Contacts of the helix formed by residues 52 - 63 (chain D) in PDB entry 1I0E
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 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D ASN 4.7 2.3 + - - -
9D LYS* 5.8 0.9 - - - -
43D ARG 6.0 3.1 - - - +
44D ASP* 6.0 0.9 - - - -
45D LYS 3.8 7.0 - - - +
46D GLU* 3.7 23.1 - - + +
50D GLY 3.9 6.2 + - - +
51D PHE* 1.3 78.6 - - - +
53D VAL* 1.3 58.1 + - - +
54D ASP* 4.2 9.5 + - - +
55D ASP* 2.6 57.7 + - - +
56D VAL* 3.0 6.1 + - - +
85D PHE* 3.6 9.0 - - - -
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Residues in contact with VAL 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 5.2 4.0 - - + -
39D TYR* 5.0 7.2 - - + -
42D LEU* 2.7 57.9 - - + +
43D ARG* 4.0 9.0 - - + -
45D LYS 4.8 1.3 - - - +
52D THR* 1.3 70.0 - - - +
54D ASP* 1.3 56.8 + - - +
55D ASP 2.6 12.1 + - - -
56D VAL* 2.6 22.7 + - + -
57D ILE* 2.7 32.6 + - + +
85D PHE* 3.2 25.4 - - + -
88D LEU* 4.8 8.7 - - + -
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Residues in contact with ASP 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASN 3.9 5.0 + - - +
9D LYS 3.5 25.7 - - - +
10D PHE* 2.7 28.9 - - + +
19D GLU* 5.0 5.0 - - - +
21D PRO* 5.9 0.9 - - - +
39D TYR* 2.7 29.3 + - - -
43D ARG* 5.4 1.9 - - - +
52D THR* 3.2 10.0 + - - +
53D VAL* 1.3 79.3 - - - +
55D ASP* 1.3 56.5 + - - +
57D ILE* 4.2 11.2 - - - +
58D GLN* 3.1 34.1 + - - +
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Residues in contact with ASP 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASN* 2.7 41.8 + - - +
50D GLY 4.0 4.2 - - - +
51D PHE* 3.6 31.8 - - + -
52D THR* 2.6 42.3 + - - +
53D VAL 2.6 3.8 + - - -
54D ASP* 1.3 71.2 - - - +
56D VAL* 1.3 63.8 + - - +
57D ILE 3.1 1.9 + - - -
58D GLN* 3.2 14.2 + - - +
59D THR* 4.5 4.0 + - - +
75D VAL* 5.1 2.8 - - - +
145D HIS* 5.4 2.2 + - - -
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D PHE* 3.5 23.1 - - + -
52D THR 3.4 14.8 - - - +
53D VAL* 2.6 21.3 + - + +
55D ASP* 1.3 72.3 - - - +
57D ILE* 1.3 69.4 + - + +
59D THR* 4.3 2.1 - - - +
74D CYS* 2.8 31.4 - - + +
75D VAL* 3.3 22.5 + - - +
81D SER* 5.2 0.4 - - - +
85D PHE* 4.2 16.2 - - + -
88D LEU* 3.9 23.3 - - + -
89D PHE* 4.2 14.6 - - + -
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Residues in contact with ILE 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 3.9 21.5 - - + -
30D MET* 3.6 19.7 - - + +
34D LEU* 4.3 21.8 - - + -
39D TYR* 4.5 11.9 - - + -
53D VAL* 2.7 38.6 + - + +
54D ASP* 4.2 9.6 - - - +
56D VAL* 1.3 84.9 - - + +
58D GLN* 1.3 67.1 + - - +
59D THR 3.3 2.7 - - - -
60D GLY* 2.9 15.4 + - - -
61D VAL* 3.0 32.0 + - + -
73D GLY 4.2 5.2 - - - -
74D CYS* 4.5 0.4 - - - -
88D LEU* 5.1 1.8 - - + -
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Residues in contact with GLN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASN* 2.9 51.4 + - - +
54D ASP* 3.1 22.0 + - - +
55D ASP 3.2 6.6 + - - +
57D ILE* 1.3 78.9 - - - +
59D THR* 1.3 62.3 + - - +
61D VAL* 3.3 14.8 + - - +
62D ASP* 2.7 50.5 + - - +
204D ALA 5.2 3.4 - - - +
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Residues in contact with THR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ASP 4.5 1.7 + - - +
56D VAL 4.3 3.4 - - - +
58D GLN* 1.3 76.5 - - - +
60D GLY* 1.3 59.1 + - - +
62D ASP* 3.5 2.1 + - - +
63D ASN* 3.0 34.8 + - - +
73D GLY 4.5 0.4 - - - -
74D CYS* 4.0 27.1 - - - +
75D VAL* 4.2 23.1 - - + -
201D LEU* 3.8 13.5 + - - +
204D ALA 3.8 20.3 + - - -
205D SER* 3.8 22.5 + - - +
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Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D HIS* 3.8 3.6 + - - -
28D ASN* 3.7 8.7 + - - -
30D MET* 3.7 10.3 - - - +
57D ILE 2.9 7.9 + - - -
59D THR* 1.3 81.4 - - - +
61D VAL* 1.3 64.8 - - - +
62D ASP 3.1 0.4 - - - -
63D ASN* 3.1 24.9 - - - +
73D GLY* 3.6 26.2 + - - -
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Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 3.6 33.2 - - + -
22D ASP 5.7 1.6 - - - +
23D LEU* 4.0 12.3 - - + -
26D HIS* 3.2 22.0 + - - +
30D MET* 3.6 7.4 - - + +
57D ILE* 3.0 32.0 + - + +
58D GLN* 3.6 20.9 - - - +
60D GLY* 1.3 76.0 - - - +
62D ASP* 1.3 61.5 + - - +
64D PRO* 4.7 0.7 - - - +
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Residues in contact with ASP 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLN* 2.7 43.9 + - - +
59D THR* 3.9 5.8 - - - +
60D GLY 3.1 0.2 - - - -
61D VAL* 1.3 83.2 - - - +
63D ASN* 1.3 70.4 + - - +
64D PRO* 3.0 12.2 - - - +
204D ALA* 4.4 14.9 - - + +
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Residues in contact with ASN 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ASN* 3.1 9.4 + - - -
59D THR* 3.0 20.1 + - - +
60D GLY* 3.1 14.7 + - - +
62D ASP* 1.3 85.8 + - - +
64D PRO* 1.3 54.8 - - - +
65D GLY* 2.7 19.5 + - - +
71D THR* 4.8 5.0 + - - +
200D PRO 3.1 18.7 + - - -
201D LEU* 2.9 48.0 - - + +
204D ALA* 3.7 10.2 - - - +
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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