Contacts of the strand formed by residues 47 - 52 (chain G) in PDB entry 5T0J
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 CYS 47 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43G ARG* 3.3 2.4 - - - +
44G GLY* 2.4 38.1 + - - +
45G LYS 3.5 0.8 - - - -
46G ASP* 1.3 82.7 - - - +
48G ALA* 1.3 55.5 + - - +
49G VAL* 5.4 0.4 - - + -
149G PRO* 3.5 5.1 - - - +
189G TRP 4.0 15.7 - - - -
190G THR 4.9 1.1 - - - -
191G PHE* 5.0 8.7 - - + -
194G THR* 3.6 33.4 - - - -
219G VAL* 4.7 4.9 - - + -
220G VAL 3.3 6.1 - - - -
221G THR* 3.2 28.9 - - + +
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Residues in contact with ALA 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G VAL 3.4 13.5 - - - +
43G ARG* 3.7 17.5 - - + -
44G GLY 4.2 0.7 - - - +
47G CYS* 1.3 75.7 - - - +
49G VAL* 1.3 63.2 + - - +
50G ILE* 4.3 1.6 + - + +
141G ILE* 5.1 1.3 - - + -
149G PRO* 4.4 4.3 - - + -
150G GLN 4.4 0.7 - - - +
151G VAL* 3.8 15.3 - - + -
194G THR* 6.1 0.4 - - - -
219G VAL* 3.4 2.8 - - - +
220G VAL* 2.8 51.4 + - + +
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Residues in contact with VAL 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G VAL 3.9 2.3 - - - +
42G VAL* 2.9 32.9 + - + +
47G CYS* 5.4 0.9 - - + -
48G ALA* 1.3 77.2 - - - +
50G ILE* 1.3 66.7 + - - +
51G VAL* 5.3 1.0 - - - +
191G PHE* 5.1 0.4 - - + -
194G THR* 3.3 49.1 - - + +
195G VAL* 4.8 7.2 - - + +
198G ALA* 4.6 10.1 - - + -
217G VAL* 3.7 20.9 - - + -
218G GLY 3.3 11.7 - - - +
219G VAL* 3.7 20.9 - - + -
230G LEU* 5.9 0.2 - - + -
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Residues in contact with ILE 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G SER* 4.9 1.6 - - - -
40G VAL 3.6 10.1 - - - +
41G ALA* 3.7 27.6 - - + -
42G VAL 4.5 1.6 - - - +
48G ALA 5.1 2.2 - - - +
49G VAL* 1.3 83.4 - - - +
51G VAL* 1.3 63.7 + - - +
52G THR* 4.2 9.0 - - - +
69G LEU* 5.4 4.6 - - + +
78G CYS 6.5 0.9 - - - -
79G VAL* 3.7 31.6 - - + -
139G ILE* 5.2 2.5 - - + -
141G ILE* 3.8 31.4 - - + -
151G VAL* 4.9 3.4 - - + -
216G GLU 4.0 0.5 - - - +
217G VAL* 3.3 5.5 - - - +
218G GLY* 2.8 40.9 + - - +
220G VAL* 5.7 0.9 - - + -
227G PHE* 5.6 6.1 - - + -
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Residues in contact with VAL 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G THR 3.6 2.2 - - - +
39G SER* 3.3 3.3 - - - -
40G VAL* 3.2 49.3 + - + +
42G VAL* 6.3 0.4 - - + -
49G VAL 5.3 1.3 - - - +
50G ILE* 1.3 72.6 - - - +
52G THR* 1.3 75.5 + - - +
53G GLN* 5.6 0.2 - - - +
198G ALA* 3.9 42.2 - - + +
199G ILE* 6.5 0.7 - - + -
201G CYS* 4.5 2.5 - - - -
202G LEU* 4.2 18.4 - - + -
215G ILE* 5.6 2.0 - - + -
216G GLU 3.8 2.0 - - - -
217G VAL* 4.2 15.0 - - + -
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Residues in contact with THR 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LEU* 3.6 31.6 - - + -
38G THR 3.7 6.7 - - - +
39G SER* 3.8 9.6 - - - -
50G ILE* 4.2 4.2 - - - +
51G VAL* 1.3 81.2 + - - +
53G GLN* 1.3 79.9 + - - +
68G HIS* 4.8 6.5 - - + -
69G LEU* 4.2 6.2 - - - +
79G VAL* 3.6 25.4 - - + +
202G LEU* 5.8 0.2 - - - -
215G ILE* 3.3 9.9 - - - +
216G GLU* 2.7 38.3 + - - +
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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