Contacts of the strand formed by residues 105 - 110 (chain Y) in PDB entry 3UBT
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 105 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1Y MET* 5.3 1.8 - - - -
3Y LEU* 3.6 25.1 - - + -
17Y PHE* 4.0 18.6 - + - -
22Y PHE* 4.1 13.9 - + - -
63Y ASP 3.9 5.8 - - - -
64Y GLY* 3.4 19.3 - - - -
65Y ILE 3.2 20.8 + - - -
66Y ILE* 4.2 11.0 - - + -
103Y PRO* 3.5 8.6 - - - +
104Y ILE* 1.3 79.2 - - - +
106Y PHE* 1.3 76.5 + - - +
107Y LEU* 5.1 0.2 - - + -
135Y TYR* 4.5 1.3 - - - -
159Y ILE* 5.4 0.7 - - + -
160Y GLY 2.9 14.6 - - - +
161Y PHE* 3.7 18.8 - - + -
320Y ILE* 3.8 36.3 - - + -
324Y LEU* 4.0 18.4 - - + -
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Residues in contact with PHE 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Y ILE* 3.0 15.7 - - + +
94Y TYR* 3.4 21.3 - + - +
98Y LEU* 3.9 33.4 - - + -
105Y PHE* 1.3 84.3 - - - +
107Y LEU* 1.3 68.7 + - - +
108Y ALA* 4.4 5.6 - - + -
130Y PHE* 3.7 43.5 - + - -
135Y TYR* 4.0 28.7 - + + -
137Y VAL* 4.3 4.5 - - + -
158Y TYR* 4.2 15.7 - - + -
159Y ILE* 3.6 5.6 - - - +
160Y GLY* 3.0 51.1 + - - +
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Residues in contact with LEU 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Y LEU* 4.0 20.6 - - + -
17Y PHE* 3.6 35.0 - - + -
65Y ILE 3.0 9.6 + - - +
66Y ILE* 4.5 9.4 - - + -
67Y GLY* 2.9 35.2 + - - +
94Y TYR* 3.6 1.7 + - - -
105Y PHE* 5.1 0.4 - - + -
106Y PHE* 1.3 76.5 - - - +
108Y ALA* 1.3 66.1 + - - +
157Y PHE* 4.1 25.4 - - + -
158Y TYR 3.4 14.6 - - - +
159Y ILE* 3.7 21.5 - - + -
316Y ILE* 4.3 17.0 - - + -
320Y ILE* 5.0 5.2 - - + -
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Residues in contact with ALA 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Y LEU* 6.4 0.2 - - - -
67Y GLY* 5.1 0.4 - - - -
68Y GLY* 4.0 21.3 - - - +
74Y TRP* 4.1 22.2 - - + -
94Y TYR* 4.0 12.6 - - + +
106Y PHE* 4.3 10.1 - - + -
107Y LEU* 1.3 79.7 - - - +
109Y GLU* 1.3 60.6 + - - +
130Y PHE* 5.5 0.9 - - + -
156Y VAL 4.0 0.2 - - - +
157Y PHE* 3.6 3.0 - - - -
158Y TYR* 2.8 40.9 + - + +
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Residues in contact with GLU 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Y LEU* 6.3 2.2 - - + -
67Y GLY* 5.9 0.2 - - - -
68Y GLY* 4.8 5.3 - - - +
69Y PRO 4.3 7.4 - - - +
71Y SER* 4.0 5.4 + - - -
74Y TRP* 3.8 14.6 - - - -
108Y ALA* 1.3 75.1 - - - +
110Y ASN* 1.3 66.6 + - - +
111Y VAL* 4.6 6.0 - - - +
153Y ARG* 5.1 1.9 + - - -
155Y ARG* 3.1 48.1 + - + +
156Y VAL 3.4 9.9 - - - +
157Y PHE* 4.1 19.3 - - + -
306Y ASN 4.9 6.2 - - - +
308Y VAL* 3.5 27.1 - - + +
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Residues in contact with ASN 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Y SER* 3.4 15.0 + - - +
74Y TRP* 3.3 37.8 - - + +
108Y ALA 4.3 0.2 + - - -
109Y GLU* 1.3 75.7 - - - +
111Y VAL* 1.3 63.2 + - - +
112Y LYS* 3.0 41.6 + - - +
115Y MET* 3.5 23.3 - - + +
126Y PHE* 4.7 0.8 - - - -
155Y ARG* 3.9 1.6 - - - +
156Y VAL* 2.8 48.9 + - + +
158Y TYR* 4.5 10.1 - - + -
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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