Contacts of the helix formed by residues 55 - 72 (chain A) in PDB entry 1IL8
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 GLU 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR 4.4 5.7 - - - +
14A SER* 4.6 8.7 - - - -
52A ASP* 2.9 23.6 + - + +
53A PRO 3.9 5.9 - - - +
54A LYS* 1.3 84.6 - - + +
56A ASN* 1.3 66.4 + - - +
57A TRP* 3.2 45.6 + - + +
58A VAL* 3.2 15.3 + - + +
59A GLN* 3.5 5.5 + - - +
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Residues in contact with ASN 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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54A LYS 4.0 3.0 + - - +
55A GLU* 1.3 74.4 + - - +
57A TRP* 1.3 65.6 + - - +
58A VAL 3.0 1.6 + - - -
59A GLN* 3.0 25.0 + - - +
60A ARG* 3.2 12.4 + - - +
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Residues in contact with TRP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR 3.4 26.9 - - - -
14A SER* 4.9 0.6 - - - -
15A LYS 4.1 6.7 - - - -
16A PRO* 3.6 56.3 - - + +
17A PHE* 3.9 24.5 - + - -
51A LEU* 4.6 4.9 - - + -
52A ASP 5.7 0.4 - - - -
55A GLU* 3.2 36.5 + - + +
56A ASN* 1.3 80.7 - - - +
58A VAL* 1.3 87.0 + - + +
60A ARG* 3.7 8.7 - - - +
61A VAL* 3.0 38.4 + - + +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.9 7.6 - - + -
51A LEU* 3.9 25.4 - - + -
52A ASP 3.5 24.0 - - - +
53A PRO* 4.0 12.3 - - + -
55A GLU* 3.2 11.6 + - + +
56A ASN 3.0 1.0 - - - -
57A TRP* 1.3 117.9 - - + +
59A GLN* 1.3 61.4 + - - +
60A ARG 3.0 4.7 - - - -
61A VAL* 3.9 3.1 - - - -
62A VAL* 2.9 41.4 + - + +
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Residues in contact with GLN 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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53A PRO* 5.5 4.9 - - + +
55A GLU 3.5 6.1 + - - +
56A ASN* 3.0 19.2 + - - +
58A VAL* 1.3 82.8 - - - +
60A ARG* 1.3 57.5 + - - +
62A VAL* 4.6 2.9 - - - +
63A GLU* 2.9 30.5 + - + +
70B GLU* 4.1 21.7 + - - +
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Residues in contact with ARG 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 ASN 3.2 10.0 + - - +
57A TRP* 3.7 11.9 - - - +
58A VAL 3.0 0.4 - - - -
59A GLN* 1.3 77.4 - - - +
61A VAL* 1.3 70.3 + - + +
62A VAL 3.0 0.9 - - - -
63A GLU* 2.9 11.0 + - - +
64A LYS* 2.9 39.0 + - + +
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Residues in contact with VAL 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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16A PRO* 5.5 0.9 - - + -
17A PHE* 2.9 45.8 - - + +
19A PRO* 3.3 30.6 - - + +
22A ILE* 6.0 0.7 - - - +
51A LEU* 5.0 0.4 - - + -
57A TRP* 3.0 37.9 + - + +
58A VAL* 3.5 11.9 - - - +
60A ARG* 1.3 77.6 - - + +
62A VAL* 1.3 70.5 + - + +
64A LYS* 4.6 2.7 - - - -
65A PHE* 3.3 16.1 + - - +
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Residues in contact with VAL 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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25A LEU* 4.2 30.1 - - + -
39A ILE* 4.6 19.3 - - + -
51A LEU* 4.0 26.7 - - + -
58A VAL* 2.9 30.0 + - + +
59A GLN* 4.4 3.6 - - - +
60A ARG 3.0 0.6 - - - -
61A VAL* 1.3 85.6 - - + +
63A GLU* 1.3 66.6 + - - +
65A PHE* 3.1 15.3 + - - +
66A LEU* 3.2 20.3 + - + +
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Residues in contact with GLU 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 GLN* 2.9 24.1 + - + +
60A ARG* 2.9 12.4 + - - +
62A VAL* 1.3 81.4 - - - +
64A LYS* 1.3 63.6 - - + +
66A LEU* 3.2 12.9 + - + +
67A LYS* 3.0 25.6 + - + +
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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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18A HIS* 4.6 16.5 + - + +
