Contacts of the helix formed by residues 42 - 53 (chain F) in PDB entry 5TWV
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 42 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F PHE* 3.2 31.3 + - + +
39F LEU* 4.8 3.8 - - - +
41F PHE* 1.3 78.5 - - - +
43F THR* 1.3 57.4 + - - +
45F PRO* 3.2 21.3 - - - +
46F ILE* 4.2 4.7 + - - +
123F TYR* 4.1 13.4 + - + +
138F ALA* 6.2 4.0 - - + -
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Residues in contact with THR 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU 3.5 20.2 + - - -
40F LEU* 4.1 7.4 - - - -
41F PHE 3.4 0.4 - - - -
42F ILE* 1.3 75.9 - - - +
44F PHE* 1.3 60.2 + - - +
45F PRO 3.3 2.0 - - - -
46F ILE* 3.2 2.9 + - - +
47F LEU* 2.7 42.4 + - - +
119F THR* 4.8 10.5 - - - -
123F TYR* 3.6 29.4 + - - -
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Residues in contact with PHE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E MET* 5.2 26.0 - - + +
78E SER 6.0 0.2 - - - +
81E CYS* 4.4 18.2 - - + -
40F LEU* 3.3 33.4 + - + -
41F PHE* 4.6 11.2 - + - -
43F THR* 1.3 78.0 - - - +
45F PRO* 1.3 68.8 - - + +
47F LEU* 4.4 6.3 - - + -
48F PHE* 2.8 39.0 + - + +
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Residues in contact with PRO 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ILE* 5.5 13.0 - - + +
78E SER* 4.6 23.3 - - - -
81E CYS* 5.7 0.2 - - + -
41F PHE 3.7 13.7 - - - +
42F ILE* 3.2 17.0 - - - +
44F PHE* 1.3 98.3 - - + +
46F ILE* 1.3 57.3 + - - +
48F PHE* 4.5 1.7 - - + +
49F ILE* 3.2 27.7 + - - +
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Residues in contact with ILE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E LEU* 5.1 19.0 - - + +
42F ILE 4.7 6.1 - - - +
43F THR 3.2 6.3 + - - +
45F PRO* 1.3 78.2 - - + +
47F LEU* 1.3 63.9 + - - +
49F ILE* 4.2 4.5 - - - +
50F GLY* 3.6 14.7 + - - -
123F TYR* 4.7 17.7 - - + +
126F ASN* 5.5 5.2 - - - +
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F THR* 2.7 28.2 + - - +
44F PHE* 4.2 5.4 - - + +
46F ILE* 1.3 73.7 - - - +
48F PHE* 1.3 63.6 + - - +
50F GLY* 3.5 2.4 + - - -
51F TRP* 3.1 21.9 + - - +
122F VAL* 4.5 22.4 - - + -
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Residues in contact with PHE 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LEU* 5.7 0.2 - - - +
73E LEU* 5.6 9.6 - - + -
74E ILE* 5.1 16.2 - - + -
44F PHE* 2.8 27.1 + - + +
45F PRO* 4.5 2.0 - - + +
47F LEU* 1.3 70.4 - - - +
49F ILE* 1.3 59.5 + - - +
51F TRP* 3.0 18.5 + - + +
52F GLY* 2.9 24.3 + - - -
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Residues in contact with ILE 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E LEU* 6.4 2.2 - - + -
62E THR* 5.8 0.9 - - - +
63E LEU* 4.8 19.3 - - + -
66E LEU* 4.4 8.6 - - + +
74E ILE* 5.1 10.0 - - + +
45F PRO 3.2 20.0 + - - +
46F ILE* 4.5 4.0 - - - +
47F LEU 3.4 0.2 - - - -
48F PHE* 1.3 78.6 - - - +
50F GLY* 1.3 58.8 + - - +
51F TRP 3.0 0.2 - - - -
52F GLY* 3.2 0.9 + - - +
53F SER* 2.8 37.5 + - - +
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Residues in contact with GLY 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E LEU* 6.5 1.6 - - - -
46F ILE 3.6 10.4 + - - -
47F LEU 3.5 7.3 + - - -
48F PHE 3.2 0.6 - - - -
49F ILE* 1.3 79.1 - - - +
51F TRP* 1.3 58.8 + - - +
53F SER* 4.3 4.9 - - - -
54F GLN* 3.5 21.8 - - - +
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Residues in contact with TRP 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E HIS* 4.0 30.7 - + - -
73E LEU* 4.6 17.3 - - + -
47F LEU 3.1 13.0 + - - +
48F PHE* 3.0 23.1 + - + +
50F GLY* 1.3 80.2 - - - +
52F GLY* 1.3 62.8 + - - +
54F GLN* 4.2 2.6 + - - +
55F SER* 3.5 21.0 + - - -
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Residues in contact with GLY 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LEU* 3.6 19.8 - - - +
70E HIS* 4.1 23.1 + - - -
48F PHE 2.9 11.6 + - - -
49F ILE 3.2 1.8 + - - -
51F TRP* 1.3 80.2 - - - +
53F SER* 1.3 59.7 + - - +
54F GLN 3.1 5.4 - - - -
55F SER* 3.1 14.5 + - - -
56F SER* 3.3 11.4 + - - -
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Residues in contact with SER 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E THR* 3.8 28.2 - - - -
66E LEU* 3.8 19.6 - - - +
49F ILE* 2.8 22.7 + - - +
50F GLY* 4.9 3.6 - - - -
52F GLY* 1.3 72.3 - - - -
54F GLN* 1.3 55.3 + - - +
55F SER 3.3 1.1 - - - -
56F SER 4.4 0.9 - - - +
57F LYS 3.0 30.2 - - - +
58F VAL* 3.1 8.3 - - - +
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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