Contacts of the strand formed by residues 18 - 26 (chain F) in PDB entry 2MF0
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 ILE 18 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E ILE* 4.1 35.2 - - + -
18E ILE* 6.1 4.0 - - + -
13F ASN* 3.0 6.5 - - - +
14F ILE* 2.8 60.3 + - + +
15F GLY* 4.6 5.2 - - - -
16F ASP 5.0 0.2 - - - +
17F ASP* 1.3 87.6 - - + +
19F THR* 1.3 67.2 + - - +
20F ILE* 4.4 6.3 - - + -
34F ILE* 4.4 1.8 - - + -
35F ASN 3.3 9.6 - - - +
36F ALA* 4.0 22.2 - - + -
37F PRO* 4.1 7.2 - - + -
40F VAL* 4.8 9.0 - - + -
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Residues in contact with THR 19 (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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1E MET* 5.1 1.0 - - + +
45E GLU* 4.4 7.0 - - - +
11F SER* 4.7 6.3 - - - +
12F ILE 3.6 10.5 - - - +
13F ASN* 3.1 20.1 + - - +
17F ASP 4.5 4.5 + - - -
18F ILE* 1.3 72.6 - - - +
20F ILE* 1.3 74.2 + - - +
21F THR* 4.5 7.6 - - - +
33F GLY 4.2 0.2 - - - +
34F ILE* 3.6 2.3 - - - +
35F ASN* 2.8 50.2 + - + +
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Residues in contact with ILE 20 (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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14E ILE* 3.8 17.9 - - + -
20E ILE* 5.2 12.8 - - + -
32E ILE* 5.9 7.0 - - + -
34E ILE* 6.4 0.2 - - + -
11F SER* 3.2 6.1 - - - -
12F ILE* 2.8 52.6 + - + +
14F ILE* 4.0 22.9 - - + -
18F ILE* 4.4 3.1 - - + -
19F THR* 1.3 75.1 - - - +
21F THR* 1.3 70.1 + - - +
22F ILE 5.1 0.2 - - - +
32F ILE* 4.3 16.2 - - + -
33F GLY 3.5 7.2 - - - +
34F ILE* 3.7 34.5 - - + -
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Residues in contact with THR 21 (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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1E MET* 4.6 10.0 - - - +
9F GLY* 4.6 7.9 - - - +
10F GLU 3.6 8.7 - - - +
11F SER* 3.0 21.7 + - - +
19F THR* 4.5 6.6 - - - +
20F ILE* 1.3 75.3 + - - +
22F ILE* 1.3 67.6 + - - +
23F LEU* 3.5 23.0 + - + +
32F ILE* 3.6 6.4 - - - +
33F GLY 2.9 36.8 + - - +
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Residues in contact with ILE 22 (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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30E VAL* 4.1 20.0 - - + -
32E ILE* 5.0 9.9 - - + -
6F ARG* 3.5 21.1 - - + +
7F LYS 3.1 25.1 - - - +
8F VAL* 3.9 14.4 - - + -
9F GLY* 2.8 32.7 + - - -
10F GLU 3.1 13.7 + - - +
20F ILE* 5.1 0.2 - - - +
21F THR* 1.3 70.9 - - - +
23F LEU* 1.3 58.2 + - - +
24F GLY 3.6 10.8 - - - +
30F VAL* 3.2 34.8 - - + -
31F ARG 3.4 10.8 - - - +
32F ILE* 4.7 6.3 - - + +
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Residues in contact with LEU 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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1E MET* 5.2 2.2 - - + -
3E ILE* 3.7 29.8 - - + -
8F VAL* 4.7 2.6 - - - +
9F GLY* 4.7 3.9 + - - +
21F THR* 3.8 28.0 - - + +
22F ILE* 1.3 72.4 - - - +
24F GLY* 1.3 55.3 + - - +
31F ARG* 2.8 31.1 + - + +
32F ILE 3.5 25.6 - - - +
33F GLY* 3.6 15.0 - - - +
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Residues in contact with GLY 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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8F VAL* 3.5 20.9 - - - -
22F ILE* 3.4 9.0 - - - +
23F LEU* 1.3 79.5 - - - +
25F VAL* 1.3 62.1 + - - -
30F VAL* 3.6 1.0 - - - -
31F ARG* 2.8 39.1 + - - +
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Residues in contact with VAL 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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25E VAL* 4.6 9.4 - - + -
27E GLY 3.9 22.2 - - - +
28E GLN* 4.4 13.9 - - - +
30E VAL* 3.8 23.6 - - + -
8F VAL* 3.8 16.4 - - + +
24F GLY* 1.3 77.7 - - - +
26F SER* 1.3 67.1 + - - +
27F GLY 4.7 10.8 - - - +
29F GLN 3.8 6.5 - - - +
30F VAL* 4.6 4.7 - - + -
31F ARG* 5.2 2.5 + - - -
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Residues in contact with SER 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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5E THR* 5.4 3.6 - - - -
25F VAL* 1.3 75.0 + - - +
27F GLY* 1.3 64.2 + - - +
28F GLN 3.2 0.7 + - - -
29F GLN* 2.8 36.3 + - - +
30F VAL* 4.7 0.2 - - - +
31F ARG* 3.5 28.1 + - - +
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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