Contacts of the helix formed by residues 27 - 38 (chain D) in PDB entry 1TF6
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 ASN 27 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D TYR* 3.0 44.1 - - + +
26D LYS* 1.3 69.6 - - - +
28D TRP* 1.3 57.6 + - - +
30D LEU* 3.4 2.8 + - - +
31D GLN* 2.8 59.6 + - - +
35F G 3.5 19.6 + - - +
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Residues in contact with TRP 28 (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 LYS* 2.8 26.2 + - + +
27D ASN* 1.3 74.4 - - - +
29D LYS* 1.3 121.6 + - + +
31D GLN* 2.8 12.5 + - + +
32D ALA* 2.8 28.4 + - + +
55D THR 5.6 4.9 - - - -
26E G 3.8 20.4 - + - -
27E A 3.6 29.4 - - - -
28E G 4.0 7.7 + - - -
35F G 4.7 7.4 + - + -
36F T 3.2 35.5 + - + +
37F C 4.2 6.8 - - - +
38F T 5.1 0.7 - - - -
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Residues in contact with LYS 29 (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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24D TYR* 3.4 28.8 - - + +
25D ASN* 2.7 33.9 + - - +
26D LYS* 2.7 30.7 + - + +
28D TRP* 1.3 115.1 - - + +
30D LEU* 1.3 66.7 + - - +
32D ALA* 2.9 11.8 + - - +
33D HIS* 3.1 9.2 + - - +
26E G 3.6 23.7 + - + -
27E A 2.8 33.2 + - - +
28E G 5.4 2.7 - - - -
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Residues in contact with LEU 30 (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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13D TYR* 3.3 17.0 - - + -
14D ILE 2.9 50.7 - - - +
15D CYS* 4.0 7.0 - - - +
16D SER* 5.0 1.6 - - - +
24D TYR* 3.1 23.8 - - + -
26D LYS 3.4 1.4 + - - -
27D ASN* 3.4 9.1 + - - +
28D TRP 3.2 0.2 - - - -
29D LYS* 1.3 77.7 - - - +
31D GLN* 1.3 58.6 + - - +
33D HIS* 2.7 25.0 + - + +
34D LEU* 2.7 52.3 + - + +
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Residues in contact with GLN 31 (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 ASN* 2.8 56.9 + - - +
28D TRP* 2.8 16.4 + - + +
30D LEU* 1.3 84.9 - - - +
32D ALA* 1.3 56.9 + - - +
34D LEU* 3.1 26.5 - - - +
35D CYS* 2.8 28.4 + - - -
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Residues in contact with ALA 32 (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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28D TRP* 2.8 19.5 + - + +
29D LYS* 3.3 10.1 - - - +
31D GLN* 1.3 71.6 - - - +
33D HIS* 1.3 68.0 + - - +
34D LEU 3.0 1.8 - - - -
35D CYS* 2.9 27.3 + - - +
36D LYS* 3.3 5.0 + - - +
55D THR* 4.1 28.1 - - - +
25E G 6.5 1.6 - - + -
26E G 6.1 0.4 - - - +
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Residues in contact with HIS 33 (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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15D CYS* 2.8 23.8 - - + -
20D CYS* 2.9 12.2 - - - -
22D ALA* 3.6 9.8 - - + +
24D TYR* 2.8 38.3 + + + +
29D LYS 3.1 1.8 + - - -
30D LEU* 2.7 16.5 + - + +
32D ALA* 1.3 74.7 - - - +
34D LEU* 1.3 57.0 + - - +
36D LYS* 2.9 43.7 + - + +
37D HIS* 3.5 11.3 - + - -
201D ZN 1.9 37.9 - - - -
26E G 4.5 6.1 + - - +
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Residues in contact with LEU 34 (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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15D CYS* 4.6 6.1 - - - -
16D SER* 4.1 30.7 - - - +
17D PHE* 4.1 25.8 - - + -
30D LEU* 2.7 33.5 + - + +
31D GLN* 3.1 34.8 - - - +
32D ALA 3.0 0.2 - - - -
33D HIS* 1.3 74.2 - - - +
35D CYS* 1.3 56.7 + - - +
36D LYS 2.9 4.5 - - - -
37D HIS* 2.9 17.2 + - + +
38D THR* 2.6 25.8 + - + +
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Residues in contact with CYS 35 (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 GLN* 2.8 30.3 - - - -
32D ALA* 2.9 10.6 + - - +
34D LEU* 1.3 76.6 - - - +
36D LYS* 1.3 56.0 + - - +
38D THR* 3.0 10.1 - - - -
39D GLY* 2.6 32.3 + - - +
40D GLU* 3.6 18.1 + - + +
42D PRO* 4.1 13.5 - - - -
55D THR* 3.3 33.2 - - + -
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Residues in contact with LYS 36 (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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32D ALA 3.3 4.5 + - - +
33D HIS* 2.9 35.3 + - + +
34D LEU 2.9 0.4 - - - -
35D CYS* 1.3 82.6 - - - +
37D HIS* 1.3 67.1 + - + +
38D THR 3.9 0.3 - - - -
39D GLY* 3.7 5.0 + - - -
25E G 2.8 44.4 + - - +
26E G 5.2 6.3 + - - -
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Residues in contact with HIS 37 (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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15D CYS* 3.5 3.6 - - - -
17D PHE* 3.0 63.3 - + + -
20D CYS* 3.9 6.1 - - + -
33D HIS* 3.5 19.4 - + - -
34D LEU* 2.9 8.8 + - - +
36D LYS* 1.3 85.6 - - + +
38D THR* 1.3 64.3 + - - +
201D ZN 1.9 37.3 - - - -
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Residues in contact with THR 38 (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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17D PHE* 5.0 12.8 - - + -
34D LEU* 2.6 19.7 + - + +
35D CYS* 3.0 14.7 - - - -
37D HIS* 1.3 81.8 - - - +
39D GLY* 1.3 56.7 + - - -
40D GLU* 4.0 26.5 + - + +
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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