Contacts of the helix formed by residues 45 - 56 (chain D) in PDB entry 2I6A
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 HIS 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D TYR* 3.7 25.4 + - - +
32D SER 5.5 1.1 - - - -
33D LEU* 4.2 17.2 - - + +
39D ILE* 3.8 14.1 - - + +
41D ALA* 3.8 15.9 - - + -
42D GLU* 3.0 52.7 - - + +
43D ASP 3.0 1.2 - - - -
44D LYS* 1.3 108.4 + - - +
46D LYS* 1.3 54.4 + - - +
47D GLU 3.1 3.1 - - - -
48D LEU* 2.6 40.6 + - + +
49D PHE* 3.9 6.6 + - + -
135D ILE* 4.5 9.9 - - + -
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Residues in contact with LYS 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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41D ALA* 5.8 0.4 - - - +
42D GLU 3.9 4.3 + - - +
43D ASP* 3.0 45.2 + - - +
45D HIS* 1.3 76.5 - - - +
47D GLU* 1.3 61.5 + - - +
48D LEU 3.4 0.3 + - - -
49D PHE* 3.5 20.2 + - - +
50D ASP* 4.1 11.8 - - - +
137D ASN* 5.4 7.2 - - - +
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Residues in contact with GLU 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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31D TYR* 3.4 25.9 + - + +
44D LYS 4.8 3.8 + - - +
45D HIS 2.8 2.9 + - - -
46D LYS* 1.3 77.3 - - - +
48D LEU* 1.3 63.2 + - - +
49D PHE 3.1 0.9 + - - -
50D ASP* 3.1 17.7 + - + +
51D GLU* 3.2 19.6 + - + +
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Residues in contact with LEU 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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27D PHE* 3.8 15.7 - - + -
31D TYR* 3.3 33.0 + - + -
33D LEU* 3.7 31.0 - - + -
45D HIS* 2.6 21.7 + - + +
47D GLU* 1.3 74.2 - - - +
49D PHE* 1.3 92.6 + - + +
51D GLU* 4.8 0.4 - - - -
52D LEU* 3.0 36.8 + - + +
124D ALA* 4.0 11.2 - - + -
126D CYS* 5.0 0.2 - - - -
135D ILE* 3.9 23.1 - - + -
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Residues in contact with PHE 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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19D ILE* 5.0 12.9 - - + +
41D ALA* 4.0 15.7 - - + -
45D HIS* 4.0 12.8 - - + -
46D LYS* 4.1 10.8 - - - +
47D GLU 3.1 1.2 - - - -
48D LEU* 1.3 96.8 - - + +
50D ASP* 1.3 63.6 + - - +
52D LEU* 4.1 5.2 - - + +
53D VAL* 3.7 24.1 + - - +
122D THR* 4.3 15.3 - - - -
123D CYS 4.3 1.3 - - - -
124D ALA* 3.4 31.2 - - + -
135D ILE* 3.5 28.0 - - + -
137D ASN* 3.8 32.8 - - + -
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Residues in contact with ASP 50 (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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46D LYS 4.1 10.8 - - - +
47D GLU* 3.1 9.6 + - + +
49D PHE* 1.3 77.8 - - - +
51D GLU* 1.3 59.9 + - - +
52D LEU 3.2 1.1 - - - -
53D VAL* 3.3 6.9 + - - +
54D LYS* 3.0 53.6 + - - +
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Residues in contact with GLU 51 (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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27D PHE* 3.5 26.1 - - + -
30D LYS* 5.6 6.1 - - - +
31D TYR* 2.4 30.0 + - - +
47D GLU* 3.2 19.2 + - + +
48D LEU 4.4 0.7 - - - +
50D ASP* 1.3 75.4 - - - +
52D LEU* 1.3 62.1 + - - +
54D LYS* 4.3 9.0 - - + -
55D LYS* 2.6 72.4 + - + +
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Residues in contact with LEU 52 (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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19D ILE* 3.9 32.1 - - + +
20D SER* 5.5 0.4 - - - -
21D ALA* 4.4 11.2 - - + +
23D VAL* 3.7 30.3 - - + -
27D PHE* 4.0 16.4 - - + -
48D LEU* 3.0 23.1 + - + +
49D PHE* 4.1 7.2 - - + +
51D GLU* 1.3 79.6 - - - +
53D VAL* 1.3 62.2 + - - +
56D PHE* 3.2 29.9 + - + +
58D VAL* 4.2 7.2 - - + +
124D ALA* 4.0 25.4 - - + -
125D ALA 5.3 0.9 - - - +
126D CYS* 4.3 7.6 - - - -
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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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19D ILE* 4.4 21.1 - - + -
49D PHE 3.7 14.3 + - - +
50D ASP* 3.3 9.3 + - - +
51D GLU 3.2 0.4 - - - -
52D LEU* 1.3 79.6 - - - +
54D LYS* 1.3 65.3 + - + +
56D PHE 3.4 14.2 - - - +
58D VAL* 4.4 16.0 - - + +
60D TYR* 4.1 22.4 - - + +
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Residues in contact with LYS 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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50D ASP* 3.0 51.1 + - - +
51D GLU* 4.0 7.0 - - + +
53D VAL* 1.3 82.9 - - + +
55D LYS* 1.3 66.0 + - + +
56D PHE 3.8 1.0 + - - +
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Residues in contact with LYS 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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51D GLU* 2.6 56.9 + - + +
54D LYS* 1.3 77.9 - - + +
56D PHE* 1.3 78.6 + - + +
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Residues in contact with PHE 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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21D ALA* 4.0 16.6 - - + -
22D VAL 3.2 19.1 - - - +
23D VAL* 3.6 28.0 - - + -
24D ASP* 3.9 21.1 - - + -
27D PHE* 3.8 31.2 - + - -
51D GLU 4.1 1.3 - - - -
52D LEU* 3.2 22.9 + - + +
53D VAL 3.4 16.3 - - - +
54D LYS 4.6 0.5 - - - +
55D LYS* 1.3 102.4 - - + +
57D LYS* 1.3 61.9 + - - +
58D VAL* 3.1 7.9 + - - +
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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