Contacts of the strand formed by residues 152 - 158 (chain G) in PDB entry 3TDK
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 LEU 152 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117G VAL* 4.6 9.0 - - + +
120G SER* 3.4 39.0 - - - +
121G ASN* 3.8 4.3 - - - +
122G GLY 3.6 15.3 - - - +
147G ASN 4.4 11.4 - - - +
148G THR* 4.6 7.4 - - + +
149G LYS* 3.5 52.8 + - + +
150G PRO 3.2 0.6 - - - +
151G ASN* 1.3 76.6 - - - +
153G ASN* 1.3 61.6 + - - +
154G LEU* 4.1 24.8 + - + -
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Residues in contact with ASN 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G GLY 2.9 14.4 + - - +
123G TYR* 3.4 31.8 - - + -
124G LYS 3.3 21.5 + - - +
151G ASN 5.5 1.1 - - - -
152G LEU* 1.3 76.3 - - - +
154G LEU* 1.3 59.3 + - - +
155G GLN* 3.1 26.0 + - - +
187G GLU* 4.1 19.4 + - - +
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Residues in contact with LEU 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G ILE* 4.0 15.5 - - + -
117G VAL* 4.3 11.9 - - + -
120G SER* 4.4 7.4 - - - +
124G LYS* 3.3 31.0 - - + +
126G VAL* 3.9 14.4 - - + -
144G PHE* 3.6 48.6 - - + +
147G ASN 6.0 0.2 - - - +
152G LEU* 4.0 27.8 + - + -
153G ASN* 1.3 75.6 + - - +
155G GLN* 1.3 66.2 + - - +
156G VAL* 4.0 5.7 + - - +
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Residues in contact with GLN 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G TYR* 3.6 30.7 - - + +
124G LYS 2.9 12.0 + - - +
125G ILE* 3.7 7.9 - - + +
126G VAL* 2.8 32.1 + - - +
153G ASN* 3.1 38.2 + - - +
154G LEU* 1.3 78.2 + - - +
156G VAL* 1.3 63.0 + - - +
187G GLU* 3.4 32.9 + - - +
188G GLY 3.5 9.0 + - - -
191G ALA* 3.8 18.1 - - + +
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Residues in contact with VAL 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G VAL* 3.4 5.6 - - - +
137G ALA* 3.8 33.2 - - + +
140G ILE* 3.9 16.8 - - + -
141G ARG* 4.1 34.5 + - + +
144G PHE* 3.7 29.8 - - + -
154G LEU 4.0 3.5 + - - +
155G GLN* 1.3 78.8 + - - +
157G LEU* 1.3 76.1 + - - +
182G GLY* 4.5 5.5 - - - -
183G ASP* 4.7 8.3 + - - +
213G THR* 4.5 5.7 + - - -
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Residues in contact with LEU 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G ILE* 3.7 20.9 - - + -
126G VAL 2.7 9.7 + - - +
127G THR* 3.3 14.3 - - + +
128G GLU* 2.8 28.3 + - - +
137G ALA* 4.9 2.6 - - - +
155G GLN* 5.5 0.2 - - + -
156G VAL* 1.3 89.8 - - - +
158G SER* 1.3 61.3 + - - +
180G ILE* 4.4 2.2 - - + -
181G GLY 3.4 14.6 - - - +
182G GLY* 3.6 13.5 - - - -
183G ASP 4.9 0.4 - - - +
188G GLY 4.6 1.8 - - - +
191G ALA* 3.2 40.2 - - + +
192G VAL* 3.9 15.3 - - + +
195G LEU* 3.9 21.8 - - + -
213G THR* 5.2 0.9 - - - -
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Residues in contact with SER 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G THR* 4.3 0.2 - - - -
128G GLU* 3.8 8.0 + - - -
133G PRO* 5.4 0.5 - - - +
137G ALA* 4.6 2.0 - - - -
157G LEU* 1.3 73.7 - - - +
159G ASN* 1.3 62.8 + - - +
160G PRO* 3.6 7.7 - - - +
179G LEU 3.9 0.3 - - - +
180G ILE* 3.4 4.5 - - - +
181G GLY* 2.6 38.2 + - - +
213G THR* 4.1 22.3 + - - -
216G SER* 2.7 24.3 + - - -
217G GLU* 3.9 19.3 + - - +
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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