19A PRO* 3.6 28.5 - - + -
60A ARG* 2.9 26.8 + - + +
61A VAL* 5.2 1.8 - - - -
63A GLU* 1.3 80.0 - - + +
65A PHE* 1.3 51.8 + - - +
67A LYS* 3.1 10.3 + - + +
68A ARG* 2.7 39.7 + - + +
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Residues in contact with PHE 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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19A PRO* 4.2 12.5 - - + +
22A ILE* 3.8 31.6 - - + -
23A LYS 3.7 22.2 - - - -
24A GLU 4.5 0.2 - - - -
25A LEU* 3.5 39.9 - - + -
61A VAL 3.3 11.2 + - - +
62A VAL* 3.1 12.9 + - - +
64A LYS* 1.3 80.2 - - - +
66A LEU* 1.3 63.1 + - + +
68A ARG* 3.6 4.2 - - + +
69A ALA* 2.8 32.9 + - + +
27B VAL* 4.0 25.6 - - + -
29B GLU* 3.2 38.4 - - + -
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Residues in contact with LEU 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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25A LEU* 5.1 8.1 - - + -
62A VAL* 3.2 22.1 + - + +
63A GLU* 3.2 12.3 + - + +
64A LYS 3.2 0.4 - - - -
65A PHE* 1.3 88.3 - - + +
67A LYS* 1.3 57.4 + - - +
69A ALA* 4.2 2.9 - - + +
70A GLU* 2.9 35.8 + - + +
25B LEU* 6.4 0.7 - - + -
27B VAL* 5.0 22.4 - - + -
39B ILE* 5.9 6.1 - - + -
66B LEU* 4.8 23.6 - - + -
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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 GLU* 3.0 19.5 + - + +
64A LYS* 3.7 13.7 - - + +
66A LEU* 1.3 78.8 - - - +
68A ARG* 1.3 57.1 + - - +
70A GLU* 3.9 8.8 - - - +
71A ASN* 3.2 27.7 + - - +
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Residues in contact with ARG 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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18A HIS* 5.5 9.3 - - - -
19A PRO* 6.0 5.6 - - + -
20A LYS* 5.7 12.1 - - - +
23A LYS* 6.2 0.2 - - - +
64A LYS 2.7 22.2 + - - +
65A PHE* 3.6 6.5 - - + +
67A LYS* 1.3 72.2 - - - +
69A ALA* 1.3 60.5 + - - +
70A GLU 3.1 1.1 - - - -
71A ASN* 3.9 3.2 - - - +
72A SER* 3.0 28.6 + - - -
29B GLU* 3.3 23.5 + - - +
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Residues in contact with ALA 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 PHE* 2.8 32.6 + - + +
66A LEU* 4.2 4.5 - - + +
68A ARG* 1.3 75.6 - - - +
70A GLU* 1.3 60.4 + - - +
72A SER* 3.8 5.7 + - - -
27B VAL* 4.7 6.5 - - + -
29B GLU* 4.0 24.2 - - + +
37B THR* 2.5 49.5 + - + +
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Residues in contact with GLU 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 LEU* 2.9 21.3 + - + +
67A LYS* 4.1 8.9 - - - +
69A ALA* 1.3 78.8 - - - +
71A ASN* 1.3 65.4 + - - +
72A SER* 3.1 7.8 + - - +
37B THR* 4.8 3.8 - - - -
53B PRO* 6.1 5.5 - - + +
59B GLN* 4.1 20.4 + - - +
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Residues in contact with ASN 71 (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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67A LYS* 3.2 18.2 + - + +
68A ARG* 4.0 4.4 - - - +
70A GLU* 1.3 75.2 - - - +
72A SER* 1.3 73.2 + - - +
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Residues in contact with SER 72 (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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68A ARG* 3.0 18.6 + - - -
69A ALA* 3.8 14.4 - - - -
70A GLU 3.1 9.2 - - - +
71A ASN* 1.3 93.4 + - - +
29B GLU* 4.3 7.1 + - - -
30B SER* 4.0 17.6 + - - -
35B ALA 4.5 5.7 + - - +
36B ASN* 4.3 19.8 - - - +
37B THR* 4.3 9.0 - - - -
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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