Contacts of the strand formed by residues 343 - 350 (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 LEU 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ALA 5.9 1.1 - - - +
252B PHE* 3.6 23.6 - - + -
282B HIS* 4.3 17.5 - - + -
283B GLU 3.4 15.3 - - - +
284B ARG* 4.7 3.4 - - - -
333B GLN* 3.6 2.1 - - - -
334B LEU* 2.8 46.6 + - + +
336B SER* 6.4 0.4 - - - -
339B ILE* 4.3 19.7 - - + +
341B TYR* 4.0 20.9 + - + +
342B ASP* 1.3 77.2 - - - +
344B SER* 1.3 62.7 + - - +
1600B ERT 3.4 31.0 - - + +
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Residues in contact with SER 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B HIS* 3.4 8.0 + - - -
283B GLU 2.9 31.2 + - - +
284B ARG* 3.8 1.4 - - - -
285B ASP* 3.0 32.8 + - - +
331B VAL* 3.5 26.2 - - - -
332B ARG 3.4 7.4 - - - -
333B GLN* 4.3 6.9 + - - -
334B LEU* 3.6 4.7 - - - -
342B ASP 4.1 2.1 + - - -
343B LEU* 1.3 76.5 - - - +
345B LEU* 1.3 61.9 + - - +
346B LEU* 4.0 6.1 - - - -
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B PRO* 4.6 8.5 - - + +
173B ALA* 3.9 31.4 - - + +
174B TYR* 4.6 2.9 - - + -
192B PHE* 4.8 9.9 - - + -
280B LEU* 3.9 40.8 - - + +
281B ILE 3.2 21.8 - - - +
282B HIS* 3.9 15.9 - - + +
331B VAL* 3.7 0.4 - - - -
332B ARG* 3.0 38.5 + - + +
334B LEU* 4.1 10.3 - - + -
344B SER* 1.3 72.7 - - - +
346B LEU* 1.3 64.4 + - - +
347B VAL* 3.7 12.4 + - + +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE 3.4 1.7 - - - +
280B LEU* 3.3 5.5 - - - -
281B ILE* 2.8 62.2 + - + +
283B GLU* 4.9 3.6 - - + +
284B ARG 5.0 5.2 - - - +
285B ASP* 4.5 5.4 - - + +
317B TRP* 3.9 48.5 - - + +
328B VAL* 4.4 8.7 - - + -
330B GLU 3.8 4.9 - - - +
331B VAL* 3.7 30.1 - - + +
344B SER* 4.6 12.8 - - - +
345B LEU* 1.3 73.9 - - - +
347B VAL* 1.3 59.2 + - - +
348B LEU* 4.0 13.4 - - + +
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 4.8 6.5 - - + -
278B ARG* 4.2 13.2 - - + -
279B ILE 3.5 2.9 - - - -
280B LEU* 3.8 20.6 - - + -
328B VAL* 3.7 0.2 - - - -
329B GLU* 3.1 54.2 + - + +
330B GLU* 3.0 23.5 + - + +
332B ARG* 4.0 32.1 - - - +
345B LEU* 4.0 8.3 - - + +
346B LEU* 1.3 72.8 - - - +
348B LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 348 (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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266B LEU* 4.4 8.3 - - + -
273B LEU* 4.9 1.0 - - - +
278B ARG* 3.4 9.9 - - - -
279B ILE* 2.8 48.4 + - + +
281B ILE* 3.8 24.0 - - + -
317B TRP* 6.0 1.3 - - + -
321B ALA* 3.9 21.5 - - + -
326B LEU* 4.0 23.8 - - + -
327B VAL 3.2 14.6 - - - +
328B VAL* 3.8 19.7 - - + -
346B LEU* 4.0 22.4 - - + +
347B VAL* 1.3 80.8 - - - +
349B ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 349 (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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273B LEU* 5.5 0.4 - - - -
277B GLY 4.8 0.2 - - - -
278B ARG* 3.2 33.4 - - - +
326B LEU* 3.3 9.7 - - - +
327B VAL* 2.8 34.5 + - + +
329B GLU* 4.0 16.5 - - + +
347B VAL 4.3 0.2 + - - -
348B LEU* 1.3 73.0 - - - +
350B PRO* 1.3 76.9 - - + +
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Residues in contact with PRO 350 (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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270B ALA* 6.5 0.2 - - + -
273B LEU* 4.5 14.4 - - + -
276B GLY 6.4 0.4 - - - +
277B GLY 4.5 11.4 - - - +
278B ARG* 4.9 3.6 - - - +
325B GLY 3.8 9.6 - - - +
326B LEU* 3.9 6.5 - - + -
327B VAL* 3.7 8.0 - - - +
349B ALA* 1.3 96.3 - - + +
351B ALA* 1.3 65.0 + - - +
352B ALA* 3.3 12.8 + - - +
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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