Contacts of the strand formed by residues 32 - 37 (chain F) in PDB entry 3SR2
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 PHE 32 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F VAL* 4.6 11.7 - - + -
23F SER 3.6 13.7 - - - +
24F TRP* 4.0 2.7 - - + +
28F LEU* 3.2 46.0 - - + -
31F GLY* 1.3 74.6 - - - +
33F VAL* 1.3 71.5 + - - +
34F ILE* 4.9 9.0 - - + -
46F THR* 4.5 1.6 - - - +
47F VAL* 3.0 64.8 + - + +
52F ILE* 3.4 26.9 - - + -
70F LEU* 4.3 20.9 - - + -
74F LEU* 4.9 10.5 - - + -
111F PHE* 4.9 8.3 - + - -
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Residues in contact with VAL 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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21F GLN* 6.0 0.2 + - - -
22F VAL* 3.7 4.0 - - - +
23F SER* 3.0 47.7 + - - +
32F PHE* 1.3 79.1 - - - +
34F ILE* 1.3 61.1 + - - +
35F THR* 5.0 3.1 + - - +
44F THR* 3.9 19.1 - - + -
45F GLY 3.2 17.7 - - - +
46F THR* 3.6 19.3 - - + +
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Residues in contact with ILE 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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20F LEU* 5.3 9.2 - - + -
21F GLN 3.6 10.5 - - - +
22F VAL* 3.7 14.6 - - + -
32F PHE* 4.9 11.4 - - + -
33F VAL* 1.3 74.4 - - - +
35F THR* 1.3 70.6 - - - +
44F THR* 3.1 7.3 - - - +
45F GLY* 2.9 39.6 + - - +
47F VAL* 5.7 6.5 - - + -
74F LEU* 4.0 35.7 - - + -
95F PHE* 5.9 3.1 - - + -
111F PHE* 4.9 16.4 - - + -
113F LEU* 3.4 28.9 - - + -
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Residues in contact with THR 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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19F PHE 3.8 0.4 - - - +
20F LEU* 3.3 7.8 - - - +
21F GLN* 2.9 60.3 + - - +
33F VAL* 5.0 2.6 + - - +
34F ILE* 1.3 81.7 + - - +
36F LEU* 1.3 64.1 + - - +
37F THR* 5.4 2.9 - - - -
42F ALA* 5.2 2.7 - - + -
43F TRP 3.1 21.5 - - - +
44F THR* 3.4 16.6 - - - +
113F LEU* 5.6 0.4 - - - -
122F VAL* 4.3 22.4 - - + -
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Residues in contact with LEU 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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8F ILE* 4.1 0.7 - - + -
10F LEU* 3.8 31.4 - - + -
18F HIS* 4.3 13.7 - - + -
19F PHE 3.3 4.3 - - - +
20F LEU* 3.3 28.3 - - + -
35F THR* 1.3 74.7 - - - +
37F THR* 1.3 64.2 + - - +
43F TRP* 2.9 75.9 + - + +
88F PHE* 4.8 9.2 - - + -
95F PHE* 3.9 17.7 - - + -
113F LEU* 4.7 13.8 - - + +
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Residues in contact with THR 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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127E ILE* 5.5 10.3 - - + -
18F HIS* 4.6 4.0 - - - -
19F PHE* 3.0 37.2 + - + +
35F THR* 4.3 4.7 - - - -
36F LEU* 1.3 72.6 - - - +
38F ASP* 1.3 59.1 + - - +
39F GLY* 3.4 16.4 - - - +
41F SER 2.3 28.0 + - - +
42F ALA* 2.6 23.5 - - - +
43F TRP* 4.7 1.1 - - - -
122F VAL* 6.2 0.9 - - - -
123F ILE* 4.8 12.1 - - + -
126F LEU* 6.2 3.6 - - + -
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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