Contacts of the helix formed by residues 28 - 43 (chain F) in PDB entry 3TMH
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 LEU 28 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F TYR* 3.9 12.2 + - - +
20F VAL* 4.7 16.4 - - + -
24F GLN* 5.5 0.7 - - - -
25F PRO* 3.5 33.4 - - + +
26F PRO* 3.8 7.2 - - + +
27F ASP* 1.3 83.5 + - - +
29F VAL* 1.3 58.7 + - + +
30F ASP 3.2 1.1 - - - -
31F PHE* 2.7 7.4 + - + +
32F ALA* 2.5 36.1 + - - +
7G PRO 5.8 4.5 - - - +
8G GLY 6.6 0.4 - - - -
9G LEU* 5.5 5.8 - - + -
12G LEU* 4.1 19.1 - - + -
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Residues in contact with VAL 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ASP* 4.0 7.6 - - - +
28F LEU* 1.3 73.2 - - + +
30F ASP* 1.3 80.1 + - - +
32F ALA* 3.7 6.6 - - - +
33F VAL* 2.7 33.7 + - - +
12G LEU* 4.6 11.9 - - + -
36G PHE* 4.6 1.6 - - - +
39G LEU* 3.9 46.9 - - + -
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Residues in contact with ASP 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ASP* 2.8 34.2 + - - +
29F VAL* 1.3 85.7 - - - +
31F PHE* 1.3 55.4 + - - +
33F VAL* 3.4 6.8 - - - +
34F GLU* 2.9 50.6 + - - +
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Residues in contact with PHE 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TYR* 3.9 29.4 - + - -
19F GLU* 4.3 9.9 - - + -
20F VAL* 4.1 18.8 - - + -
23F GLN* 3.4 39.3 - - - -
25F PRO* 3.8 20.0 - - + -
27F ASP* 3.3 22.0 + - - +
28F LEU* 2.7 16.4 + - + +
30F ASP* 1.3 74.8 - - - +
32F ALA* 1.3 54.6 + - - -
34F GLU* 3.9 8.3 - - - -
35F TYR* 2.8 48.1 + + + +
38F ARG* 3.2 22.1 + - - -
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Residues in contact with ALA 32 (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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16F TYR* 3.5 28.9 - - + +
28F LEU 2.5 17.4 + - - +
29F VAL* 3.7 4.0 - - - +
31F PHE* 1.3 70.4 - - - +
33F VAL* 1.3 67.4 + - - +
35F TYR* 3.0 1.6 + - - +
36F PHE* 2.9 31.9 + - + -
12G LEU* 5.1 1.3 - - + -
36G PHE* 3.5 35.9 - - + -
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Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F VAL 2.7 24.2 + - - +
30F ASP* 3.4 9.4 - - - +
32F ALA* 1.3 77.5 - - - +
34F GLU* 1.3 63.3 + - + +
36F PHE* 3.3 2.6 + - - +
37F THR* 2.7 36.4 + - - +
33G VAL* 4.0 4.2 - - - +
36G PHE* 2.7 41.2 - - - +
37G THR* 2.8 32.3 - - + +
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Residues in contact with GLU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ASP* 4.5 1.8 - - - +
30F ASP* 2.9 43.7 + - - +
31F PHE* 3.9 6.4 - - - +
33F VAL* 1.3 84.6 - - + +
35F TYR* 1.3 54.6 + - - +
37F THR* 3.3 7.2 + - - -
38F ARG* 2.9 65.4 + - - +
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Residues in contact with TYR 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 4.8 1.7 + - + +
15F GLY* 3.4 8.7 - - - -
16F TYR* 3.4 43.3 + + + -
19F GLU* 3.8 24.9 - - + +
31F PHE* 2.8 34.6 + + + +
32F ALA* 3.4 4.7 - - - +
34F GLU* 1.3 77.8 - - - +
36F PHE* 1.3 74.7 + + - +
38F ARG* 2.7 26.4 - - - +
39F LEU* 3.0 59.3 + - + +
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Residues in contact with PHE 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 3.1 32.8 - - + -
13F LEU* 5.8 4.5 - - + -
16F TYR* 3.7 37.7 - + + -
32F ALA 2.9 24.9 + - - +
35F TYR* 1.3 81.1 - + - +
37F THR* 1.3 60.0 + - - +
38F ARG 3.3 0.2 - - - -
39F LEU* 3.1 18.4 - - + +
40F ARG 2.9 23.6 + - - -
16G TYR* 6.0 1.3 - + - -
29G VAL* 4.3 3.7 - - + +
32G ALA* 3.6 15.9 - - + -
33G VAL* 2.9 34.1 - - + +
36G PHE* 3.3 39.0 - + - -
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Residues in contact with THR 37 (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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33F VAL* 2.7 28.0 + - - +
34F GLU* 3.5 8.2 - - - -
35F TYR 3.3 0.2 - - - -
36F PHE* 1.3 75.6 - - - +
38F ARG* 1.3 66.5 + - - +
40F ARG* 3.4 6.0 + - - +
41F GLU* 2.9 49.5 + - + +
33G VAL* 3.0 21.8 - - + +
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Residues in contact with ARG 38 (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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31F PHE* 3.2 25.7 + - - -
34F GLU* 2.9 50.3 + - + +
35F TYR* 2.7 49.9 - - + +
37F THR* 1.3 77.3 - - - +
39F LEU* 1.3 64.6 + - + +
41F GLU* 4.0 3.7 - - - +
42F ALA* 3.0 23.0 + - - +
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Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 4.0 12.1 - - + -
35F TYR* 3.0 52.9 + - + +
36F PHE* 3.1 35.7 - - + +
37F THR 3.1 0.8 - - - -
38F ARG* 1.3 74.1 - - + +
40F ARG* 1.3 58.9 + - - +
42F ALA* 2.7 34.5 + - + +
43F ARG* 2.9 7.4 + - - +
29G VAL* 4.4 16.6 - - + -
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Residues in contact with ARG 40 (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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36F PHE 2.9 14.1 + - - +
37F THR* 4.2 6.8 - - - +
39F LEU* 1.3 72.4 - - - +
41F GLU* 1.3 95.9 + - - +
43F ARG* 2.8 28.6 + - + +
29G VAL* 4.3 14.7 - - + +
30G ASP* 2.6 53.5 + - - +
33G VAL* 3.1 39.5 - - + +
34G GLU* 3.4 12.7 + - - +
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Residues in contact with GLU 41 (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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37F THR* 2.9 33.9 + - + +
38F ARG* 4.2 3.4 - - - +
40F ARG* 1.3 112.5 + - - +
42F ALA* 1.3 66.2 + - - +
43F ARG 4.4 1.9 - - - -
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Residues in contact with ALA 42 (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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38F ARG 3.0 15.8 + - - +
39F LEU* 2.7 24.4 + - + +
41F GLU* 1.3 75.7 - - - +
43F ARG* 1.3 61.8 + - - +
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Residues in contact with ARG 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 2.9 9.7 + - - +
40F ARG* 2.8 25.1 + - + +
41F GLU 4.4 1.8 - - - -
42F ALA* 1.3 78.9 - - - +
29G VAL* 5.5 7.6 - - + -
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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