Contacts of the strand formed by residues 28 - 36 (chain F) in PDB entry 4PJO
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 GLU 28 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72E LYS* 4.1 16.6 + - - -
20F MET* 3.2 33.3 - - + +
21F VAL 3.1 13.7 - - - +
22F LYS* 4.0 30.8 + - + +
26F GLY 4.3 1.8 - - - +
27F MET* 1.3 77.3 - - - +
29F TYR* 1.3 69.6 + - - +
48F GLU 3.9 0.2 - - - +
49F GLU* 3.7 1.2 - - - +
50F TYR* 2.9 41.9 + - + +
53F GLY* 3.6 30.9 + - - +
71F TYR* 4.8 2.3 + - - -
73F ARG* 4.6 4.3 + - - -
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Residues in contact with TYR 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ASN* 4.6 3.6 + - - -
107D ILE* 5.7 0.2 - - - +
108D VAL* 4.1 21.9 - - + +
20F MET* 3.4 3.3 - - - -
21F VAL 2.8 34.0 + - - +
23F LEU* 3.6 36.1 - - + -
27F MET* 4.2 21.7 - - + -
28F GLU* 1.3 75.2 - - - +
30F LYS* 1.3 61.8 + - - +
44F LEU* 3.7 15.3 - - + +
47F THR* 3.8 17.0 - - + -
48F GLU 3.4 5.8 - - - -
49F GLU* 2.6 28.1 + - + -
59F LEU* 3.3 35.2 - - + -
62F VAL* 5.0 3.6 - - + -
64F ILE* 4.3 13.2 - - + -
40K GLY* 4.6 1.9 - - - -
41K ILE* 4.2 7.1 - - - +
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Residues in contact with LYS 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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18F PRO* 5.8 4.5 - - + -
19F VAL 3.3 9.2 - - - +
20F MET* 3.4 25.3 - - + +
29F TYR* 1.3 73.2 - - - +
31F GLY* 1.3 62.8 + - - +
44F LEU* 4.3 0.4 - - - -
46F ASN 3.6 1.9 - - - +
47F THR* 3.1 6.0 - - - -
48F GLU* 2.8 46.6 + - + +
50F TYR* 3.2 41.5 + - + -
75F VAL 4.0 20.6 - - - +
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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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18F PRO* 4.1 5.2 - - - -
19F VAL* 2.9 36.1 + - - +
30F LYS* 1.3 78.5 - - - +
32F TYR* 1.3 62.1 + - - -
33F LEU 3.1 5.2 + - - -
44F LEU* 4.1 8.9 - - - +
45F ALA 3.4 11.2 - - - -
46F ASN 4.0 4.7 - - - -
47F THR* 4.3 2.5 - - - -
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Residues in contact with TYR 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 GLY 3.6 22.9 - - - +
17F LYS 3.7 2.5 - - - -
18F PRO* 3.5 33.2 - - + +
31F GLY* 1.3 70.9 - - - -
33F LEU* 1.3 67.7 + - - +
34F VAL* 3.1 8.1 + - + +
44F LEU* 3.6 0.8 - - - -
45F ALA* 2.8 45.5 + - + +
46F ASN* 4.0 24.2 - - + -
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Residues in contact with LEU 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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11F LEU* 4.3 8.5 - - + +
14F LEU* 3.9 32.3 - - + +
15F THR* 4.0 8.3 - - + -
16F GLY* 2.9 28.8 + - - -
17F LYS 3.2 5.3 + - - -
19F VAL* 3.6 14.6 - - + -
31F GLY 3.1 6.9 + - - -
32F TYR* 1.3 70.2 - - - +
34F VAL* 1.3 59.0 + - - +
35F SER 3.4 26.5 - - - +
36F VAL* 3.6 18.8 - - + -
42F MET* 4.4 7.2 - - + -
43F GLN 3.6 9.4 - - - +
44F LEU* 4.4 10.8 - - + -
72F ILE* 3.7 27.4 - - + -
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Residues in contact with VAL 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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26D THR 5.6 1.3 - - - +
15F THR* 4.2 11.8 - - - +
16F GLY 5.2 0.3 + - - -
32F TYR* 3.2 17.9 - - + +
33F LEU* 1.3 74.5 - - - +
35F SER* 1.3 63.9 + - - +
43F GLN* 3.0 43.8 + - + +
44F LEU 4.1 2.0 - - - -
45F ALA* 3.6 24.0 - - + +
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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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26D THR 4.0 7.6 - - - -
27D GLY* 3.4 19.9 + - - -
28D PRO* 3.3 8.0 - - - +
15F THR* 5.0 3.8 - - - -
33F LEU* 3.4 3.9 - - - +
34F VAL* 1.3 80.5 - - - +
36F VAL* 1.3 74.0 + - - +
42F MET* 3.7 0.5 - - - -
43F GLN* 2.6 55.5 + - - +
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Residues in contact with VAL 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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27D GLY* 5.0 2.3 - - - -
28D PRO* 3.7 6.8 - - - +
8F LYS* 6.3 1.8 - - + -
11F LEU* 4.3 26.7 - - + -
12F ASN* 5.6 3.8 - - - +
15F THR* 4.6 8.1 - - + +
33F LEU* 3.6 28.3 - - + -
35F SER* 1.3 87.4 - - - +
37F ASP* 1.3 75.6 + - - +
40F MET* 3.9 19.1 - - + -
41F ASN 3.4 14.4 - - - +
42F MET* 4.3 4.0 - - + -
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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