Contacts of the helix formed by residues 42 - 53 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B PHE* 3.2 30.6 + - + +
39B LEU* 4.8 3.4 - - - +
41B PHE* 1.3 79.1 - - - +
43B THR* 1.3 58.0 + - - +
44B PHE 3.5 0.2 - - - -
45B PRO* 3.2 22.4 - - - +
46B ILE* 4.2 4.2 + - - +
123B TYR* 4.1 13.6 + - + +
138B ALA* 6.2 3.8 - - + -
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU 3.5 19.1 + - - -
40B LEU* 4.1 7.9 - - - -
41B PHE 3.4 0.2 - - - -
42B ILE* 1.3 76.5 - - - +
44B PHE* 1.3 58.9 + - - +
45B PRO 3.3 2.2 - - - -
46B ILE* 3.2 3.0 + - - +
47B LEU* 2.7 41.8 + - - +
119B THR* 4.8 10.8 - - - -
123B TYR* 3.6 29.1 + - - -
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A MET* 5.2 25.4 - - + +
81A CYS* 4.4 17.3 - - + -
40B LEU* 3.3 34.5 + - + -
41B PHE* 4.6 11.0 - + - -
42B ILE 3.5 0.2 - - - -
43B THR* 1.3 77.0 - - - +
45B PRO* 1.3 70.2 - - + +
47B LEU* 4.4 5.8 - - + -
48B PHE* 2.8 38.8 + - + +
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Residues in contact with PRO 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 5.5 14.0 - - + +
78A SER* 4.6 22.7 - - - -
81A CYS* 5.7 0.2 - - + -
41B PHE 3.7 13.9 - - - +
42B ILE* 3.2 16.4 - - - +
44B PHE* 1.3 99.2 - - + +
46B ILE* 1.3 57.9 + - - +
48B PHE* 4.5 1.5 - - + +
49B ILE* 3.2 27.0 + - - +
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 5.1 18.6 - - + +
42B ILE 4.2 5.8 + - - +
43B THR* 3.2 5.4 + - - +
45B PRO* 1.3 79.1 - - + +
47B LEU* 1.3 64.8 + - - +
49B ILE* 4.2 3.6 - - - +
50B GLY* 3.6 15.0 + - - -
123B TYR* 4.7 18.2 - - + +
126B ASN* 5.5 5.2 - - - +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B THR* 2.7 27.6 + - - +
44B PHE* 4.2 5.2 - - + +
46B ILE* 1.3 74.4 - - - +
48B PHE* 1.3 63.2 + - - +
50B GLY* 3.5 2.6 + - - -
51B TRP* 3.1 22.1 + - - +
122B VAL* 4.5 21.5 - - + -
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 5.6 9.9 - - + -
74A ILE* 5.1 15.5 - - + -
44B PHE* 2.8 26.5 + - + +
45B PRO* 4.5 2.2 - - + +
47B LEU* 1.3 70.5 - - - +
49B ILE* 1.3 60.5 + - - +
51B TRP* 3.0 18.2 + - + +
52B GLY* 2.9 24.6 + - - -
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 6.4 2.0 - - + -
62A THR* 5.8 1.1 - - - +
63A LEU* 4.8 18.6 - - + -
66A LEU* 4.4 9.1 - - + +
74A ILE* 5.1 10.0 - - + +
45B PRO 3.2 19.6 + - - +
46B ILE* 4.5 3.8 - - - +
47B LEU 3.4 0.4 - - - -
48B PHE* 1.3 78.4 - - - +
50B GLY* 1.3 58.5 + - - +
51B TRP 3.0 0.2 - - - -
52B GLY 3.2 0.2 + - - -
53B SER* 2.8 37.9 + - - +
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Residues in contact with GLY 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 6.5 1.6 - - - -
46B ILE 3.6 10.2 + - - -
47B LEU 3.5 7.2 + - - -
48B PHE 3.2 0.6 - - - -
49B ILE* 1.3 78.5 - - - +
51B TRP* 1.3 58.9 - - - +
53B SER* 4.3 5.6 - - - -
54B GLN* 3.5 22.2 - - - +
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Residues in contact with TRP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A HIS* 4.0 31.9 - + - -
73A LEU* 4.6 17.0 - - + -
47B LEU 3.1 13.6 + - - +
48B PHE* 3.0 22.9 + - + +
50B GLY* 1.3 81.2 - - - +
52B GLY* 1.3 61.7 + - - +
54B GLN* 4.3 2.2 - - - +
55B SER* 3.5 21.1 + - - -
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.6 18.4 - - - +
70A HIS* 4.1 23.3 + - - -
48B PHE 2.9 12.0 + - - -
49B ILE 3.2 1.7 + - - -
51B TRP* 1.3 79.1 - - - +
53B SER* 1.3 59.9 + - - +
54B GLN 3.1 5.2 - - - -
55B SER* 3.1 14.7 + - - -
56B SER* 3.3 11.6 + - - -
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A THR* 3.8 28.4 - - - +
66A LEU* 3.8 19.6 - - - +
49B ILE* 2.8 24.1 + - - +
50B GLY* 4.9 3.4 - - - -
52B GLY* 1.3 71.4 - - - +
54B GLN* 1.3 56.7 + - - +
55B SER 3.3 1.1 - - - -
56B SER 4.4 1.1 - - - -
57B LYS 3.0 30.3 - - - +
58B VAL* 3.1 7.2 - - - +
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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