Contacts of the strand formed by residues 37 - 45 (chain C) in PDB entry 5DO7
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 SER 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C HIS* 1.3 76.9 - - - +
38C LEU* 1.3 63.1 + - - +
75C TYR* 4.9 2.9 - - - -
76C VAL 3.8 3.1 - - - -
77C GLU* 4.8 0.7 - - - +
114C TYR 4.1 3.6 + - - -
115C VAL* 3.3 8.8 - - - +
116C ASN* 2.7 40.4 + - - +
244C ILE* 4.3 1.9 - - - +
345C MET* 3.3 52.4 - - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C SER* 1.3 76.0 + - - +
39C GLY* 1.3 57.7 + - - +
40C ILE* 5.6 2.7 - - + -
74C LEU* 3.8 1.7 - - - +
75C TYR* 3.6 3.8 - - - -
76C VAL* 2.8 46.4 + - + +
99C MET* 6.3 2.7 - - + -
113C VAL* 3.9 14.6 - - + -
114C TYR 3.6 0.7 - - - -
115C VAL* 3.7 29.6 - - + -
129C PHE* 4.1 15.7 - - + -
213C VAL* 3.5 30.1 - - + -
215C LEU* 5.6 0.7 - - + -
244C ILE* 3.5 27.8 - - + -
246C VAL* 4.9 10.8 - - + -
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Residues in contact with GLY 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C SER* 5.0 0.2 + - - -
38C LEU* 1.3 74.7 - - - +
40C ILE* 1.3 63.0 + - - -
74C LEU 3.0 9.6 - - - -
75C TYR* 4.6 1.9 - - - -
113C VAL* 3.0 11.8 - - - +
114C TYR* 2.8 43.6 + - - -
342C ILE* 3.6 18.8 - - - -
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 5.6 4.0 - - + -
39C GLY* 1.3 80.3 - - - +
41C LEU* 1.3 62.1 + - - +
43C ALA* 3.6 30.3 - - + -
72C VAL* 4.2 11.0 - - + +
73C SER* 3.0 7.6 - - - -
74C LEU* 2.8 61.6 + - + +
95C LEU* 5.3 5.8 - - + -
99C MET* 4.1 26.0 - - - -
112C GLU 4.1 9.6 - - - +
113C VAL* 4.1 18.2 - - + +
114C TYR 4.8 0.2 - - - +
342C ILE* 3.9 11.0 - - - +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 1.3 73.1 - - - +
42C HIS* 1.3 107.3 + - + +
43C ALA* 3.1 4.2 + - - +
72C VAL 3.4 1.1 - - - -
73C SER* 4.1 3.1 - - - -
111C GLY* 3.7 0.5 - - - -
112C GLU 3.4 25.7 + - - +
114C TYR* 4.6 15.0 - - + +
339C LEU* 3.8 25.1 - - + -
342C ILE* 3.5 24.6 - - + +
343C GLU* 5.6 4.7 - - + +
346C LYS* 5.1 12.1 - - - +
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Residues in contact with HIS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 1.3 103.1 - - + +
43C ALA* 1.3 59.2 + - - +
71C ASP* 3.4 35.9 - - + +
72C VAL 2.8 12.9 + - - -
73C SER* 4.0 5.2 - - - -
110C LEU* 3.7 10.7 - - + +
111C GLY* 3.0 19.7 + - - -
330C LYS* 4.8 12.9 + - - -
339C LEU* 4.4 11.9 - - + +
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 3.6 27.4 - - + -
41C LEU 4.2 1.6 - - - +
42C HIS* 1.3 73.6 - - - +
44C SER* 1.3 60.9 + - - +
69C LEU* 4.4 5.5 - - + +
70C LYS 3.4 1.6 + - - -
71C ASP 2.8 18.4 + - - -
72C VAL* 2.8 26.2 + - + +
109C PHE* 5.1 9.0 - - + -
110C LEU 3.1 10.5 - - - +
111C GLY* 3.9 4.5 - - - -
112C GLU 5.1 0.7 - - - +
113C VAL* 6.0 0.9 - - + -
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Residues in contact with SER 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA* 1.3 75.1 - - - +
45C TYR* 1.3 63.7 + - - +
69C LEU* 2.3 31.0 + - - +
70C LYS* 3.2 14.2 - - - +
71C ASP* 3.5 7.2 + - - -
108C THR* 6.0 0.4 - - - -
109C PHE* 3.4 8.7 - - - -
110C LEU* 2.8 52.5 + - - +
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Residues in contact with TYR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C SER* 1.3 75.7 + - - +
46C SER* 1.3 68.7 + - - +
67C GLN 2.8 24.0 + - - -
68C ILE* 2.8 33.5 + - + -
69C LEU* 2.8 32.4 + - + +
94C THR* 4.5 13.5 - - + -
98C ALA* 4.9 16.4 - - + -
103C LEU* 3.8 5.7 + - - +
104C GLY* 3.3 40.2 + - - -
106C ALA* 4.2 8.2 + - - +
108C THR* 3.1 25.3 - - - +
109C PHE* 4.0 22.0 - + + -
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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