Contacts of the strand formed by residues 46 - 51 (chain O) in PDB entry 3SDI
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 VAL 46 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40O ILE 3.4 19.7 - - - +
41O LYS* 4.0 8.7 - - + -
42O ALA 4.5 0.2 - - - +
45O GLY* 1.3 79.9 - - - +
47O VAL* 1.3 64.8 + - - +
48O ILE* 4.3 0.4 - - - +
139O ALA* 3.7 27.6 - - + -
140O GLY 4.4 3.1 - - - +
147O SER* 3.7 45.3 - - + +
148O LEU* 4.1 15.3 - - + -
186O LEU* 4.0 2.6 - - - +
213O ALA 4.1 0.2 - - - +
214O ILE* 3.3 5.2 - - - +
215O ILE* 2.8 36.0 + - + +
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Residues in contact with VAL 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O LEU* 5.1 0.5 - - - +
39O GLY* 3.0 6.6 - - - -
40O ILE* 2.9 44.9 + - + +
46O VAL* 1.3 76.2 - - - +
48O ILE* 1.3 69.0 + - - +
186O LEU* 4.8 1.8 - - + -
189O ALA* 3.7 33.2 - - + +
190O ILE* 4.2 6.1 - - + +
193O ALA* 4.3 12.1 - - + -
212O LEU* 3.6 32.1 - - + -
213O ALA 3.5 9.9 - - - +
214O ILE* 4.5 9.6 - - + -
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Residues in contact with ILE 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O LEU 3.3 10.1 - - - +
39O GLY* 4.1 0.4 - - - -
47O VAL* 1.3 78.8 - - - +
49O ALA* 1.3 61.1 + - - +
67O VAL* 3.7 26.5 - - + +
75O GLY* 3.8 11.2 - - - +
76O ALA* 3.7 36.1 - - - +
77O VAL* 3.8 15.0 - - + +
137O LEU* 4.4 7.0 - - + +
139O ALA* 3.9 23.6 - - + -
148O LEU* 4.1 14.4 - - + -
212O LEU* 3.4 3.6 - - - +
213O ALA* 2.9 40.3 + - + +
215O ILE* 5.8 2.9 - - + -
221O PHE* 5.1 0.4 - - + -
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Residues in contact with ALA 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O SER* 3.2 2.9 - - - -
38O LEU* 2.9 53.3 + - + +
47O VAL* 4.7 0.2 - - + -
48O ILE* 1.3 75.7 - - - +
50O THR* 1.3 64.6 + - - +
67O VAL* 5.1 0.9 - - - -
77O VAL* 4.5 3.8 - - - +
193O ALA* 4.7 3.8 - - + -
197O LEU* 4.2 10.5 - - + -
211O GLU 3.3 6.1 - - - -
212O LEU* 3.3 30.5 - - + -
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Residues in contact with THR 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O THR 2.9 22.2 + - - -
37O SER* 3.4 13.1 - - - -
49O ALA* 1.3 77.9 - - - +
51O GLU* 1.3 60.8 + - - +
66O LYS* 3.2 51.6 + - + +
67O VAL* 4.5 0.2 - - + -
77O VAL* 3.8 13.0 - - + -
78O TYR 4.4 0.2 + - - -
197O LEU* 3.8 14.6 - - - +
210O ILE* 3.7 3.5 - - - -
211O GLU* 3.0 40.2 + - + +
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Residues in contact with GLU 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O VAL* 3.4 25.0 - - + +
36O THR* 3.9 4.5 + - - +
50O THR* 1.3 78.8 + - - +
52O LYS* 1.3 63.5 + - - +
53O LYS* 3.3 36.5 + - - +
66O LYS* 3.3 23.7 + - - +
197O LEU* 5.3 2.0 - - + -
200O SER* 4.8 3.8 + - - +
202O VAL* 3.6 46.7 - - + +
203O GLU* 4.4 9.8 + - - +
204O GLY 5.9 0.2 + - - -
209O THR* 3.4 12.8 - - + +
210O ILE* 4.3 2.9 - - + -
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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