Contacts of the strand formed by residues 41 - 48 (chain A) in PDB entry 1STU
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 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.2 3.7 - - - +
38A VAL* 2.5 43.2 + - + +
39A GLY* 5.4 0.7 - - - -
40A SER* 1.3 97.8 - - - +
42A VAL* 1.3 74.8 + - + +
43A THR* 4.9 1.1 - - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LYS* 5.2 8.5 - - - +
35A ALA* 4.6 16.8 - - + -
36A CYS 4.2 1.1 - - - +
37A ILE* 3.7 31.6 - - + +
40A SER 5.8 0.2 - - - +
41A ILE* 1.3 85.8 - - + +
43A THR* 1.3 71.2 + - - +
44A GLU* 4.2 6.5 - - + +
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Residues in contact with THR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A CYS* 2.7 45.5 + - - +
38A VAL* 4.5 10.0 - - - +
41A ILE* 4.5 1.0 + - - +
42A VAL* 1.3 83.3 + - - +
44A GLU* 1.3 55.8 + - - +
61A MET* 3.5 32.6 - - - +
64A GLU* 3.4 41.5 - - + +
65A LEU* 5.3 0.5 - - - +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.1 30.2 - - - +
22A ARG* 5.0 0.8 + - - -
33A ILE* 3.3 23.7 - - + +
34A THR 2.9 14.4 - - - +
35A ALA* 3.1 22.6 - - + +
36A CYS* 4.1 2.2 - - - -
42A VAL* 5.1 6.4 - - + +
43A THR* 1.3 83.2 - - - +
45A GLY* 1.3 61.0 + - - +
60A LYS* 3.8 20.7 + - - +
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE 3.1 0.2 - - - +
33A ILE* 4.0 1.3 - - - +
34A THR* 2.7 35.1 + - - +
44A GLU* 1.3 78.7 - - - +
46A GLU* 1.3 65.2 + - - -
47A GLY 3.0 7.4 + - - -
56A ARG* 4.3 2.2 - - - -
57A ALA* 3.9 17.2 + - - -
60A LYS* 4.1 15.3 - - - -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASN* 4.2 17.7 + - + +
32A PHE 3.0 9.2 - - - +
33A ILE* 3.4 35.2 - - + +
45A GLY* 1.3 71.9 - - - -
47A GLY* 1.3 62.3 + - - +
48A ASN 3.4 3.1 + - - -
56A ARG* 3.7 9.5 + - - +
60A LYS* 4.2 19.1 + - - +
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE 2.8 26.6 + - - +
45A GLY 3.0 6.7 + - - -
46A GLU* 1.3 71.4 - - - +
48A ASN* 1.3 57.3 + - - -
49A GLY 2.8 13.0 + - - +
52A VAL* 2.9 17.4 - - - +
53A SER* 3.8 4.7 + - - +
56A ARG* 2.9 29.4 - - - +
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Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A MET* 4.2 12.5 - - - +
30A LYS* 3.3 20.7 + - - +
31A ASN* 2.7 29.2 + - - +
46A GLU 3.4 6.0 + - - +
47A GLY* 1.3 66.5 - - - -
49A GLY* 1.3 60.3 + - - +
52A VAL* 2.8 17.2 - - - +
56A ARG* 3.9 20.2 - - - +
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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