Contacts of the helix formed by residues 40 - 62 (chain A) in PDB entry 2DOB
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU 3.8 1.0 - - - +
39A PRO* 1.3 82.7 - - + +
41A PRO* 1.3 72.3 - - + +
42A ASN* 2.6 37.9 + - - +
43A MSE 3.0 41.4 + - + +
44A SER* 2.9 23.1 + - - -
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Residues in contact with PRO 41 (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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39A PRO 4.2 3.8 - - - +
40A LYS* 1.3 87.4 - - + +
42A ASN* 1.3 59.2 + - + +
44A SER* 2.6 23.8 + - - +
45A ALA* 2.9 18.0 + - - +
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Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 2.6 38.7 + - - +
41A PRO* 1.3 78.2 - - + +
43A MSE 1.3 68.5 + - - +
45A ALA* 3.4 8.2 + - - +
46A SER* 3.0 27.7 + - - -
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Residues in contact with MSE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.0 24.0 - - + -
38A LEU* 3.2 28.8 - - + +
39A PRO* 3.3 24.5 - - + -
40A LYS* 3.0 64.7 + - + +
42A ASN* 1.3 84.6 + - - +
44A SER* 1.3 67.2 + - - +
46A SER* 3.0 10.0 + - - -
47A CYS 2.9 18.9 + - - -
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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
----------------------------------------------------------
35A CYS* 3.4 29.2 - - - +
36A ASP* 4.4 11.2 + - - -
38A LEU* 3.9 11.8 - - - +
40A LYS 2.9 9.9 + - - -
41A PRO* 2.6 30.3 + - - +
43A MSE 1.3 75.5 - - - +
45A ALA* 1.3 55.3 + - - +
47A CYS* 3.2 3.5 + - - +
48A LYS* 3.0 38.1 + - - +
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Residues in contact with ALA 45 (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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41A PRO 2.9 17.9 + - - +
42A ASN* 3.6 8.5 - - - +
43A MSE 3.2 0.2 - - - -
44A SER* 1.3 78.7 + - - +
46A SER* 1.3 61.3 + - - +
48A LYS* 3.2 12.1 + - - +
49A GLU* 3.1 20.6 + - - +
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Residues in contact with SER 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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2A LEU* 4.1 14.7 - - - +
6A ILE* 4.2 3.6 - - - +
42A ASN 3.0 14.5 + - - -
43A MSE 3.0 17.5 + - - -
45A ALA* 1.3 74.0 - - - +
47A CYS* 1.3 66.3 + - - +
49A GLU* 3.2 14.5 - - - +
50A ILE* 3.1 28.2 + - - +
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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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6A ILE* 3.8 29.4 - - + -
10A VAL* 5.6 1.3 - - - -
35A CYS* 2.0 48.5 - - + -
38A LEU* 3.5 19.5 - - + -
43A MSE 2.9 13.6 + - - +
44A SER 3.3 7.4 - - - +
46A SER* 1.3 78.2 + - - +
48A LYS* 1.3 61.4 + - - +
50A ILE* 3.2 3.5 + - - +
51A VAL* 3.0 29.1 + - - +
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Residues in contact with LYS 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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32A GLU* 3.4 42.7 - - + +
35A CYS* 3.7 17.3 - - + -
36A ASP* 2.8 32.7 + - - -
44A SER* 3.0 23.3 + - - +
45A ALA* 3.2 10.5 + - - +
47A CYS* 1.3 76.9 - - - +
49A GLU* 1.3 55.8 + - - +
51A VAL* 3.4 5.4 + - - +
52A ASP* 2.9 30.5 + - - +
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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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45A ALA 3.1 11.9 + - - +
46A SER* 3.2 19.1 - - - +
47A CYS 3.2 0.4 - - - -
48A LYS* 1.3 73.4 - - - +
50A ILE* 1.3 80.1 + - + +
52A ASP* 3.8 5.2 - - - +
53A SER* 2.8 41.4 + - - -
54A TYR* 4.4 8.7 - - - -
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Residues in contact with ILE 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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3A PRO* 3.7 38.8 - - + +
6A ILE* 3.9 30.7 - - + -
7A CYS* 4.8 8.3 - - - +
10A VAL* 5.2 4.7 - - + -
46A SER* 3.1 16.4 + - - +
47A CYS 3.6 6.7 - - - +
49A GLU* 1.3 93.4 - - + +
51A VAL* 1.3 59.5 + - - +
54A TYR* 2.7 56.5 + - + +
58A ILE* 6.2 0.9 - - + -
78A LEU* 4.7 11.0 - - + -
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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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10A VAL* 3.9 26.9 - - + -
28A LEU* 4.1 20.9 - - + +
31A LEU* 4.0 26.9 - - + +
32A GLU* 4.3 13.0 - - + +
35A CYS* 3.7 19.1 - - - -
47A CYS* 3.0 19.0 + - - +
48A LYS* 3.7 8.5 - - - +
50A ILE* 1.3 77.4 - - + +
52A ASP* 1.3 58.5 + - - +
55A LEU* 2.9 42.6 + - + +
56A PRO* 3.9 0.5 - - - +
