Contacts of the strand formed by residues 69 - 75 (chain C) in PDB entry 5BOU
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 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C ILE* 3.0 26.7 + - + -
66C ASP* 3.1 16.7 + - + +
67C SER 3.8 0.2 - - - -
68C HIS* 1.3 116.2 - - + +
70C VAL* 1.3 69.6 + - - +
102C VAL* 4.4 12.8 - - + +
104C VAL* 4.5 17.3 - - + -
107C LEU* 4.6 11.9 - - + -
133C ILE* 3.8 24.2 - - + -
134C ALA 3.4 14.8 - - - +
219C ILE* 5.0 0.2 - - - -
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 3.5 23.8 - - + -
62C VAL* 4.0 16.4 - - + -
63C SER 3.4 6.3 - - - +
64C LYS* 4.0 16.6 - - + -
65C ILE* 4.4 2.7 - - - -
69C VAL* 1.3 78.4 - - - +
71C LEU* 1.3 61.6 + - - +
132C LEU 4.0 0.4 - - - +
133C ILE* 3.5 7.8 - - - +
134C ALA* 2.9 45.0 + - + +
211C THR* 5.1 3.1 - - + -
213C VAL* 4.4 15.0 - - + -
219C ILE* 3.8 30.7 - - + -
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Residues in contact with LEU 71 (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 LEU* 4.7 0.2 - - - -
61C LYS 3.9 1.2 - - - +
62C VAL* 3.6 3.0 - - - -
63C SER* 2.7 39.4 + - - +
65C ILE* 3.7 31.4 - - + -
70C VAL* 1.3 76.2 - - - +
72C SER* 1.3 75.9 + - - +
73C PHE* 4.5 5.6 - - + -
80C SER* 5.9 0.9 - - - -
83C LEU* 5.4 3.1 - - + +
84C ILE* 4.0 27.9 - - + +
87C ALA* 5.1 1.6 - - + -
107C LEU* 5.0 0.4 - - + -
111C VAL* 4.6 14.8 - - + -
131C THR* 4.2 19.1 - - + -
132C LEU 3.5 3.6 - - - -
133C ILE* 3.8 28.7 - - + -
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Residues in contact with SER 72 (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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31C ALA* 4.4 4.6 - - - +
32C VAL 5.4 0.7 + - - -
42C LEU* 3.8 18.8 - - - +
44C CYS* 4.0 21.2 - - - -
61C LYS 3.7 13.5 - - - -
62C VAL* 4.2 3.8 - - - -
71C LEU* 1.3 80.1 - - - +
73C PHE* 1.3 63.8 + - - +
131C THR* 3.3 4.7 - - - -
132C LEU* 2.9 51.8 + - - +
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Residues in contact with PHE 73 (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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31C ALA* 4.0 7.5 - - - +
60C SER 5.2 2.7 - - - -
61C LYS* 3.3 67.7 + - + +
63C SER* 5.8 0.4 - - - -
71C LEU* 4.5 7.9 - - + -
72C SER* 1.3 80.3 + - - +
74C SER* 1.3 74.8 + - - +
75C GLY 4.0 4.7 - - - -
76C LEU 4.1 1.1 - - - -
77C ASN* 3.5 33.4 - - + -
80C SER* 3.2 39.0 - - - -
84C ILE* 4.8 7.6 - - + -
129C VAL* 3.9 13.2 - - + -
130C SER 3.3 13.5 - - - +
131C THR* 4.2 5.2 - - + +
162C ILE* 4.2 4.9 - - - -
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Residues in contact with SER 74 (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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25C VAL* 3.6 13.2 - - - +
28C GLY 4.7 0.7 - - - -
29C THR 2.8 25.8 + - - -
31C ALA* 3.6 3.1 - - - +
61C LYS* 4.6 2.0 - - - +
73C PHE* 1.3 78.3 + - - +
75C GLY* 1.3 57.9 + - - +
129C VAL* 3.6 1.9 - - - -
130C SER 3.0 30.4 + - - -
162C ILE* 3.2 26.5 + - - +
163C GLY* 3.7 21.5 - - - -
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Residues in contact with GLY 75 (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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24C ALA 3.7 20.9 - - - -
25C VAL* 4.0 1.6 - - - -
28C GLY* 3.8 15.9 - - - -
61C LYS* 5.3 1.1 + - - +
73C PHE* 4.0 3.3 - - - -
74C SER* 1.3 74.4 - - - +
76C LEU* 1.3 67.6 + - - -
77C ASN* 3.3 16.6 + - - -
128C GLY 3.3 9.6 - - - -
129C VAL* 4.6 0.4 - - - -
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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