Contacts of the helix formed by residues 43 - 63 (chain A) in PDB entry 1M12
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 LEU 43 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 4.8 13.7 - - + -
6A GLU* 3.3 32.8 - - + +
7A VAL* 4.6 9.9 - - + +
36A CYS* 5.0 1.1 - - - -
39A LEU* 4.6 20.2 - - + -
40A PRO* 3.3 19.6 + - + +
41A LYS 3.1 0.4 - - - -
42A SER* 1.3 94.2 - - - +
44A SER* 1.3 70.3 + - - +
46A GLU* 2.9 25.1 - - - +
47A CYS* 3.4 14.4 + - - +
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A CYS* 3.9 15.1 - - - -
39A LEU 5.7 0.4 - - - -
40A PRO 3.7 5.6 + - - -
41A LYS* 3.3 28.0 + - - -
42A SER 3.5 0.2 - - - -
43A LEU* 1.3 78.3 - - - +
45A GLU* 1.3 76.0 + - - +
47A CYS* 2.7 30.7 - - - -
48A GLN* 3.3 2.1 + - - +
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS 5.8 0.7 - - - +
44A SER* 1.3 87.1 + - - +
46A GLU* 1.3 74.5 + - + +
47A CYS 2.8 6.3 + - - -
48A GLN* 2.9 22.1 + - - +
49A GLU* 3.2 15.9 + - - +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.9 26.5 - - + +
4A TYR* 4.0 28.7 - - + +
7A VAL* 5.0 8.5 - - + -
42A SER 3.2 19.1 - - - +
43A LEU* 2.9 35.5 - - - +
45A GLU* 1.3 82.2 + - + +
47A CYS* 1.3 59.1 + - - +
49A GLU* 3.7 3.5 + - - +
50A VAL* 2.9 31.3 + - - +
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Residues in contact with CYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.2 22.6 - - + +
11A LEU* 5.5 1.8 - - + -
36A CYS* 2.0 53.6 - - + -
39A LEU* 4.7 6.3 - - + -
43A LEU 3.4 6.9 + - - +
44A SER* 2.7 15.0 + - - +
45A GLU 2.9 0.8 - - - -
46A GLU* 1.3 79.5 - - - +
48A GLN* 1.3 77.7 + - - +
50A VAL* 3.0 1.0 + - - -
51A VAL* 2.6 46.9 + - + +
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A CYS* 5.8 3.4 - - - +
44A SER* 4.3 3.1 - - - +
45A GLU* 2.9 19.6 + - - +
47A CYS* 1.3 89.2 - - - +
49A GLU* 1.3 65.3 + - + +
51A VAL* 4.7 1.8 - - - +
52A ASP* 2.4 72.2 + - - +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 4.8 12.8 - - + +
45A GLU* 3.2 11.6 + - + +
46A GLU* 4.0 8.7 - - - +
47A CYS 3.1 0.6 - - - -
48A GLN* 1.3 84.2 - - + +
50A VAL* 1.3 58.1 + - + +
52A ASP* 4.7 2.2 - - - +
53A THR* 2.8 47.2 + - - +
54A TYR* 4.2 1.2 - - - -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.6 29.6 - - + +
7A VAL* 4.5 10.5 - - + -
8A CYS* 5.0 6.1 - - + -
11A LEU* 3.9 21.3 - - + -
46A GLU 2.9 23.5 + - - +
47A CYS* 3.0 6.5 + - - +
49A GLU* 1.3 77.6 - - - +
51A VAL* 1.3 57.7 + - - +
54A TYR* 2.6 43.8 + - + +
58A ILE* 4.2 15.3 - - + -
77A LEU* 4.3 20.6 - - + -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.6 36.3 - - + -
32A PHE* 3.2 50.8 - - + +
35A MET* 6.5 0.2 - - + -
36A CYS* 5.9 1.8 - - + +
47A CYS* 2.6 34.8 + - + +
48A GLN* 4.7 0.9 - - - +
50A VAL* 1.3 73.3 - - - +
52A ASP* 1.3 66.0 + - - +
54A TYR 5.1 0.2 - - - -
55A GLY* 2.7 32.5 + - - +
58A ILE* 5.9 0.7 - - - -
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLN* 2.4 66.2 + - - +
49A GLU* 4.4 2.2 - - - +
51A VAL* 1.3 81.3 - - - +
53A THR* 1.3 62.0 + - - +
55A GLY 4.3 1.4 + - - -
56A SER 5.7 0.3 + - - -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 2.8 33.7 + - - -
52A ASP* 1.3 79.4 - - - +
54A TYR* 1.3 86.3 + - + +
55A GLY 3.5 1.4 + - - -
56A SER 5.3 0.7 + - - -
57A SER* 4.4 2.8 + - - -