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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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28A LEU* 4.8 13.8 - - - +
32A GLU* 4.9 10.0 + - - +
48A LYS 2.9 18.2 + - - +
49A GLU* 3.9 6.1 - - - +
51A VAL* 1.3 80.6 - - - +
53A SER* 1.3 65.5 + - - +
56A PRO* 3.8 14.9 - - - +
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Residues in contact with SER 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 38.3 + - - -
52A ASP* 1.3 80.5 + - - +
54A TYR* 1.3 79.3 + - - +
56A PRO* 4.6 6.3 - - - +
57A VAL* 4.7 4.3 - - - +
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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* 4.4 11.2 - - - -
50A ILE* 2.7 41.5 + - + +
53A SER* 1.3 90.9 - - - +
55A LEU* 1.3 65.5 + - - +
56A PRO* 3.3 2.7 - - - -
57A VAL* 3.0 14.6 - - + +
58A ILE* 2.9 37.3 + - + +
76A LEU* 4.1 28.1 + - + -
78A LEU* 4.0 34.4 - - + +
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Residues in contact with LEU 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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10A VAL* 4.1 11.4 - - + +
14A ALA* 4.1 9.4 - - + -
24A GLU 4.4 1.6 - - - +
27A ILE* 4.1 15.3 - - + -
28A LEU* 3.7 28.5 - - + +
31A LEU* 3.9 27.6 - - + -
50A ILE 4.0 0.4 + - - -
51A VAL* 2.9 31.8 + - + +
54A TYR* 1.3 71.4 - - - +
56A PRO* 1.3 69.8 - - + +
58A ILE* 3.1 10.2 + - + +
59A LEU* 2.9 53.1 + - + +
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Residues in contact with PRO 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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28A LEU* 4.3 8.1 - - + -
51A VAL 3.9 0.4 - - - +
52A ASP 3.8 20.0 - - - +
53A SER 4.6 5.2 - - - +
54A TYR 3.6 1.8 - - - -
55A LEU* 1.3 102.4 - - + +
57A VAL* 1.3 61.2 + - - +
59A LEU* 3.3 9.3 + - + +
60A ASP* 3.3 26.4 + - - +
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Residues in contact with VAL 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 SER 4.7 3.8 - - - +
54A TYR* 3.0 33.7 - - + +
56A PRO* 1.3 78.5 - - - +
58A ILE* 1.3 67.8 + - + +
60A ASP* 3.1 11.5 + - + +
61A ILE* 2.9 37.4 + - + +
76A LEU* 4.3 20.6 - - + -
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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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7A CYS* 4.5 7.0 - - - -
10A VAL* 3.8 24.7 - - + -
11A VAL* 4.0 35.4 - - + -
14A ALA* 4.7 1.3 - - + -
50A ILE* 6.2 0.9 - - + -
54A TYR* 2.9 34.3 + - + +
55A LEU* 3.1 13.7 + - + +
57A VAL* 1.3 79.0 - - - +
59A LEU* 1.3 63.8 + - - +
61A ILE* 3.1 7.7 + - - +
62A ILE* 2.9 42.8 + - + +
72A VAL* 4.5 3.8 - - + -
76A LEU* 3.9 23.6 - - + -
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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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14A ALA* 4.2 16.4 - - + -
18A LEU* 4.1 16.4 - - + +
24A GLU* 3.6 50.0 - - + +
27A ILE* 4.2 10.8 - - + -
55A LEU* 2.9 39.4 + - + +
56A PRO* 3.6 10.8 - - + +
57A VAL 3.2 0.2 - - - -
58A ILE* 1.3 77.1 - - - +
60A ASP* 1.3 63.4 + - - +
62A ILE* 3.6 25.5 - - + +
63A LYS* 3.1 24.9 - - - +
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Residues in contact with ASP 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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24A GLU* 5.3 0.3 - - - +
56A PRO* 3.3 13.5 + - - +
57A VAL* 3.1 15.7 + - + +
59A LEU* 1.3 78.4 - - - +
61A ILE* 1.3 65.9 + - + +
63A LYS* 3.4 38.3 + - - +
64A GLY* 4.0 1.9 + - - -
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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 VAL* 2.9 30.9 + - + +
58A ILE* 3.1 6.7 + - - +
60A ASP* 1.3 77.7 - - + +
62A ILE* 1.3 58.6 + - - +
63A LYS 3.1 0.2 - - - -
64A GLY* 2.9 21.7 + - - -
66A MSE 3.2 50.3 + - + +
72A VAL* 4.1 17.3 - - + +
75A ALA* 5.4 2.0 - - + -
76A LEU* 3.9 32.1 - - + -
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Residues in contact with ILE 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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11A VAL* 4.5 4.9 - - + +
14A ALA* 4.3 13.9 - - + -
15A GLY* 4.5 9.0 - - - +
18A LEU* 3.5 32.1 - - + -
58A ILE* 2.9 29.7 + - + +
59A LEU* 3.6 22.2 - - + +
61A ILE* 1.3 71.5 - - - +
63A LYS* 1.3 59.3 + - + +
64A GLY 3.0 11.9 + - - +
66A MSE 3.3 7.6 - - - +
67A SER* 3.9 38.2 - - - +
72A VAL* 4.1 11.7 - - + -
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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