Contacts of the strand formed by residues 216 - 222 (chain B) in PDB entry 1TAD
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 CYS 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B VAL* 5.1 0.2 - - + -
31B LYS 3.3 2.2 + - - +
32B LEU* 3.4 10.7 - - + -
33B LEU 3.0 23.7 + - - -
214B VAL* 3.2 6.9 - - - +
215B THR* 1.3 82.8 - - - +
217B ILE* 1.3 77.1 + - - +
218B ILE* 4.3 6.1 - - - -
258B THR* 4.7 0.4 - - - -
259B SER* 3.1 18.4 - - - +
261B VAL* 4.3 9.0 - - - -
335B VAL* 4.2 17.3 - - - -
338B ILE* 6.4 0.4 - - - -
339B ILE* 3.9 34.1 - - + -
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.4 13.5 - - + +
35B LEU* 4.1 18.8 - - + -
214B VAL* 3.8 13.7 - - + -
216B CYS* 1.3 81.4 - - - +
218B ILE* 1.3 69.6 + - - +
219B PHE* 4.1 4.7 - - + +
249B ILE* 4.2 12.6 - - + -
255B PHE* 3.5 52.5 - - + -
258B THR* 4.1 7.2 - - - +
259B SER 2.8 11.8 + - - +
260B ILE* 3.4 15.0 - - + -
261B VAL* 2.7 32.7 + - - -
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.8 32.3 - - + -
33B LEU 2.9 8.1 + - - +
34B LEU* 3.6 24.3 - - + +
35B LEU 3.0 25.1 + - - +
45B ILE* 5.5 1.6 - - + -
194B MET* 4.9 1.8 - - + -
216B CYS* 4.4 9.4 - - - -
217B ILE* 1.3 77.2 - - - +
219B PHE* 1.3 58.2 + - - +
220B ILE* 3.8 3.5 + - + -
261B VAL* 3.3 11.4 - - + -
263B PHE* 3.7 52.7 - - + -
332B PHE* 4.1 15.3 - - + -
335B VAL* 4.3 6.5 - - + -
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Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.4 17.5 - - + -
36B GLY* 4.0 16.8 - - - -
37B ALA 4.7 0.9 - - - -
207B TRP* 5.3 0.2 - + - -
217B ILE* 3.8 7.0 - - + -
218B ILE* 1.3 71.7 - - - +
220B ILE* 1.3 64.2 + - - +
242B SER* 3.7 24.5 - - - -
245B LEU* 3.9 24.7 - - + -
246B PHE* 3.6 60.1 - + + -
249B ILE* 4.3 17.0 - - + -
260B ILE* 5.1 1.8 - - + -
261B VAL 2.7 13.4 + - - +
262B LEU* 3.3 17.3 - - + +
263B PHE 2.7 31.2 + - - -
303B PHE* 4.3 2.9 - + - -
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Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.6 24.9 - - + -
35B LEU 2.8 15.6 + - - +
36B GLY* 3.5 12.6 - - - -
37B ALA 4.2 1.4 + - - -
40B SER* 3.4 46.1 + - - +
41B GLY 3.9 0.2 - - - -
42B LYS* 3.6 26.7 - - + +
45B ILE* 3.8 17.5 - - + -
218B ILE* 4.1 8.7 - - + -
219B PHE* 1.3 79.7 - - - +
221B ALA* 1.3 62.6 + - - +
242B SER* 4.8 0.5 + - - -
263B PHE* 3.4 15.7 - - + +
265B ASN* 3.6 20.9 - - + +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B SER* 4.5 0.9 - - - -
219B PHE* 4.0 4.2 + - + -
220B ILE* 1.3 75.3 - - - +
222B ALA* 1.3 64.4 + - - +
223B LEU 3.4 0.9 + - - -
239B MET* 5.9 0.4 - - + -
242B SER* 3.4 23.8 - - - +
262B LEU* 4.4 3.6 - - + -
263B PHE 2.9 9.6 + - - +
264B LEU* 3.5 11.4 - - + +
265B ASN* 2.8 25.4 + - - -
303B PHE* 3.5 26.7 - - + -
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLU 5.7 0.2 - - - -
40B SER* 4.3 16.8 - - - -
221B ALA* 1.3 70.7 - - - +
223B LEU* 1.3 64.9 + - - +
224B SER* 4.4 1.1 - - - +
225B ALA* 3.1 33.4 + - + +
228B MET* 6.4 0.4 - - - -
239B MET* 3.3 10.1 - - - +
242B SER* 5.2 1.4 + - - -
265B ASN 3.6 7.2 - - - -
266B LYS* 3.9 31.2 - - + +
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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