Contacts of the strand formed by residues 166 - 171 (chain A) in PDB entry 1TUB
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 LYS 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.4 19.1 - - + +
154A MET* 1.4 77.3 + - + +
157A LEU* 3.1 15.7 - - + +
158A SER* 2.4 27.3 - - - +
164A LYS 3.9 9.2 - - - +
165A SER* 1.3 77.6 - - - +
167A LEU* 1.2 62.6 + - - +
168A GLU* 4.2 0.4 + - - -
197A HIS* 1.7 23.1 + - + -
198A SER* 3.8 11.7 - - - +
199A ASP* 2.6 31.6 + - - +
200A CYS 3.5 0.3 - - - +
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Residues in contact with LEU 167 (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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4A CYS* 5.6 0.2 - - - -
134A GLY* 5.2 0.9 - - - -
135A PHE 2.4 26.9 + - - +
136A SER* 3.3 4.2 - - - -
137A VAL* 2.9 14.1 + - - +
165A SER 4.4 5.4 - - - +
166A LYS* 1.2 83.6 - - - +
168A GLU* 1.3 65.1 + - - +
169A PHE* 5.6 4.7 - - + -
199A ASP* 4.3 5.2 - - + -
200A CYS* 3.3 28.9 - - + +
202A PHE* 4.3 15.5 - - + -
238A ILE* 5.3 3.8 - - + -
239A THR* 5.8 0.2 - - - +
252A LEU* 3.2 52.7 - - + +
255A PHE* 4.4 15.0 - - + -
256A GLN* 4.9 2.7 - - + +
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Residues in contact with GLU 168 (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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137A VAL* 3.0 20.6 - - + +
139A HIS* 3.4 9.5 - - + -
154A MET* 1.6 65.7 - - + +
166A LYS* 4.4 1.1 - - + -
167A LEU* 1.3 79.3 - - - +
169A PHE* 1.3 69.3 + - - +
193A THR* 3.0 27.3 - - - +
198A SER* 4.2 8.7 - - - -
199A ASP 5.9 0.2 - - - +
200A CYS 3.6 5.0 + - - +
201A ALA* 3.1 13.6 - - + +
202A PHE* 3.0 26.3 + - - -
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Residues in contact with PHE 169 (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 ILE* 4.2 9.6 - - + -
136A SER* 5.0 10.8 - - - -
137A VAL 2.4 20.4 + - - +
138A PHE* 4.0 31.4 - + + -
139A HIS* 2.9 29.5 + - - +
167A LEU* 6.0 4.0 - - + -
168A GLU* 1.3 80.6 - - - +
170A SER* 1.2 62.9 + - - +
201A ALA* 5.8 0.2 - - - -
202A PHE* 3.1 30.5 - + + -
203A MET* 5.2 0.9 - - - -
204A VAL* 5.8 1.3 - - + -
231A ILE* 5.1 8.3 - - + -
234A ILE* 4.5 9.2 - - + -
235A VAL* 2.8 46.2 - - + -
238A ILE* 4.0 19.1 - - + -
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Residues in contact with SER 170 (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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139A HIS* 3.2 6.1 - - - -
141A PHE* 3.1 16.2 - - - -
169A PHE* 1.2 80.0 - - - +
171A ILE* 1.3 60.6 + - - +
201A ALA* 5.8 1.8 - - - -
202A PHE 2.3 14.1 + - - -
203A MET* 0.5 171.5 - - - +
204A VAL* 2.8 29.5 + - - +
231A ILE* 5.2 0.7 - - - +
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Residues in contact with ILE 171 (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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12A ALA* 3.9 28.3 - - + +
16A ILE* 4.6 18.2 - - + -
139A HIS 3.1 10.8 + - - +
140A SER* 3.5 3.1 - - - -
141A PHE* 3.2 21.7 + - - +
170A SER* 1.3 76.8 - - - +
172A TYR* 1.3 59.7 - - - +
203A MET* 2.2 8.6 - - - +
204A VAL* 3.4 16.6 - - + +
206A ASN* 3.3 32.3 - - + +
228A ASN* 5.3 0.9 - - - +
231A ILE* 5.0 5.6 - - + -
500A GTP 3.5 41.7 - - + +
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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