU 56 (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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5E LYS* 5.1 9.3 - - - +
52E ASP* 2.9 27.6 + - + +
53E GLU* 3.8 17.3 - - - +
55E ARG* 1.3 77.9 - - + +
57E SER* 1.3 60.1 + - - +
58E ASP* 3.2 2.5 + - - +
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Residues in contact with SER 57 (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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53E GLU 3.0 16.9 + - - -
54E ALA* 3.8 0.3 - - - -
56E GLU* 1.3 76.4 - - - +
58E ASP* 1.3 68.4 + - - +
59E THR* 2.7 41.3 + - - +
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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
------------------------------------------------------------
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