Contacts of the helix formed by residues 39 - 48 (chain I) in PDB entry 2IUO
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 ALA 39 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156C PHE* 2.7 56.2 + - + +
38I LEU* 1.3 74.5 - - - +
40I GLU* 1.3 65.4 + - - +
41I ALA* 4.2 2.2 - - + +
42I PHE* 3.1 4.6 + - - +
43I VAL* 3.0 21.7 + - - +
127I LYS* 6.4 0.2 - - - -
1159I SO4 3.3 20.9 - - - +
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Residues in contact with GLU 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I PHE 4.0 6.3 - - - +
30I ALA* 3.3 42.7 + - - +
33I ALA* 4.0 11.4 - - + +
38I LEU 3.5 0.6 + - - -
39I ALA* 1.3 69.6 - - - +
41I ALA* 1.3 57.3 + - - +
43I VAL* 4.0 0.5 - - - +
44I THR* 2.8 37.0 + - - +
1159I SO4 2.8 34.7 + - - +
111J LEU* 3.7 22.6 - - + +
114J GLU* 3.4 12.1 - - - +
115J LYS* 3.3 27.8 + - - +
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Residues in contact with ALA 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C PHE* 4.5 8.3 - - + -
39I ALA* 3.3 2.5 - - + +
40I GLU* 1.3 77.9 - - - +
42I PHE* 1.3 62.9 + - - +
45I ALA* 3.1 25.8 + - - +
128I LEU* 3.8 39.9 - - + +
129I ASP* 5.1 3.4 - - + -
1159I SO4 4.3 1.4 + - - +
104J TYR* 3.9 5.0 - - + -
107J THR* 3.6 8.5 - - + +
111J LEU* 4.0 18.3 - - + +
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Residues in contact with PHE 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C THR* 5.0 1.8 - - + -
154C LYS 4.1 5.2 - - - -
155C PRO* 3.5 42.2 - - + -
156C PHE* 3.7 46.7 - + + +
38I LEU* 4.0 23.8 - - + -
39I ALA 3.1 9.6 + - - +
41I ALA* 1.3 75.8 - - - +
43I VAL* 1.3 68.6 + - - +
45I ALA* 3.4 5.5 + - - +
46I ALA* 3.1 18.0 + - - +
51I GLN* 3.6 37.8 - - + +
52I ALA 3.4 26.7 - - - -
53I LEU* 4.3 5.4 - - + -
104J TYR* 4.3 1.1 - - - -
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Residues in contact with VAL 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I PHE 5.7 0.4 - - - +
32I ILE* 4.7 2.5 - - + -
33I ALA* 4.1 21.8 - - + +
36I THR* 3.7 15.9 - - - +
38I LEU* 3.5 33.0 - - + +
39I ALA 3.0 19.8 + - - +
40I GLU 4.2 0.2 - - - +
42I PHE* 1.3 77.0 - - - +
44I THR* 1.3 64.3 + - - +
46I ALA* 3.1 11.3 + - - +
47I LEU* 3.1 22.9 + - + +
53I LEU* 4.3 15.7 - - + -
61I VAL* 4.2 25.4 - - + -
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Residues in contact with THR 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I PHE* 3.4 43.3 + - + +
40I GLU* 2.8 25.2 + - - +
43I VAL* 1.3 75.1 - - - +
45I ALA* 1.3 66.1 + - - +
46I ALA 3.2 0.5 + - - -
47I LEU* 3.2 11.7 + - - +
48I LEU* 3.0 42.8 + - + +
107J THR* 3.7 23.3 - - + -
110J ALA* 4.1 10.3 - - + -
111J LEU* 3.8 6.5 - - + +
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Residues in contact with ALA 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I ALA 3.1 18.4 + - - +
42I PHE 3.7 4.3 - - - +
43I VAL 3.4 0.2 - - - -
44I THR* 1.3 75.4 - - - +
46I ALA* 1.4 60.6 + - - +
48I LEU* 3.3 4.2 + - - -
49I GLY 3.2 4.9 + - - -
50I GLN* 2.8 35.9 + - + +
51I GLN* 3.8 18.4 - - + -
103J VAL 4.8 0.2 - - - +
104J TYR* 3.8 15.5 - - + -
107J THR* 3.1 21.6 + - - +
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Residues in contact with ALA 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ARG* 3.0 18.0 + - - +
42I PHE* 3.1 13.3 + - + +
43I VAL 3.3 9.6 - - - +
44I THR 3.1 0.4 - - - -
45I ALA* 1.4 71.9 - - - +
47I LEU* 1.3 66.3 + - - +
48I LEU 3.0 1.8 - - - -
49I GLY* 2.9 11.6 + - - -
51I GLN* 3.5 26.8 - - + +
52I ALA 4.6 0.2 - - - -
53I LEU* 3.5 34.5 - - + +
75I LEU* 3.8 5.3 - - + +
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Residues in contact with LEU 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ARG* 4.7 1.2 + - - +
14I LEU* 5.6 0.3 - - - +
15I ALA* 3.2 25.1 + - - +
18I ILE* 3.8 35.4 - - + +
29I PHE* 4.1 29.6 - - + -
32I ILE* 4.1 26.2 - - + -
43I VAL* 3.1 18.8 + - + +
44I THR* 3.5 8.3 - - - +
46I ALA* 1.3 76.2 - - - +
48I LEU* 1.3 63.6 + - + +
49I GLY 3.4 1.4 + - - -
53I LEU* 4.8 2.9 - - + -
61I VAL* 4.4 19.7 - - + -
65I LEU* 4.3 13.5 - - + -
75I LEU* 4.0 13.5 - - + +
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Residues in contact with LEU 48 (chain I).
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 26.5 - - + +
12I LEU* 3.5 19.1 - - - +
15I ALA* 3.8 8.7 - - + +
18I ILE* 6.2 0.2 - - + -
19I LEU* 4.1 27.1 - - + -
29I PHE* 4.9 4.5 - - + -
44I THR* 3.0 25.4 + - + +
45I ALA* 3.3 7.6 + - - +
46I ALA 3.0 1.0 - - - -
47I LEU* 1.3 84.2 - - + +
49I GLY* 1.3 59.0 + - - +
50I GLN* 3.5 8.5 + - + +
83I CYS* 5.5 0.2 - - - +
106J THR* 3.5 47.3 + - - +
107J THR* 3.8 13.7 - - - +
110J ALA* 4.2 5.4 - - + -
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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
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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