Contacts of the strand formed by residues 273 - 283 (chain A) 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 LEU 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A LYS* 4.5 3.4 - - - +
245A ALA 3.6 7.4 - - - +
246A ASP 4.6 0.2 - - - +
248A ILE* 3.6 31.2 - - + +
269A CYS 3.1 3.4 + - - +
270A ALA* 3.3 19.6 + - - +
271A GLU 4.7 2.4 - - - +
272A ALA* 1.3 76.8 - - - +
274A GLU* 1.3 65.0 + - - +
275A PRO* 4.7 0.5 - - - +
277A GLY* 3.8 27.8 - - - +
278A ARG* 3.6 21.3 - - - +
279A ILE* 4.1 25.4 - - + +
326A LEU* 4.9 2.9 - - + -
348A LEU 5.0 0.4 - - - +
350A PRO* 4.2 24.2 - - + -
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ARG* 5.3 3.5 + - - -
244A LYS* 3.3 37.3 - - + +
245A ALA* 3.2 23.2 + - - +
246A ASP* 3.9 22.4 + - - +
272A ALA 3.5 2.6 + - - -
273A LEU* 1.3 79.2 - - - +
275A PRO* 1.3 82.6 - - + +
276A GLY 3.3 0.3 + - - -
277A GLY* 3.1 15.5 + - - -
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Residues in contact with PRO 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ASP* 4.7 5.2 - - - +
273A LEU 4.7 0.7 - - - +
274A GLU* 1.3 99.0 - - + +
276A GLY* 1.3 56.6 + - - +
277A GLY 3.4 2.4 + - - -
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A GLU 3.3 0.4 + - - -
275A PRO* 1.3 71.5 - - - +
277A GLY* 1.3 66.0 + - - +
278A ARG* 3.6 18.8 + - - +
350A PRO* 5.8 4.7 - - - +
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Residues in contact with GLY 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ASP* 3.0 24.5 - - - -
273A LEU* 3.8 17.9 - - - +
274A GLU 3.1 15.7 + - - -
275A PRO 3.3 2.2 + - - -
276A GLY* 1.3 78.5 - - - +
278A ARG* 1.3 77.4 + - - -
350A PRO* 3.8 5.8 - - - +
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Residues in contact with ARG 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TYR* 3.4 27.3 + - + +
246A ASP 3.1 5.9 + - - -
247A ALA* 3.2 6.8 - - - +
248A ILE 3.0 22.5 + - - -
273A LEU* 3.6 6.8 - - - +
276A GLY* 3.6 18.3 + - - +
277A GLY* 1.3 88.6 + - - -
279A ILE* 1.3 63.6 + - - +
280A LEU* 4.2 3.1 + - + -
329A GLU* 2.7 34.6 + - - -
347A VAL* 3.9 20.8 - - + +
348A LEU 3.5 14.6 - - - +
349A ALA* 3.3 21.0 - - - +
350A PRO* 3.9 5.5 - - - +
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ILE* 3.2 14.4 - - + +
250A LEU* 4.1 25.1 - - + -
266A LEU* 4.2 5.8 - - + +
269A CYS* 3.5 30.5 - - + -
270A ALA 3.9 9.0 - - - +
273A LEU* 4.1 21.7 - - + +
278A ARG* 1.3 76.7 - - - +
280A LEU* 1.3 64.6 + - - +
281A ILE* 4.1 13.2 + - + -
326A LEU* 3.9 28.9 - - + -
346A LEU 3.7 0.5 - - - +
347A VAL* 3.5 2.8 - - - -
348A LEU* 2.8 44.5 + - + +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PRO 5.4 1.6 - - - +
174A TYR* 3.5 48.7 - - + +
176A TRP* 4.1 18.8 - - + -
192A PHE* 5.0 7.0 - - + -
247A ALA* 4.9 3.6 - - + -
248A ILE 2.9 8.2 + - - +
249A ILE* 3.5 32.7 - - + +
250A LEU* 2.9 27.2 + - - +
278A ARG* 4.4 8.1 - - + +
279A ILE* 1.3 78.7 - - - +
281A ILE* 1.3 62.4 + - - +
282A HIS* 4.1 0.6 + - + -
345A LEU* 3.7 23.6 - - + -
346A LEU 3.3 4.5 - - - +
347A VAL* 4.5 5.6 - - + -
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LEU* 3.4 12.1 - - + +
254A LEU* 3.5 28.3 - - + -
266A LEU* 4.2 4.7 - - + -
279A ILE* 4.2 12.1 - - + -
280A LEU* 1.3 75.0 - - - +
282A HIS* 1.3 61.4 + - - +
283A GLU* 4.3 14.1 - - + +
317A TRP* 3.8 31.6 - - + -
344A SER 3.5 1.4 - - - +
345A LEU* 3.3 5.5 - - - -
346A LEU* 2.8 59.5 + - + +
348A LEU* 3.8 30.5 - - + -
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Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ALA 4.4 5.4 + - - -
167A PHE* 4.2 17.9 - + - -
170A PRO* 3.8 30.8 - - + +
192A PHE* 3.8 18.4 - + + -
249A ILE* 5.3 0.2 - - + -
250A LEU 3.0 7.7 + - - -
251A SER* 2.9 30.0 - - - +
252A PHE* 2.8 36.9 + + - -
280A LEU 4.1 1.1 + - - +
281A ILE* 1.3 71.5 - - - +
283A GLU* 1.3 56.9 + - - +
334A LEU* 5.9 2.9 - - + +
343A LEU* 3.5 38.8 - - + +
344A SER 3.4 11.0 + - - -
345A LEU* 4.3 9.5 - - + +
600A ERT 5.1 1.4 - - - -
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LEU 5.0 0.9 - - - +
252A PHE* 4.0 24.3 + - + -
253A VAL 4.2 2.1 + - - -
254A LEU* 3.3 17.7 + - - +
255A LEU* 3.1 55.2 + - + +
281A ILE* 3.8 10.4 - - + +
282A HIS* 1.3 77.9 - - - +
284A ARG* 1.3 66.8 + - - +
310A ALA 4.9 1.2 - - - +
311A LEU* 4.1 5.0 - - + +
312A ARG* 5.3 0.2 + - - -
317A TRP* 3.5 24.9 - - + -
343A LEU* 3.4 14.4 - - - +
344A SER* 2.8 31.8 + - - +
346A LEU* 5.3 1.7 - - + +
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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
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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