Contacts of the strand formed by residues 119 - 124 (chain A) in PDB entry 3TAU
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 ILE 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.5 9.2 - - + -
7A LEU 2.8 10.5 + - - +
8A ILE* 3.6 28.1 - - + +
9A VAL 2.8 31.8 + - - +
117A GLU 3.9 9.6 - - - +
118A GLY* 1.3 77.3 - - - +
120A PHE* 1.3 57.0 + - - +
121A ILE* 3.8 6.2 + - + -
164A ASP* 3.6 5.8 - - - +
165A TYR* 3.8 31.9 - - + -
182A ILE* 3.9 14.6 - - + -
186A GLU* 3.7 35.2 - - + +
192A ARG* 4.4 10.3 - - - +
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.6 35.7 - - + -
108A ALA* 3.9 8.3 - - + -
111A VAL* 3.9 10.3 - - + -
112A ARG* 3.4 52.0 - - + -
115A MSE 3.4 22.4 - - + -
116A PRO 4.5 4.7 - - - -
118A GLY* 3.3 23.6 - - - -
119A ILE* 1.3 70.3 - - - +
121A ILE* 1.3 62.1 + - - +
162A SER 4.6 1.8 - - - +
163A TYR* 3.7 26.9 - + + +
164A ASP* 2.9 46.3 + - - +
165A TYR 3.1 9.2 + - - +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.7 27.4 - - + -
9A VAL 2.8 13.4 + - - +
10A LEU* 3.6 20.1 - - + +
11A SER 2.9 27.5 + - - +
100A PHE* 5.3 0.4 - - + -
119A ILE* 4.3 12.1 - - + +
120A PHE* 1.3 77.0 - - - +
122A PHE* 1.3 61.5 + - - +
123A LEU 3.6 0.2 + - - -
163A TYR* 3.6 5.0 - - - -
165A TYR* 3.4 7.6 - - + +
167A VAL* 3.8 31.9 - - + -
179A ILE* 4.3 19.7 - - + +
182A ILE* 4.0 31.4 - - + -
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A SER 3.8 1.1 - - - -
12A GLY* 3.9 14.4 - - - -
13A PRO* 3.7 24.9 - - + -
105A VAL* 4.4 2.2 - - + -
121A ILE* 1.3 72.5 - - - +
123A LEU* 1.3 62.8 + - - +
124A THR* 3.2 24.6 + - + -
125A PRO* 5.0 0.9 - - + -
156A GLU* 4.1 24.9 - - + -
159A MSE 3.7 29.4 - - + -
160A MSE 3.9 31.9 - - + -
163A TYR* 3.6 38.3 - + + -
165A TYR 2.8 15.6 + - - +
166A ALA* 3.3 3.9 - - - -
167A VAL 2.9 25.7 + - - -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.0 16.8 - - + +
11A SER 2.8 20.8 + - - +
12A GLY* 3.5 15.4 - - - -
13A PRO* 3.6 5.0 - - - +
16A VAL* 3.5 25.3 - - + +
17A GLY 3.8 2.7 - - - -
18A LYS* 3.7 32.1 - - + +
21A VAL* 3.8 23.3 - - + -
121A ILE 3.6 1.0 + - - -
122A PHE* 1.3 70.4 - - - +
124A THR* 1.3 57.6 + - - +
167A VAL* 3.4 21.5 - - + +
169A ASN* 3.8 20.0 - - + -
175A ALA* 4.1 19.3 - - + -
179A ILE* 4.9 0.7 - - + -
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Residues in contact with THR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.5 5.0 - - - +
122A PHE* 3.2 24.2 + - + -
123A LEU* 1.3 73.0 - - - +
125A PRO* 1.4 84.0 - - + +
126A PRO* 3.5 0.5 - - - +
128A LEU* 3.7 19.1 - - + -
160A MSE 4.7 3.7 - - + -
166A ALA* 3.8 13.0 - - - +
167A VAL 2.7 15.7 + - - -
168A VAL* 3.5 10.0 - - + -
169A ASN 3.0 22.9 + - - -
197B TYR* 3.6 25.7 + - + +
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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