Contacts of the strand formed by residues 245 - 251 (chain B) in PDB entry 1TW2
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 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B HIS* 3.7 21.1 - - + +
182B VAL 4.4 0.4 - - - -
183B LEU* 3.8 24.0 - - + +
243B ARG* 5.4 0.2 - - - +
244B LYS* 1.3 76.8 - - - +
246B ASP* 1.3 61.7 + - - +
247B ALA 3.5 14.6 - - - +
248B ILE* 3.8 6.1 - - + -
272B ALA 2.9 7.7 + - - -
273B LEU* 3.6 9.8 - - - +
274B GLU* 3.1 29.7 + - - +
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Residues in contact with ASP 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 5.3 1.6 + - - -
178B ASN 4.4 7.2 - - - +
179B VAL* 4.2 12.2 - - + +
180B ARG* 3.0 63.2 + - - +
181B HIS* 3.0 20.4 + - - +
245B ALA* 1.3 73.9 - - - +
247B ALA* 1.3 61.0 + - - +
273B LEU* 4.4 1.1 - - - -
274B GLU* 3.6 18.3 - - - +
275B PRO 5.0 3.6 - - - +
277B GLY* 3.0 30.1 - - - -
278B ARG 3.1 3.9 + - - -
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 4.5 12.3 - - + -
176B TRP* 4.0 26.5 - - + -
179B VAL* 4.2 6.1 - - + -
181B HIS 3.3 2.8 + - - -
182B VAL* 3.3 15.9 - - + +
183B LEU 3.0 23.2 + - - -
245B ALA* 3.7 1.2 - - - +
246B ASP* 1.3 78.1 - - - +
248B ILE* 1.3 65.6 + - - +
249B ILE* 4.2 0.7 - - + -
278B ARG 3.4 8.7 - - - +
280B LEU* 4.5 6.5 - - + -
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 3.3 12.8 - - + +
185B VAL* 3.7 26.7 - - + -
245B ALA* 3.8 15.7 - - + -
247B ALA* 1.3 80.3 - - - +
249B ILE* 1.3 60.3 - - - +
269B CYS* 3.4 44.2 - - + +
272B ALA* 4.0 25.6 - - + +
273B LEU* 3.9 15.5 - - + -
278B ARG 3.1 7.1 + - - -
279B ILE* 3.3 15.4 - - + +
280B LEU* 2.8 29.6 + - - +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TRP* 4.2 4.0 - - + -
182B VAL* 3.6 23.3 - - + -
183B LEU 2.9 9.3 + - - +
184B ASP* 3.4 25.4 - - + +
185B VAL* 2.9 26.6 + - - +
192B PHE* 3.5 37.0 - - + -
196B ILE* 4.1 22.4 - - + -
247B ALA* 5.4 0.2 - - + -
248B ILE* 1.3 73.8 - - - +
250B LEU* 1.3 69.8 + - - +
251B SER 4.0 6.1 - - - +
280B LEU* 3.4 37.7 - - + +
282B HIS* 5.4 0.2 - - + -
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Residues in contact with LEU 250 (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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185B VAL* 3.6 39.3 - - + +
248B ILE 5.1 0.4 - - - +
249B ILE* 1.3 74.4 - - - +
251B SER* 1.3 60.1 + - - +
252B PHE 3.7 0.9 + - - -
253B VAL* 4.2 16.0 + - + -
254B LEU* 4.1 19.4 - - + +
265B ILE* 3.9 14.6 - - + -
266B LEU* 3.6 32.1 - - + -
269B CYS* 3.9 16.8 - - - -
279B ILE* 4.2 11.2 - - + -
280B LEU 2.8 10.5 + - - +
281B ILE* 3.4 12.2 - - + +
282B HIS 3.0 23.5 + - - +
283B GLU* 5.2 0.5 - - - +
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Residues in contact with SER 251 (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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167B PHE* 3.7 5.5 - - - -
184B ASP* 4.6 2.3 + - - -
185B VAL 4.6 0.2 + - - -
192B PHE* 3.8 24.2 - - - -
249B ILE* 4.0 3.5 - - - +
250B LEU* 1.3 70.8 - - - +
252B PHE* 1.3 67.4 - - - +
253B VAL* 3.2 5.3 + - - +
282B HIS* 3.2 30.3 - - - -
1635B SAH 2.7 57.7 + - - +
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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
------------------------------------------------------------
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