Contacts of the helix formed by residues 22 - 35 (chain F) in PDB entry 1M5P
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 LYS 22 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E A 4.2 18.2 + - - -
32E A 3.3 32.3 + - - -
20F LYS 4.6 9.1 + - - +
21F ILE* 1.3 78.1 - - - +
23F LYS* 1.3 56.0 + - - +
24F ASP* 3.4 18.4 - - - +
25F GLU* 3.2 13.6 + - + +
26F LEU* 2.7 34.1 + - - +
47F ARG* 4.2 14.2 - - - +
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Residues in contact with LYS 23 (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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43E U 4.7 7.2 + - - -
21F ILE 3.8 1.2 + - - -
22F LYS* 1.3 72.2 - - - +
24F ASP* 1.3 57.5 + - - +
26F LEU* 3.1 6.1 + - - +
27F LYS* 2.6 58.1 + - + +
45F VAL* 2.6 47.2 + - + +
46F SER* 3.8 3.6 - - - +
47F ARG* 4.2 16.6 - - + +
101F CA 2.8 26.3 - - - -
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Residues in contact with ASP 24 (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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22F LYS* 4.0 19.2 - - - +
23F LYS* 1.3 77.7 + - - +
25F GLU* 1.3 75.4 + - - +
27F LYS* 3.8 7.4 - - - +
28F LYS* 2.9 27.9 + - - +
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Residues in contact with GLU 25 (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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21F ILE* 3.6 13.9 - - + -
22F LYS* 3.2 20.4 + - + +
24F ASP* 1.3 90.0 + - - +
26F LEU* 1.3 61.6 + - - +
28F LYS* 3.5 26.7 + - - +
29F SER* 3.0 26.4 + - - -
78F TYR* 3.1 30.3 + - + +
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Residues in contact with LEU 26 (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 LEU* 4.6 27.1 - - + -
18F ASN* 5.0 7.0 - - + +
21F ILE* 3.3 27.5 - - + +
22F LYS 2.7 19.4 + - - +
23F LYS* 3.5 4.3 - - - +
25F GLU* 1.3 72.5 - - - +
27F LYS* 1.3 68.4 + - - +
29F SER* 3.4 3.9 + - - -
30F LEU* 2.9 36.1 + - + +
45F VAL* 3.6 26.2 - - + -
47F ARG* 5.3 4.3 - - - -
53F GLY 6.0 2.7 - - - +
54F GLN 4.9 2.0 - - - +
77F PHE* 3.6 31.2 - - + -
78F TYR* 4.7 2.0 - - + -
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Residues in contact with LYS 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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23F LYS* 2.6 45.7 + - + +
24F ASP* 3.8 6.1 - - - +
26F LEU* 1.3 75.7 - - - +
28F LYS* 1.3 64.6 + - - +
30F LEU* 3.1 6.5 + - - +
31F HIS* 3.0 22.0 + - - +
42F ASP* 4.7 7.1 + - - -
43F ILE* 2.9 44.9 + - + +
44F LEU* 5.0 3.0 - - - +
45F VAL* 4.2 15.3 - - + +
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Residues in contact with LYS 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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24F ASP 2.9 15.7 + - - +
25F GLU* 3.5 33.1 + - - +
27F LYS* 1.3 75.1 - - - +
29F SER* 1.3 68.0 + - - +
31F HIS* 3.1 10.2 + - - +
32F ALA* 3.0 21.9 + - + +
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Residues in contact with SER 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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25F GLU* 3.0 13.1 + - - -
26F LEU 3.9 1.3 - - - -
28F LYS* 1.3 82.0 - - - +
30F LEU* 1.3 65.0 + - - +
32F ALA* 2.8 18.3 + - - +
33F ILE* 2.9 23.6 + - - +
77F PHE* 3.6 22.2 - - - -
78F TYR* 2.6 30.4 + - - -
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Residues in contact with LEU 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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14F ILE* 4.1 14.8 - - + -
17F LEU* 4.6 3.6 - - + -
26F LEU* 2.9 31.3 + - + +
27F LYS 3.3 7.4 - - - +
29F SER* 1.3 76.9 - - - +
31F HIS* 1.3 58.7 + - - +
33F ILE* 3.2 0.7 + - - -
34F PHE* 2.9 67.2 + - + +
43F ILE* 4.2 20.6 - - + -
45F VAL* 4.3 2.0 - - + -
55F ALA* 3.7 28.3 - - + -
57F VAL* 4.6 1.8 - - + -
77F PHE* 3.8 13.7 - - + -
82F MET* 4.3 12.6 - - + -
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Residues in contact with HIS 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 LYS 3.0 8.7 + - - +
28F LYS* 3.1 12.8 + - - +
30F LEU* 1.3 76.8 - - - +
32F ALA* 1.3 58.3 + - - +
35F SER* 2.9 49.7 + - - -
40F ILE* 3.9 37.0 - - + +
43F ILE* 3.6 25.0 - - + +
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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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28F LYS* 3.0 13.4 + - + +
29F SER* 2.8 13.1 + - - +
31F HIS* 1.3 80.4 - - - +
33F ILE* 1.3 69.0 + - + +
34F PHE 3.7 0.2 + - - -
35F SER* 4.3 9.2 + - - -
36F ARG* 5.3 2.8 + - - +
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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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29F SER* 2.9 27.7 + - - +
30F LEU 3.8 2.7 - - - +
32F ALA* 1.3 87.4 - - + +
34F PHE* 1.3 72.4 + - + +
36F ARG* 4.1 9.9 - - - +
37F PHE* 4.0 8.0 - - - -
72F MET* 3.0 37.2 - - + +
75F PHE* 4.3 20.4 - - + -
77F PHE* 3.9 23.1 - - + -
82F MET* 5.3 0.9 - - - -
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Residues in contact with PHE 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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12F ILE* 4.2 11.0 - - + -
14F ILE* 3.6 20.9 - - + -
30F LEU* 2.9 55.4 + - + +
33F ILE* 1.3 87.2 - - + +
35F SER* 1.3 63.8 + - - +
36F ARG 3.0 5.2 + - - -
37F PHE* 3.2 19.7 + + - -
40F ILE* 3.8 13.9 - - + -
57F VAL* 4.7 8.1 - - + -
59F PHE* 3.8 14.7 - + + -
68F ALA* 4.0 19.7 - - + -
72F MET* 3.6 30.5 - - + -
82F MET* 3.7 23.1 - - + -
84F ILE* 4.0 9.2 - - + -
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Residues in contact with SER 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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31F HIS* 2.9 42.5 + - - -
32F ALA* 4.3 7.4 + - - -
33F ILE 3.8 0.8 - - - -
34F PHE* 1.3 72.2 - - - +
36F ARG* 1.3 62.8 + - - +
37F PHE 3.1 2.5 + - - -
38F GLY 3.3 16.0 + - - +
40F ILE* 3.7 12.3 - - - +
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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