Contacts of the helix formed by residues 45 - 56 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C TYR* 3.6 26.4 + - - +
32C SER 5.0 1.1 - - - -
33C LEU* 4.1 14.9 - - + +
39C ILE* 3.7 14.9 - - + +
41C ALA* 3.7 18.6 - - + -
42C GLU* 2.8 50.8 - - + +
43C ASP 2.9 1.0 - - - -
44C LYS* 1.3 112.3 + - + +
46C LYS* 1.3 59.6 + - - +
47C GLU 3.1 3.1 - - - -
48C LEU* 2.8 37.8 + - + +
49C PHE* 3.6 9.0 - - + -
135C ILE* 4.5 6.7 - - + -
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLU 4.5 9.0 + - - +
43C ASP* 2.9 43.5 + - - +
45C HIS* 1.3 76.6 - - - +
47C GLU* 1.3 60.3 + - - +
48C LEU 3.5 0.2 + - - -
49C PHE* 3.7 14.1 + - - +
50C ASP* 3.4 17.5 + - - +
137C ASN* 6.1 0.9 - - - +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TYR* 3.4 20.6 + - + +
43C ASP 5.1 0.2 + - - -
44C LYS 4.7 3.3 + - - +
45C HIS 3.1 0.6 - - - -
46C LYS* 1.3 76.3 - - - +
48C LEU* 1.3 66.7 + - - +
49C PHE 3.2 0.5 + - - -
50C ASP* 3.3 7.8 + - + +
51C GLU* 3.2 34.7 + - + +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.7 15.8 - - + -
31C TYR* 3.3 43.0 - - + -
33C LEU* 3.9 25.6 - - + -
45C HIS* 2.8 21.2 + - + +
47C GLU* 1.3 79.5 - - - +
49C PHE* 1.3 77.8 + - + +
51C GLU* 4.2 0.2 - - - +
52C LEU* 3.1 33.6 + - + +
124C ALA* 3.9 24.0 - - + -
126C CYS* 4.9 1.8 - - - -
135C ILE* 4.1 15.3 - - + -
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Residues in contact with PHE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.7 11.1 - - + +
41C ALA* 4.1 13.9 - - + -
45C HIS* 3.6 16.4 - - + -
46C LYS* 3.7 8.9 + - - +
47C GLU 3.2 0.8 - - - -
48C LEU* 1.3 91.8 - - + +
50C ASP* 1.3 67.2 + - - +
52C LEU* 4.0 6.3 - - + +
53C VAL* 3.6 23.0 + - - +
122C THR* 3.9 22.4 - - - -
123C CYS 4.4 1.1 - - - -
124C ALA* 3.8 20.2 - - + -
135C ILE* 3.3 32.3 - - + -
137C ASN* 3.6 28.0 - - + -
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Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LYS 3.4 15.2 - - - +
47C GLU* 3.3 9.2 + - + +
49C PHE* 1.3 78.1 - - - +
51C GLU* 1.3 65.5 + - - +
52C LEU 3.3 0.3 + - - -
53C VAL* 3.4 5.5 + - - +
54C LYS* 3.1 51.5 + - - +
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.5 24.8 - - + -
30C LYS* 5.8 4.0 - - - +
31C TYR* 2.3 33.3 + - - +
47C GLU* 3.2 21.0 + - + +
48C LEU 4.2 0.4 - - - +
50C ASP* 1.3 76.3 - - - +
52C LEU* 1.3 61.2 + - - +
54C LYS* 4.1 9.2 - - + +
55C LYS* 2.6 67.7 + - + +
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.7 33.7 - - + +
20C SER* 5.3 0.2 - - - -
21C ALA* 3.9 22.0 - - + +
23C VAL* 3.7 30.1 - - + -
27C PHE* 3.9 13.5 - - + -
48C LEU* 3.1 22.1 + - + +
49C PHE* 4.0 7.2 - - + +
50C ASP 3.2 0.4 - - - -
51C GLU* 1.3 75.1 - - - +
53C VAL* 1.3 56.9 + - - +
56C PHE* 3.0 40.5 + - + +
58C VAL* 4.9 1.8 - - + +
124C ALA* 3.9 25.6 - - + -
125C ALA 5.0 0.9 - - - +
126C CYS* 4.4 10.5 - - - -
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.3 18.8 - - + -
49C PHE 3.6 11.6 + - - +
50C ASP* 3.4 8.3 + - - +
51C GLU 3.3 0.2 - - - -
52C LEU* 1.3 79.5 - - - +
54C LYS* 1.3 68.7 + - + +
56C PHE 3.4 12.8 - - - +
58C VAL* 3.9 17.2 - - + +
60C TYR* 3.8 25.4 - - + +
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Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ASP* 3.1 48.5 + - - +
51C GLU* 3.8 7.2 - - + +
53C VAL* 1.3 83.3 - - + +
55C LYS* 1.3 63.9 + - + +
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Residues in contact with LYS 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C GLU* 2.6 52.5 + - + +
54C LYS* 1.3 78.1 - - + +
56C PHE* 1.3 87.3 + - + +
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Residues in contact with PHE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 4.0 9.6 - - + -
22C VAL 3.4 24.9 - - - +
23C VAL* 3.8 18.6 - - + -
24C ASP* 3.6 26.9 - - - -
27C PHE* 3.7 30.3 - + - -
51C GLU 4.1 1.6 - - - -
52C LEU* 3.0 21.0 + - - +
53C VAL 3.4 14.6 - - - +
54C LYS 5.0 0.2 - - - +
55C LYS* 1.3 107.5 - - + +
57C LYS* 1.3 64.8 + - - +
58C VAL* 3.2 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