Contacts of the strand formed by residues 144 - 150 (chain D) in PDB entry 3T0E
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 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C LEU* 3.3 28.3 - - + -
131C VAL* 4.4 7.6 - - + -
133C LEU* 4.3 10.1 - - + -
172C VAL* 4.8 15.3 - - + -
127D VAL* 3.4 4.2 - - - +
128D PHE* 2.7 55.9 + - + -
143D LEU* 1.3 83.5 - - - +
145D CYS* 1.3 69.2 + - - +
146D LEU* 4.9 5.6 - - + -
159D TRP* 4.3 3.1 - - - -
191D SER* 5.3 4.5 - - - -
192D SER 3.7 7.4 - - - +
193D ARG* 3.7 19.7 - - + -
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Residues in contact with CYS 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D VAL* 4.1 12.1 - - - -
126D ALA 3.9 11.4 - - - -
127D VAL* 4.9 0.9 - - - -
144D VAL* 1.3 76.3 - - - +
146D LEU* 1.3 66.6 + - - +
147D ALA 4.1 0.7 - - - -
157D LEU* 4.6 9.1 - - + +
159D TRP* 3.3 18.8 - - + -
190D LEU 3.7 0.9 - - - +
191D SER* 3.2 8.8 - - - -
192D SER 2.9 33.1 + - - +
210D CYS* 2.0 48.5 - - - -
212D VAL* 5.3 1.6 - - - -
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Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ASP* 6.1 1.1 - - + +
131C VAL* 4.7 2.2 - - + -
172C VAL* 6.3 1.1 - - + -
174C TRP* 3.3 72.0 - - + +
124D GLU 3.4 5.4 - - - +
125D VAL* 4.7 0.2 - - - -
126D ALA* 3.1 33.2 + - + +
128D PHE* 3.8 31.4 - - + -
144D VAL* 4.3 4.0 + - + +
145D CYS* 1.3 74.6 - - - +
147D ALA* 1.3 59.9 + - - +
148D THR* 3.9 11.1 + - + +
190D LEU 3.6 14.8 - - - +
191D SER* 3.8 11.7 - - - -
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PRO* 4.1 11.0 - - + -
124D GLU 3.6 5.8 - - - -
125D VAL* 3.5 25.4 - - + -
145D CYS* 4.1 1.2 - - - -
146D LEU* 1.3 71.4 - - - +
148D THR* 1.3 61.5 + - - +
150D PHE* 4.2 7.1 - - + -
157D LEU* 4.9 3.6 - - + -
189D SER* 3.5 1.6 - - - -
190D LEU* 3.0 38.3 + - + +
212D VAL* 3.5 20.9 - - + -
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Residues in contact with THR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TRP* 3.8 19.3 - - + +
123D PRO* 3.3 3.3 - - - +
124D GLU* 2.7 46.7 + - - +
146D LEU* 3.9 15.0 + - + -
147D ALA* 1.3 78.1 - - - +
149D GLY* 1.3 65.5 + - - +
150D PHE* 3.5 2.9 - - - -
179D GLU* 4.1 2.5 - - - -
188D TYR 3.7 2.0 - - - -
189D SER* 2.9 28.7 - - - +
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Residues in contact with GLY 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PHE* 3.5 1.6 - - - +
122D PRO 2.6 24.3 - - - +
124D GLU* 4.5 4.2 + - - +
148D THR* 1.3 77.9 - - - +
150D PHE* 1.3 52.2 + - - +
179D GLU* 3.2 12.3 + - - -
187D ARG* 2.8 40.9 + - - -
188D TYR 3.1 6.5 + - - -
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Residues in contact with PHE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PHE* 3.3 17.7 - - - +
122D PRO 3.5 10.1 - - - -
123D PRO* 3.6 24.5 - - + -
147D ALA* 4.2 13.2 - - + -
148D THR 4.6 0.7 - - - -
149D GLY* 1.3 75.3 - - - +
151D TYR* 1.3 68.6 + - - +
152D PRO 4.5 2.7 - - - -
153D ASP* 4.8 3.4 - - - -
155D VAL* 3.3 46.4 - - + -
176D PRO* 4.7 4.3 - - + -
187D ARG* 3.2 6.4 - - - +
188D TYR* 2.9 68.0 + + + +
189D SER* 3.4 2.9 - - - -
190D LEU* 4.3 12.3 - - + -
212D VAL* 4.9 2.5 - - + -
214D PHE* 4.1 4.9 - + + -
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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