Contacts of the strand formed by residues 204 - 209 (chain B) in PDB entry 1TD2
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 ALA 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B VAL* 4.4 18.6 - - + -
169B ARG* 4.1 9.0 - - - +
197B LEU* 6.0 0.2 - - + -
198B LEU 3.5 7.6 - - - -
199B VAL* 4.3 15.9 - - + -
203B GLU* 1.3 81.7 - - - +
205B TRP* 1.3 64.0 + - - +
286B LYS* 3.7 6.2 - - - +
287B LEU* 2.9 41.6 + - + +
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Residues in contact with TRP 205 (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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197B LEU* 3.5 8.6 - - - +
198B LEU* 2.9 39.3 + - + +
203B GLU* 3.3 20.6 + - - -
204B ALA* 1.3 81.5 - - - +
206B HIS* 1.3 60.5 + - - +
240B LEU* 4.0 29.9 - - + +
241B GLN* 2.9 51.6 - - + -
244B LEU* 3.8 18.6 - - + +
284B ALA* 3.9 17.7 - - + -
285B THR 3.5 6.5 - - - -
286B LYS* 3.6 54.8 - - + +
287B LEU* 4.9 0.7 - - - -
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL* 4.6 1.0 - - + +
184B LEU* 4.0 8.0 - - + +
189B TYR* 3.6 25.3 - + - -
193B ARG* 3.7 12.9 + - - -
195B GLU* 2.7 51.2 + - + +
196B MET 3.8 4.7 + - - -
197B LEU* 3.3 21.7 - - + +
205B TRP* 1.3 74.1 - - - +
207B ILE* 1.3 69.3 + - - +
208B SER* 4.3 2.0 - - - -
244B LEU* 4.2 0.7 - - - -
283B SER 4.3 0.2 - - - +
284B ALA* 3.2 5.0 - - - -
285B THR* 2.7 53.1 + - - +
287B LEU* 4.1 15.3 - - + -
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Residues in contact with ILE 207 (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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195B GLU* 3.4 1.6 - - - -
196B MET* 2.9 42.6 + - + +
206B HIS* 1.3 82.6 + - - +
208B SER* 1.3 73.8 + - - +
244B LEU* 3.4 27.8 - - + +
245B GLU* 3.5 41.1 - - + +
248B THR* 3.3 41.7 - - + +
282B PHE* 3.9 9.9 - - + +
283B SER 3.9 10.5 - - - +
284B ALA* 3.9 8.3 - - + +
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ARG* 2.9 36.5 + - - -
194B PHE* 2.8 14.8 - - - -
195B GLU* 3.6 16.6 - - - -
206B HIS* 4.3 2.6 - - - -
207B ILE* 1.3 80.6 - - - +
209B ARG* 1.3 64.1 + - - +
248B THR* 4.2 2.6 - - - +
282B PHE* 3.8 21.0 - - - +
283B SER 4.8 4.4 + - - +
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Residues in contact with ARG 209 (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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193B ARG* 3.5 5.3 - - - +
194B PHE* 2.6 93.0 + - + +
208B SER* 1.3 76.4 - - - +
210B PRO* 1.3 90.3 + - + +
211B LEU* 4.2 5.1 - - - +
212B VAL* 4.5 10.3 - - - +
218B GLN* 5.8 4.6 - - - +
222B VAL* 3.9 19.2 - - - +
248B THR* 3.8 22.8 - - + +
251B VAL* 4.4 11.1 - - - +
252B TYR* 3.9 24.7 - - - +
255B MET* 4.4 14.0 - - - +
282B PHE* 4.1 12.3 - - + -
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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