Contacts of the helix formed by residues 26 - 37 (chain F) in PDB entry 1MVW
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 THR 26 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F LYS 4.3 1.1 - - - +
25F ILE* 1.3 76.4 - - - +
27F ALA* 1.3 60.2 + - - +
28F SER* 3.0 21.2 + - - -
29F GLN* 2.9 45.8 + - - +
30F VAL* 3.5 5.5 - - - +
61F ALA* 3.5 28.7 - - - +
62F ALA* 4.4 1.3 - - - -
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Residues in contact with ALA 27 (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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25F ILE 3.7 0.6 + - - -
26F THR* 1.3 72.0 - - - +
28F SER* 1.3 60.1 + - - +
29F GLN 3.3 0.9 + - - -
30F VAL* 3.3 25.5 + - - +
31F GLY 4.4 1.7 + - - -
46F ILE* 5.9 0.5 - - - +
50F LEU* 4.9 10.4 - - + +
56F GLU 5.6 0.9 - - - +
57F GLU* 4.5 31.4 - - + +
61F ALA* 3.6 25.7 - - + +
63F ILE* 4.1 12.6 - - + +
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Residues in contact with SER 28 (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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26F THR* 3.0 17.4 + - - -
27F ALA* 1.3 78.3 - - - +
29F GLN* 1.3 62.8 + - - +
30F VAL 3.4 0.4 + - - -
31F GLY* 4.4 4.0 + - - -
32F ASP* 4.1 10.2 - - - +
57F GLU* 5.8 9.8 - - - +
61F ALA* 5.4 0.2 - - - +
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Residues in contact with GLN 29 (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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17F PHE* 3.0 32.9 + - - +
18F ASP* 5.4 1.2 - - - -
19F ARG* 4.5 15.7 + - - +
24F LYS 5.2 0.2 - - - +
25F ILE* 3.6 15.9 - - + +
26F THR* 2.9 46.5 + - - +
28F SER* 1.3 80.2 - - - +
30F VAL* 1.3 60.3 + - - +
31F GLY 3.3 2.2 - - - -
32F ASP* 3.1 11.1 + - - +
33F ILE* 3.0 34.9 + - + +
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Residues in contact with VAL 30 (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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25F ILE 4.4 0.4 - - - +
26F THR 3.5 16.6 - - - +
27F ALA* 3.3 19.4 + - - +
29F GLN* 1.3 76.0 - - - +
31F GLY* 1.3 62.9 + - - +
33F ILE* 4.0 0.3 - - - +
34F ALA* 3.0 25.9 + - + +
46F ILE* 5.4 7.2 - - + -
50F LEU* 5.5 7.0 - - + -
63F ILE* 3.9 17.7 - - + -
68F PHE* 3.7 39.6 - - + -
71F MET* 3.9 20.4 - - + -
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Residues in contact with GLY 31 (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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27F ALA 4.4 1.8 + - - -
28F SER 4.4 3.6 + - - -
29F GLN 3.3 0.8 - - - -
30F VAL* 1.3 81.2 - - - +
32F ASP* 1.3 64.1 + - - +
34F ALA* 3.3 10.7 + - - +
35F ARG* 3.3 19.7 + - - +
43F ASN* 5.5 2.0 - - - -
46F ILE* 3.7 37.3 - - - +
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Residues in contact with ASP 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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799D MET* 2.2 63.4 - - + +
17F PHE* 6.1 0.4 - - - -
28F SER 4.1 11.8 - - - +
29F GLN* 3.1 10.0 + - - +
31F GLY* 1.3 77.1 - - - +
33F ILE* 1.3 59.6 + - + +
35F ARG* 3.3 8.9 + - - +
36F ALA* 3.0 26.2 + - - +
43F ASN* 5.5 2.6 + - - -
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Residues in contact with ILE 33 (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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14F PHE* 3.8 16.8 - - + -
17F PHE* 3.5 52.0 - - + -
25F ILE* 3.4 35.2 - - + -
29F GLN* 3.0 22.8 + - + +
31F GLY 3.3 0.2 - - - -
32F ASP* 1.3 77.6 - - + +
34F ALA* 1.3 60.0 + - - +
35F ARG 3.2 0.2 - - - -
36F ALA* 3.2 6.4 + - - -
37F LEU* 3.0 38.8 + - + +
68F PHE* 3.5 20.4 - - + -
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Residues in contact with ALA 34 (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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30F VAL* 3.0 19.9 + - + +
31F GLY* 3.6 6.3 - - - +
33F ILE* 1.3 74.4 - - - +
35F ARG* 1.3 62.4 + - - +
37F LEU* 3.1 11.4 + - - +
38F GLY 3.3 0.5 + - - -
39F GLN* 3.0 25.7 + - + +
41F PRO* 4.3 20.4 - - + -
46F ILE* 5.7 0.2 - - + -
68F PHE* 4.7 4.7 - - + -
72F LEU* 4.1 23.1 - - + -
75F ALA* 5.4 3.4 - - + -
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Residues in contact with ARG 35 (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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792D ALA 3.9 1.8 + - - -
795D ARG* 2.1 72.8 + - - +
796D GLY* 3.5 23.3 - - - +
799D MET* 3.9 23.8 - - + +
800D ARG* 4.5 15.4 - - - +
31F GLY 3.3 16.3 + - - +
32F ASP* 3.4 15.2 + - - +
33F ILE 3.2 0.2 - - - -
34F ALA* 1.3 77.1 - - - +
36F ALA* 1.3 55.6 + - - +
38F GLY* 3.1 18.4 + - - -
39F GLN 2.9 20.7 + - - +
40F ASN* 4.7 2.9 - - - +
41F PRO* 3.2 29.6 + - + +
42F THR* 4.1 0.8 - - - +
43F ASN* 3.6 16.1 + - - +
46F ILE* 4.7 0.8 - - - +
118F MET* 5.8 0.2 - - - -
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Residues in contact with ALA 36 (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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799D MET* 5.4 6.3 - - + +
800D ARG* 6.0 2.2 - - - +
803D TYR* 3.7 44.3 - - + -
806D MET* 6.1 0.4 - - - -
17F PHE* 3.8 19.5 - - + -
32F ASP 3.0 17.0 + - - +
33F ILE* 3.2 6.2 + - - +
35F ARG* 1.3 74.9 - - - +
37F LEU* 1.3 64.0 + - - +
38F GLY 3.4 0.4 - - - -
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Residues in contact with LEU 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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10F PHE* 3.6 40.9 - - + -
13F ALA* 3.9 27.6 - - + -
14F PHE* 3.6 28.5 - - + -
17F PHE* 5.4 0.9 - - + -
33F ILE* 3.0 22.5 + - + +
34F ALA* 3.1 6.4 + - - +
36F ALA* 1.3 81.7 - - - +
38F GLY* 1.3 59.1 + - - +
39F GLN* 3.7 1.9 - - - +
68F PHE* 5.0 1.6 - - + -
72F LEU* 3.6 34.5 - - + -
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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