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Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU 4.2 3.4 - - - -
50A VAL* 2.6 29.9 + - + +
53A THR* 1.3 99.1 - - + +
55A GLY* 1.3 57.4 + - - +
56A SER 3.7 0.4 - - - -
57A SER* 3.3 21.8 - - - +
58A ILE* 3.0 40.6 + - + +
75A LEU* 4.3 23.3 + - + -
77A LEU* 3.7 38.1 - - + +
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 5.1 2.5 - - - -
32A PHE* 4.1 20.4 - - - -
51A VAL* 2.7 27.7 + - - -
52A ASP 4.3 1.4 + - - -
53A THR 3.5 3.0 - - - -
54A TYR* 1.3 71.0 - - - +
56A SER* 1.3 66.9 + - - +
57A SER 3.1 1.1 - - - -
58A ILE* 4.1 2.5 - - - +
59A LEU* 3.2 26.7 + - - +
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 5.3 9.0 - - - +
52A ASP 5.7 0.4 + - - -
53A THR 5.3 0.6 + - - -
55A GLY* 1.3 74.7 - - - +
57A SER* 1.3 55.2 + - - +
59A LEU* 3.8 5.6 - - - +
60A SER* 2.4 39.8 + - - -
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A THR 4.4 2.1 + - - -
54A TYR* 3.3 34.9 + - - +
56A SER* 1.3 77.7 - - - +
58A ILE* 1.3 72.1 + - - +
60A SER* 3.0 11.3 + - - -
61A ILE* 2.9 25.5 + - - +
75A LEU* 4.4 11.4 - - - +
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A CYS* 4.8 13.2 - - - -
11A LEU* 4.7 15.9 - - + -
12A VAL* 4.4 10.8 - - + +
15A VAL* 5.5 6.1 - - + -
32A PHE* 6.2 3.8 - - + -
50A VAL* 4.2 17.7 - - + -
51A VAL* 5.9 0.4 - - - -
54A TYR* 3.0 32.1 + - + +
55A GLY* 4.1 3.1 - - - +
57A SER* 1.3 82.8 + - - +
59A LEU* 1.3 66.7 + - - +
60A SER 3.0 1.0 + - - -
61A ILE* 3.1 14.4 + - - +
62A LEU* 3.2 30.6 + - + +
71A VAL* 4.2 15.4 - - + +
75A LEU* 3.8 22.7 - - + -
77A LEU* 5.6 0.7 - - + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 4.7 9.6 - - + -
19A ILE* 5.2 1.1 - - + -
25A GLU* 3.4 38.4 - - + +
28A ILE* 4.2 33.0 - - + -
29A LEU* 3.4 29.6 - - + -
32A PHE* 5.1 6.5 - - + -
55A GLY 3.2 16.2 + - - +
56A SER* 4.2 3.8 - - - +
58A ILE* 1.3 81.5 - - - +
60A SER* 1.3 61.9 + - - +
62A LEU* 3.9 9.1 + - + +
63A LEU* 3.3 30.6 + - + +
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A SER* 2.4 30.1 + - - -
57A SER* 3.0 7.8 + - - -
59A LEU* 1.3 77.9 - - - +
61A ILE* 1.3 66.2 + - - +
63A LEU* 3.5 17.2 + - - +
64A GLU* 3.8 12.5 + - - +
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A SER* 2.9 20.8 + - - +
58A ILE* 3.7 7.0 - - - +
60A SER* 1.3 75.3 - - - +
62A LEU* 1.3 57.2 + - - +
63A LEU 3.0 2.2 - - - -
64A GLU* 2.6 38.9 + - + +
66A VAL* 3.9 22.7 + - + -
71A VAL* 4.1 13.0 - - + -
74A MET* 3.6 32.5 - - + -
75A LEU* 3.8 27.6 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.7 12.1 - - + -
15A VAL* 3.5 26.5 - - + -
16A THR* 3.9 28.0 - - + -
19A ILE* 3.9 20.1 - - + +
58A ILE* 3.2 37.1 + - + +
59A LEU* 3.9 9.0 - - - +
61A ILE* 1.3 79.0 - - - +
63A LEU* 1.3 63.1 + - + +
64A GLU 3.3 0.3 + - - -
65A GLU* 3.5 10.9 + - - -
66A VAL 4.4 10.6 + - - +
68A PRO* 4.7 11.7 - - + -
71A VAL* 4.6 8.5 - - + +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.5 18.6 - - + -
25A GLU* 4.6 19.3 - - + +
59A LEU* 3.3 29.6 - - + +
60A SER* 3.8 10.5 - - - +
61A ILE 2.8 1.0 + - - -
62A LEU* 1.3 81.8 - - + +
64A GLU* 1.3 62.6 + - + +
65A GLU* 3.0 17.4 + - - +
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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