Contacts of the helix formed by residues 25 - 35 (chain F) in PDB entry 1MA1
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 SER 25 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F TYR 4.4 0.2 - - - -
21F GLU* 4.0 11.9 - - - +
22F PRO* 4.8 3.9 + - - -
23F HIS 4.2 0.6 - - - -
24F ILE* 1.3 76.8 - - - +
26F ARG* 1.3 64.6 + - - +
27F GLU* 3.4 8.0 + - - +
28F GLN 2.9 16.5 + - - -
29F LEU* 2.9 23.0 + - - +
174F ILE* 5.0 0.2 - - - +
175F ASP* 2.7 36.4 + - - -
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Residues in contact with ARG 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 TYR* 3.1 38.8 - - + +
18F ASP* 4.0 11.9 - - + +
21F GLU* 3.1 20.9 + - - +
25F SER* 1.3 74.0 - - - +
27F GLU* 1.3 76.3 + - - +
29F LEU* 3.9 0.5 - - - +
30F THR* 2.5 42.6 + - - +
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Residues in contact with GLU 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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177E ARG* 2.6 32.9 + - - -
25F SER* 3.2 8.1 + - - +
26F ARG* 1.3 96.0 - - - +
28F GLN* 1.3 65.2 + - - +
30F THR* 3.3 4.8 + - - -
31F ILE* 2.9 29.6 + - + +
174F ILE* 3.5 24.5 - - + +
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Residues in contact with GLN 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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173E TYR* 5.0 0.8 - - - -
24F ILE* 3.8 10.3 - - + -
25F SER* 2.9 11.9 + - - +
27F GLU* 1.3 76.2 - - - +
29F LEU* 1.3 62.7 + - - +
31F ILE* 3.5 4.3 - - - +
32F HIS* 3.3 19.8 + - + +
170F HIS 2.9 24.2 + - - -
171F ALA* 3.4 22.1 - - - +
172F TYR* 3.1 11.9 - - - -
174F ILE* 3.0 47.9 + - + +
175F ASP* 3.1 32.2 + - + +
183F TYR* 6.0 0.2 - - + -
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Residues in contact with LEU 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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13F LEU* 3.5 27.8 - - + -
15F TYR* 4.1 4.7 - - + -
16F PRO 4.4 0.4 - - - +
17F TYR* 3.6 33.0 - - + +
20F LEU* 3.7 37.7 - - + -
24F ILE* 4.0 10.8 - - + -
25F SER 2.9 16.2 + - - +
28F GLN* 1.3 75.5 - - - +
30F THR* 1.3 65.1 + - - +
32F HIS* 3.5 3.9 + - - +
33F HIS* 3.1 19.0 + - + +
84F TRP* 3.8 28.3 - - + -
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Residues in contact with THR 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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17F TYR* 3.3 31.5 - - + +
26F ARG* 2.5 29.1 + - - +
27F GLU* 3.3 5.4 + - - -
29F LEU* 1.3 79.0 - - - +
31F ILE* 1.3 60.4 + - - +
34F GLN* 2.8 55.6 + - + +
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Residues in contact with ILE 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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173E TYR* 3.1 26.9 - - + +
177E ARG* 3.8 21.3 - - + -
178E ASN* 3.5 20.9 - - + +
27F GLU* 2.9 21.3 - - + +
28F GLN* 3.5 8.7 - - - +
30F THR* 1.3 75.7 - - + +
32F HIS* 1.3 65.8 + - - +
34F GLN* 4.8 0.2 - - - -
35F LYS* 2.9 43.4 + - + +
36F HIS* 3.4 2.0 + - - +
174F ILE* 3.7 16.8 - - + -
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Residues in contact with HIS 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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173E TYR* 5.2 0.2 + - - -
28F GLN* 3.3 21.2 + - - +
29F LEU* 3.8 5.7 - - - +
31F ILE* 1.3 77.6 - - - +
33F HIS* 1.3 58.5 + - - +
36F HIS* 3.4 13.3 + - + +
37F HIS* 3.0 25.3 + - - +
80F HIS* 3.2 13.1 + + - -
83F PHE* 3.8 18.0 - + - -
84F TRP* 3.4 18.9 - + + -
166F ASP* 2.4 14.9 + - + -
170F HIS* 3.3 19.0 - + - +
171F ALA* 3.2 30.1 + - + -
183F TYR* 5.1 0.2 - - - -
206F FE 2.1 30.8 - - - -
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Residues in contact with HIS 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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10F LEU* 3.6 23.5 - - + +
11F PRO 2.7 29.1 + - - -
12F GLU* 4.6 2.0 - - - -
13F LEU* 3.2 34.7 - - + +
17F TYR* 2.7 33.1 + - + -
29F LEU* 3.1 18.5 + - + +
30F THR 3.9 2.5 - - - +
32F HIS* 1.3 78.4 - - - +
34F GLN* 1.3 63.5 + - - +
37F HIS* 3.2 26.8 - - - +
38F GLN 3.4 4.9 + - - -
84F TRP* 3.5 26.9 - - + -
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Residues in contact with GLN 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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10F LEU* 4.6 12.2 - - - +
17F TYR* 2.9 40.6 + - - +
30F THR* 2.8 36.1 + - + +
31F ILE* 4.8 0.2 - - - -
33F HIS* 1.3 80.8 - - - +
35F LYS* 1.3 72.6 + - + +
38F GLN* 3.1 21.3 - - - +
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Residues in contact with LYS 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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178E ASN* 3.6 41.2 - - + +
31F ILE* 2.9 34.1 + - + +
34F GLN* 1.3 87.9 - - + +
36F HIS* 1.3 62.7 + - + +
38F GLN* 3.6 3.2 - - - +
39F ALA* 3.0 26.2 + - - +
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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