Contacts of the helix formed by residues 47 - 70 (chain A) in PDB entry 1IL0
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 THR 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASP 4.5 0.2 - - - -
46A GLN* 1.3 84.7 - - + +
48A GLU* 1.3 61.4 + - - +
49A ASP* 3.5 11.7 + - - +
50A ILE* 2.9 40.6 + - + +
51A LEU* 3.3 26.0 + - - +
92A THR* 4.0 6.5 - - - -
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Residues in contact with GLU 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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47A THR* 1.3 72.7 - - - +
49A ASP* 1.3 62.1 + - - +
51A LEU* 3.6 13.8 - - - +
52A ALA* 2.8 32.5 + - + +
90A THR* 4.1 16.3 + - - -
91A SER* 5.8 1.0 - - - -
92A THR* 4.1 15.4 - - + +
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Residues in contact with ASP 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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47A THR* 3.4 9.9 + - - +
48A GLU* 1.3 76.9 + - - +
50A ILE* 1.3 66.9 + - + +
52A ALA* 3.2 8.3 + - - +
53A LYS* 2.9 24.8 + - - +
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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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45A ASP* 3.3 38.1 - - + +
46A GLN* 4.1 7.2 - - + +
47A THR* 2.9 44.6 + - + +
48A GLU 3.2 0.2 - - - -
49A ASP* 1.3 76.7 - - + +
51A LEU* 1.3 57.9 + - - +
53A LYS* 3.1 10.0 + - + +
54A SER* 2.9 35.9 + - - +
350A NAD 4.0 17.0 - - - +
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Residues in contact with LEU 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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43A LEU* 3.3 38.3 - - + +
44A VAL 4.1 0.2 - - - -
45A ASP* 3.7 23.1 - - + +
47A THR 3.3 9.5 + - - +
48A GLU* 3.3 17.7 + - - +
50A ILE* 1.3 78.7 - - - +
52A ALA* 1.3 57.5 + - - +
54A SER* 3.7 5.2 - - - +
55A LYS* 3.0 33.1 + - - +
90A THR* 4.0 18.5 - - + +
91A SER* 3.6 22.4 - - - +
92A THR* 3.6 31.2 - - + -
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Residues in contact with ALA 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 GLU* 2.8 22.5 + - + +
49A ASP* 3.4 10.5 - - - +
51A LEU* 1.3 72.9 - - - +
53A LYS* 1.3 58.4 + - - +
55A LYS* 4.0 2.8 - - - +
56A LYS* 3.0 30.2 + - - +
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Residues in contact with LYS 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 ASP 2.9 13.2 + - - +
50A ILE* 3.1 11.2 + - + +
52A ALA* 1.3 75.6 - - - +
54A SER* 1.3 59.3 - - - +
56A LYS* 3.2 13.0 + - + +
57A GLY* 2.8 27.0 + - - -
293A LYS 4.5 14.6 + - - -
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Residues in contact with SER 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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23A GLY* 2.7 34.1 + - - -
28A ALA* 4.6 5.6 - - - +
43A LEU* 4.1 20.2 - - - -
50A ILE* 2.9 24.9 + - - +
51A LEU* 3.7 6.7 - - - +
53A LYS* 1.3 76.7 - - - +
55A LYS* 1.3 57.8 + - - +
57A GLY* 2.9 5.5 + - - -
58A ILE* 2.8 31.7 + - - +
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Residues in contact with LYS 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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43A LEU* 4.9 2.9 - - + +
51A LEU 3.0 16.9 + - - +
52A ALA* 4.4 2.9 - - - +
54A SER* 1.3 76.4 - - - +
56A LYS* 1.3 62.8 + - - +
58A ILE* 3.7 13.4 - - + +
59A GLU* 3.1 21.3 + - - +
85A LEU* 3.0 43.6 + - + +
86A SER* 4.9 2.4 + - - +
88A ILE* 2.8 32.9 + - + +
89A ALA* 5.0 0.8 - - - +
90A THR* 4.0 24.6 - - + +
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Residues in contact with LYS 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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52A ALA 3.0 20.7 + - - +
53A LYS* 3.3 13.2 - - + +
55A LYS* 1.3 77.6 - - - +
57A GLY* 1.3 58.1 + - - +
59A GLU* 3.0 32.3 + - + +
60A GLU* 3.0 33.9 + - - +
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Residues in contact with GLY 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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28A ALA* 6.1 0.2 - - - -
53A LYS 2.8 15.1 + - - -
54A SER* 3.4 4.3 - - - -
56A LYS* 1.3 74.0 - - - +
58A ILE* 1.3 64.1 + - - +
60A GLU* 3.1 13.0 + - - +
61A SER* 3.0 22.9 + - - -
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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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28A ALA* 3.3 43.3 - - + +
31A ALA* 4.3 1.8 - - + -
32A GLN* 3.6 32.3 - - + +
43A LEU* 4.1 18.8 - - + -
54A SER 2.8 17.0 + - - +
55A LYS* 3.7 12.8 - - - +
56A LYS 3.3 0.2 - - - -
57A GLY* 1.3 75.0 - - - +
59A GLU* 1.3 57.3 + - - +
61A SER* 3.4 3.0 + - - -
62A LEU* 3.0 30.9 + - + +
85A LEU* 4.2 9.6 - - + -
88A ILE* 4.1 28.5 - - + -
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Residues in contact with GLU 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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55A LYS 3.1 11.5 + - - +
