Contacts of the strand formed by residues 109 - 115 (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 PHE 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ALA* 5.1 8.3 - - + -
44C SER 3.4 11.2 - - - -
45C TYR* 4.0 17.5 - + + -
98C ALA* 5.6 10.1 - - + -
99C MET* 6.1 5.2 - - + -
104C GLY 5.3 3.6 - - - +
108C THR* 1.3 81.8 + - - +
110C LEU* 1.3 65.1 + - - +
111C GLY 3.8 21.9 + - - +
112C GLU* 5.0 3.1 - - + -
113C VAL* 4.6 13.9 - - + -
120C LEU* 5.8 1.6 - - + -
122C ARG* 4.7 22.4 - - + +
125C PHE* 4.0 31.0 - + - -
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Residues in contact with LEU 110 (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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42C HIS* 3.7 15.5 - - + +
43C ALA* 3.1 5.4 - - - +
44C SER* 2.8 46.3 + - - +
71C ASP* 3.6 25.4 - - - +
108C THR* 4.2 9.2 + - + +
109C PHE* 1.3 80.2 - - - +
111C GLY* 1.3 63.4 + - - +
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Residues in contact with GLY 111 (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 3.7 3.8 - - - -
42C HIS* 3.0 20.4 - - - -
43C ALA* 3.9 2.5 - - - -
109C PHE* 3.8 17.8 - - - +
110C LEU* 1.3 84.1 - - - +
112C GLU* 1.3 72.3 + - - +
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Residues in contact with GLU 112 (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* 4.1 2.0 - - - +
41C LEU* 3.4 27.5 + - - +
43C ALA* 5.1 1.0 - - - +
109C PHE* 5.0 4.9 - - + -
111C GLY* 1.3 83.5 - - - +
113C VAL* 1.3 67.1 + - - +
114C TYR* 4.0 28.4 + - + +
119C ALA* 4.0 19.6 - - + +
120C LEU 5.0 8.5 - - - +
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Residues in contact with VAL 113 (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* 3.9 21.5 - - + -
39C GLY 3.0 18.2 - - - +
40C ILE* 4.1 22.9 - - + +
99C MET* 5.4 9.0 - - + -
109C PHE* 4.6 10.3 - - + -
112C GLU* 1.3 79.0 - - - +
114C TYR* 1.3 57.6 + - - +
115C VAL* 4.0 6.1 - - + -
119C ALA* 3.7 1.7 - - - +
120C LEU* 2.8 46.1 + - + +
125C PHE* 4.4 23.3 - - + -
129C PHE* 4.8 7.9 - - + -
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Residues in contact with TYR 114 (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* 3.9 4.7 + - - +
38C LEU* 3.6 1.4 - - - -
39C GLY* 2.8 44.5 + - - +
41C LEU* 4.6 17.1 - - + +
112C GLU* 4.0 31.7 + - + +
113C VAL* 1.3 72.3 - - - +
115C VAL* 1.3 60.0 + - - +
116C ASN 4.1 0.2 - - - -
117C GLY 4.0 15.3 - - - +
118C ARG 3.8 1.3 - - - +
119C ALA* 3.5 28.9 - - + -
342C ILE* 4.6 28.5 - - + +
345C MET* 5.5 6.1 - - + +
346C LYS* 4.5 33.6 + - + -
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Residues in contact with VAL 115 (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 3.3 9.4 - - - +
38C LEU* 3.7 23.3 - - + -
113C VAL* 3.8 16.4 + - + +
114C TYR* 1.3 75.6 - - - +
116C ASN* 1.3 78.2 + - + +
117C GLY 3.4 0.2 - - - -
118C ARG* 3.0 20.4 + - - +
120C LEU* 4.4 19.1 - - + +
128C CYS* 3.8 28.9 - - - +
129C PHE* 4.7 5.2 - - + -
213C VAL* 6.1 3.6 - - + -
355C PRO* 4.9 8.0 - - + +
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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