Contacts of the helix formed by residues 52 - 63 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ASN 4.8 2.6 + - - -
9B LYS* 5.8 1.0 - - - -
43B ARG 6.0 3.1 - - - +
44B ASP 6.0 0.7 - - - -
45B LYS 3.8 6.3 - - - +
46B GLU* 3.7 23.3 - - + +
50B GLY 3.8 7.1 + - - +
51B PHE* 1.3 79.2 - - - +
53B VAL* 1.3 58.7 + - - +
54B ASP* 4.1 9.5 + - - +
55B ASP* 2.6 54.4 + - - +
56B VAL* 3.0 5.9 + - - +
85B PHE* 3.6 9.2 - - - -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 5.2 4.3 - - + -
39B TYR* 5.0 8.3 - - + -
42B LEU* 2.8 57.9 - - + +
43B ARG* 4.0 9.0 - - - -
45B LYS 4.8 0.7 - - - +
52B THR* 1.3 70.3 - - - +
54B ASP* 1.3 56.3 + - - +
55B ASP 2.6 11.8 + - - -
56B VAL* 2.6 22.8 + - + -
57B ILE* 2.7 32.0 + - + +
85B PHE* 3.2 24.2 - - + -
88B LEU* 4.8 8.5 - - + -
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASN 3.8 5.5 + - - +
9B LYS 3.5 25.5 - - - +
10B PHE* 2.7 25.8 - - + +
19B GLU* 5.0 5.6 - - - +
21B PRO* 5.9 0.7 - - - +
39B TYR* 2.7 31.8 + - - -
43B ARG* 5.4 2.1 - - - +
52B THR* 3.2 9.7 + - - +
53B VAL* 1.3 79.4 - - - +
55B ASP* 1.3 55.9 + - - +
57B ILE* 4.0 11.7 - - - +
58B GLN* 3.1 33.6 + - - +
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Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASN* 2.8 41.8 + - - +
50B GLY 3.9 4.0 - - - +
51B PHE* 3.5 34.8 - - + -
52B THR* 2.6 42.4 + - - +
53B VAL 2.6 4.0 + - - -
54B ASP* 1.3 69.3 - - - +
56B VAL* 1.3 62.8 + - - +
57B ILE 3.1 2.4 + - - -
58B GLN* 3.2 14.7 + - - +
59B THR* 4.5 3.8 + - - +
75B VAL* 5.1 2.8 - - - +
145B HIS* 5.4 2.6 + - - -
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PHE* 3.5 24.2 - - + -
52B THR 3.4 13.7 - - - +
53B VAL* 2.6 17.7 + - + +
55B ASP* 1.3 72.7 - - - +
57B ILE* 1.3 72.9 + - + +
59B THR* 4.3 2.1 - - - +
74B CYS* 2.8 31.7 - - + +
75B VAL 3.3 20.1 + - - +
81B SER* 5.1 0.4 - - - +
85B PHE* 4.2 15.9 - - + -
88B LEU* 3.9 24.5 - - + -
89B PHE* 4.2 15.5 - - + -
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PRO* 3.9 21.3 - - + -
30B MET* 3.6 18.4 - - + +
34B LEU* 4.3 22.9 - - + -
39B TYR* 4.5 11.7 - - + -
53B VAL* 2.7 43.7 + - + +
54B ASP* 4.2 10.1 - - - +
56B VAL* 1.3 78.4 - - + +
58B GLN* 1.3 67.9 + - - +
59B THR 3.3 2.9 - - - -
60B GLY* 2.9 14.7 + - - -
61B VAL* 3.0 31.9 + - + -
73B GLY 4.2 4.9 - - - -
74B CYS* 4.5 0.7 - - - -
88B LEU* 5.1 2.0 - - + -
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASN* 2.9 50.2 + - - +
54B ASP* 3.1 23.1 + - - +
55B ASP 3.2 6.0 + - - +
57B ILE* 1.3 77.8 - - - +
59B THR* 1.3 62.1 + - - +
61B VAL* 3.3 14.6 + - - +
62B ASP* 2.7 50.7 + - - +
204B ALA 5.3 3.6 - - - +
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASP 4.5 2.4 + - - +
56B VAL 4.3 3.1 - - - +
58B GLN* 1.3 75.8 - - - +
60B GLY* 1.3 60.4 + - - +
62B ASP* 3.8 1.7 - - - +
63B ASN* 3.0 34.7 + - - +
73B GLY* 5.4 0.4 - - - -
74B CYS* 4.0 26.2 - - - +
75B VAL* 4.2 22.9 - - + -
201B LEU* 3.8 13.9 + - - +
204B ALA 3.8 19.4 + - - -
205B SER* 3.8 22.8 + - - +
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B HIS* 3.8 4.0 + - - -
28B ASN* 3.7 8.9 + - - -
30B MET* 3.8 10.8 - - - +
57B ILE 2.9 7.9 + - - -
59B THR* 1.3 82.2 - - - +
61B VAL* 1.3 64.4 + - - +
63B ASN* 3.1 24.2 - - - +
73B GLY* 3.5 26.4 + - - -
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PRO* 3.6 32.1 - - + -
22B ASP 5.7 1.6 - - - +
23B LEU* 4.0 12.3 - - + -
26B HIS* 3.2 22.3 + - - +
30B MET* 3.7 7.8 - - + +
57B ILE* 3.0 32.5 + - + +
58B GLN* 3.3 21.1 + - - +
60B GLY* 1.3 75.8 - - - +
62B ASP* 1.3 62.2 + - - +
64B PRO* 4.7 0.5 - - - +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLN* 2.7 43.1 + - - +
59B THR* 3.9 6.1 - - - +
61B VAL* 1.3 84.1 - - - +
63B ASN* 1.3 69.2 + - - +
64B PRO* 3.0 11.4 - - - +
204B ALA* 4.5 14.1 - - + +
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ASN* 3.2 9.7 + - - -
59B THR* 3.0 19.7 + - - +
60B GLY* 3.1 14.4 + - - +
62B ASP* 1.3 86.6 + - - +
64B PRO* 1.3 54.9 - - - +
65B GLY* 2.7 20.4 + - - +
71B THR* 4.8 4.8 + - - +
200B PRO 3.1 20.5 + - - -
201B LEU* 2.9 47.7 - - + +
204B ALA* 3.7 9.6 - - - +
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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