Contacts of the strand formed by residues 109 - 113 (chain C) in PDB entry 4AOR
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 MET 109 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 4.2 2.5 - - + -
59C VAL* 3.5 6.4 - - - +
60C SER* 2.9 39.5 + - - +
61C ALA 3.4 29.2 - - - +
62C ALA* 3.7 5.2 - - - -
64C CYS* 3.9 23.6 - - + +
65C TYR* 3.8 35.9 - - - -
69C ILE* 4.6 2.7 - - + -
93C SER* 4.3 3.8 - - - -
94C ILE 3.4 15.5 - - - +
95C VAL* 4.2 3.4 - - - -
108C ILE* 1.3 78.4 - - - +
110C LEU* 1.3 73.3 + - - +
111C ILE* 3.8 28.5 - - + -
238C TRP* 4.7 0.9 - - - -
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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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53C ILE* 4.1 13.9 - - + -
57C TRP* 4.0 18.2 - - + -
58C VAL 3.5 6.1 - - - +
59C VAL* 3.7 28.9 - - + -
92C LYS 3.9 0.3 - - - +
93C SER* 3.6 1.4 - - - -
94C ILE* 2.8 46.8 + - + +
108C ILE* 5.6 0.4 - - + -
109C MET* 1.3 74.5 - - - +
111C ILE* 1.3 61.6 + - - +
112C LYS 4.2 0.2 + - - -
238C TRP* 3.9 18.3 - - + -
239C ILE* 3.8 28.9 - - + +
242C THR* 3.7 32.5 - - + -
243C ILE* 4.7 5.2 - - + -
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Residues in contact with ILE 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* 3.8 39.9 - - + -
57C TRP* 3.3 8.7 - - - -
58C VAL* 2.8 51.3 + - + +
60C SER* 4.8 1.8 - - - -
69C ILE* 4.2 13.5 - - + -
71C VAL* 4.1 14.4 - - + -
90C ALA* 3.5 27.8 - - + -
92C LYS 3.3 2.5 - - - +
93C SER* 3.8 13.5 - - - +
109C MET* 3.8 20.6 - - + +
110C LEU* 1.3 77.0 - - - +
112C LYS* 1.3 67.7 + - - +
113C LEU* 3.9 2.1 + - + +
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Residues in contact with LYS 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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56C GLN* 3.3 34.5 - - + +
57C TRP* 3.5 32.0 - - + +
90C ALA* 3.5 3.6 - - - -
91C SER* 2.7 51.6 + - - +
92C LYS* 2.8 34.9 + - + +
111C ILE* 1.3 75.3 - - - +
113C LEU* 1.3 60.6 + - - +
246C ASN* 2.8 29.2 + - - +
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Residues in contact with LEU 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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52C LEU* 4.2 13.9 - - + -
55C SER 3.6 22.0 - - - +
56C GLN* 2.9 39.6 + - + +
57C TRP 4.4 0.4 - - - +
58C VAL* 4.3 8.5 - - + -
71C VAL* 3.6 40.6 - - + -
73C LEU* 4.6 4.0 - - + -
88C ILE* 3.8 17.7 - - + +
89C SER 3.7 3.6 - - - +
91C SER* 3.5 4.1 + - - -
111C ILE* 4.6 2.9 - - + +
112C LYS* 1.3 76.0 - - - +
114C LYS* 1.3 65.3 + - - +
115C SER 3.3 16.9 + - - +
117C ALA* 4.2 15.0 - - + -
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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