56A LYS* 3.0 21.2 + - - +
58A ILE* 1.3 75.5 - - - +
60A GLU* 1.3 68.1 + - - +
62A LEU* 3.0 4.7 + - - +
63A ARG* 2.8 65.1 + - + +
81A VAL* 4.4 0.9 - - + -
85A LEU* 3.6 33.7 - - + +
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Residues in contact with GLU 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 LYS* 3.0 53.9 + - - +
57A GLY* 3.1 10.5 + - - +
59A GLU* 1.3 88.6 - - - +
61A SER* 1.3 61.5 + - - +
63A ARG* 3.4 10.3 + - + +
64A LYS* 3.2 39.9 + - - +
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Residues in contact with SER 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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32A GLN* 2.9 33.0 + - - -
57A GLY 3.0 12.6 + - - -
58A ILE* 3.5 3.6 - - - -
59A GLU 3.1 0.2 - - - -
60A GLU* 1.3 78.3 - - - +
62A LEU* 1.3 58.9 + - - +
64A LYS* 3.5 14.8 + - - +
65A VAL* 3.1 23.4 + - - +
164A PRO* 4.2 1.6 - - - +
351A CAA 2.9 31.9 + - - -
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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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32A GLN* 3.7 28.3 - - + +
36A ALA* 5.0 1.8 - - + -
58A ILE* 3.0 25.1 + - + +
59A GLU* 3.0 5.6 + - - +
61A SER* 1.3 76.1 - - - +
63A ARG* 1.3 59.9 + - - +
65A VAL* 3.1 8.2 + - + +
66A ALA* 2.7 29.6 + - - +
80A PHE* 3.8 25.4 - - + -
81A VAL* 3.7 33.3 - - + +
84A THR* 3.6 29.4 - - + -
85A LEU* 3.8 19.5 - - + -
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Residues in contact with ARG 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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59A GLU* 2.8 53.3 + - + +
60A GLU* 3.7 9.4 - - + +
62A LEU* 1.3 76.7 - - - +
64A LYS* 1.3 56.2 + - + +
66A ALA* 3.0 6.9 + - - -
67A LYS* 2.7 59.6 + - + +
78A ASP* 3.9 25.9 + - - +
81A VAL* 3.8 31.7 - - - +
85A LEU* 5.4 1.4 - - - +
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Residues in contact with LYS 64 (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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60A GLU* 3.2 27.8 + - - +
61A SER* 3.6 12.9 - - - +
63A ARG* 1.3 77.2 - - + +
65A VAL* 1.3 63.5 + - + +
67A LYS* 3.7 6.2 + - - +
68A LYS* 3.1 47.5 + - - +
351A CAA 5.0 28.7 + - + +
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Residues in contact with VAL 65 (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 GLN* 4.7 7.0 - - - +
61A SER 3.1 17.0 - - - +
62A LEU* 3.1 13.6 + - + +
64A LYS* 1.3 76.9 - - - +
66A ALA* 1.3 52.6 + - - +
68A LYS* 3.3 6.3 + - - +
69A LYS* 2.8 57.6 + - + +
80A PHE* 4.2 19.5 - - + -
164A PRO* 6.0 0.9 - - + -
351A CAA 4.1 22.4 - - + +
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Residues in contact with ALA 66 (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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62A LEU 2.7 16.8 + - - +
63A ARG* 3.0 10.5 + - - +
65A VAL* 1.3 69.2 - - - +
67A LYS* 1.3 55.8 + - + +
68A LYS 2.8 11.6 + - - -
69A LYS 2.9 0.2 + - - -
70A PHE* 2.6 46.4 + - + -
77A GLY* 4.1 17.7 - - - +
80A PHE* 4.9 2.2 - - + -
81A VAL* 3.9 20.2 - - + -
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Residues in contact with LYS 67 (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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63A ARG* 2.7 43.9 + - + +
64A LYS* 4.1 6.7 - - - +
66A ALA* 1.3 72.2 - - + +
68A LYS* 1.3 61.7 + - + +
70A PHE 4.7 3.1 - - - -
71A ALA* 4.1 17.1 - - - +
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Residues in contact with LYS 68 (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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64A LYS* 3.1 35.9 + - - +
65A VAL* 3.3 3.8 + - - +
66A ALA 2.8 1.8 + - - -
67A LYS* 1.3 81.2 - - + +
69A LYS* 1.3 65.1 + - - +
70A PHE 3.6 0.4 - - - -
71A ALA* 4.5 8.7 + - - +
351A CAA 3.3 63.8 + - + +
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Residues in contact with LYS 69 (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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65A VAL* 2.8 33.0 + - + +
68A LYS* 1.3 81.0 - - + +
70A PHE* 1.3 92.1 + - + +
71A ALA 3.7 1.5 + - - -
80A PHE* 4.8 16.2 - - - -
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Residues in contact with PHE 70 (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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66A ALA* 2.6 28.1 + - - +
67A LYS* 5.1 1.3 - - - -
69A LYS* 1.3 115.7 - - + +
71A ALA* 1.3 60.9 + - - +
72A GLU 3.4 2.9 - - - +
73A ASN* 3.6 17.0 - - + +
74A PRO* 3.4 19.1 - - - +
76A ALA* 3.9 27.1 - - + -
77A GLY* 3.6 19.3 - - - -
80A PHE* 4.2 31.4 - + + -
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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
------------------------------------------------------------
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