Contacts of the helix formed by residues 40 - 49 (chain D) in PDB entry 2I2X
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 ILE 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D PRO* 3.8 21.8 - - + -
37D ASP* 3.3 31.0 + - + +
39D LEU* 1.3 76.8 - - + +
41D TYR* 1.3 69.1 + - - +
43D ILE* 3.1 17.3 + - - +
44D ALA* 3.2 8.4 + - + +
72D LEU* 5.6 4.7 - - + -
75D ASP* 3.4 41.1 - - + +
76D ALA* 3.7 17.7 - - + +
79D VAL* 4.6 4.5 - - + -
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Residues in contact with TYR 41 (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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31D GLU* 3.2 35.9 + - - -
34D TYR* 3.8 21.5 - + + -
35D PRO* 3.3 28.9 + - - +
36D LYS* 4.7 5.6 - - + -
37D ASP 4.5 0.2 - - - -
38D GLU* 3.9 18.6 - - - +
39D LEU 3.3 0.2 - - - -
40D ILE* 1.3 78.2 - - - +
42D PRO* 1.4 82.5 - - + +
43D ILE 2.7 12.6 + - - -
44D ALA* 2.9 14.8 + - - +
45D LYS* 3.1 38.3 + - + +
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Residues in contact with PRO 42 (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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38D GLU 3.1 28.9 - - - +
39D LEU 3.6 8.7 - - - +
41D TYR* 1.4 97.9 - - + +
43D ILE* 1.3 56.6 + - + -
45D LYS* 4.4 5.4 - - + +
46D ALA* 3.2 25.7 + - - +
54D ASP* 4.4 5.7 - - - +
58D GLY* 5.5 6.7 - - - -
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Residues in contact with ILE 43 (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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39D LEU 3.7 17.3 - - - +
40D ILE* 3.3 9.2 - - - +
41D TYR 2.7 5.7 + - - -
42D PRO* 1.3 74.0 - - + +
44D ALA* 1.3 64.7 + - - +
46D ALA* 2.9 8.4 + - - +
47D ILE* 2.9 28.0 + - + +
54D ASP 5.2 2.0 - - - -
55D VAL* 4.6 10.3 - - + +
58D GLY* 3.3 36.3 - - - +
59D LEU* 4.3 10.5 - - + -
62D ALA* 4.3 9.0 - - + -
72D LEU* 4.4 1.6 - - + -
76D ALA* 3.6 28.3 - - + +
77D LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 44 (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 TYR* 3.9 19.1 - - + -
35D PRO* 4.2 18.6 - - + -
40D ILE* 3.2 7.9 + - + +
41D TYR* 2.9 8.8 + - - +
43D ILE* 1.3 77.6 - - - +
45D LYS* 1.3 62.6 + - - +
47D ILE* 3.2 4.5 + - - +
48D PHE* 3.1 22.7 + - - +
76D ALA 4.6 3.5 + - - +
79D VAL 4.9 0.2 - - - -
80D GLY* 3.7 32.5 - - - +
83D VAL* 5.7 0.4 - - + -
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Residues in contact with LYS 45 (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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31D GLU* 4.6 5.0 + - - +
34D TYR* 3.5 35.5 - - + +
41D TYR* 3.1 40.9 + - + +
42D PRO* 4.4 7.9 - - + +
44D ALA* 1.3 78.1 - - - +
46D ALA* 1.3 61.6 + - - +
48D PHE* 3.5 2.1 + - - +
49D GLU* 3.2 48.3 + - - +
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Residues in contact with ALA 46 (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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42D PRO 3.2 20.5 + - - +
43D ILE 2.9 6.9 + - - +
45D LYS* 1.3 75.4 - - - +
47D ILE* 1.3 65.0 + - - +
49D GLU* 3.3 7.4 + - - +
50D GLY 3.2 2.8 + - - -
51D GLU* 3.1 28.1 + - - +
54D ASP* 3.8 31.0 - - + +
55D VAL* 3.8 16.1 - - + +
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Residues in contact with ILE 47 (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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43D ILE* 2.9 23.9 + - + +
44D ALA 3.2 6.5 + - - +
46D ALA* 1.3 71.4 - - - +
48D PHE* 1.3 54.3 + - - +
49D GLU 3.0 1.8 - - - -
50D GLY* 2.7 19.1 + - - +
55D VAL* 3.7 20.0 - - + -
76D ALA 5.0 0.9 - - - +
77D LEU* 3.7 38.8 - - + +
80D GLY 3.8 26.7 - - - +
81D MET* 3.8 19.7 - - - -
84D VAL* 4.1 5.4 - - + -
101D SER* 2.7 26.6 + - - -
104D ALA* 4.7 2.7 - - - -
105D MET* 4.2 24.9 - - + +
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Residues in contact with PHE 48 (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 PRO* 3.7 32.1 - - + -
27D GLU* 4.5 17.0 - - + -
30D ALA* 3.8 11.2 - - + -
34D TYR* 3.2 28.9 - - + +
44D ALA 3.1 11.3 + - - +
45D LYS 3.7 3.4 - - - +
47D ILE* 1.3 77.3 - - - +
49D GLU* 1.3 69.9 + - + +
83D VAL* 4.3 5.6 - - + -
84D VAL* 3.8 21.3 - - + -
87D LEU* 3.7 25.1 - - + -
93D ILE* 4.1 18.2 - - + +
97D ASN* 4.8 7.1 - - + +
101D SER* 3.5 12.0 + - - -
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Residues in contact with GLU 49 (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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45D LYS* 3.2 48.8 + - + +
46D ALA* 3.8 7.0 - - - +
47D ILE 3.0 1.2 - - - -
48D PHE* 1.3 88.7 - - + +
50D GLY* 1.3 62.8 + - - +
51D GLU* 3.3 25.5 + - + +
54D ASP* 5.2 3.1 - - - +
100D MET* 3.9 17.6 - - - +
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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