Contacts of the strand formed by residues 373 - 380 (chain B) in PDB entry 1TUB
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 MET 373 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B ALA 5.5 1.3 - - - +
286B LEU* 2.9 48.6 - - + +
291B LEU* 3.7 24.7 - - + +
319B PHE* 6.2 0.7 - - + -
321B GLY* 3.1 35.0 - - - +
322B ARG 4.7 0.4 - - - -
323B MET* 3.7 38.6 - - + +
359B PRO* 4.0 1.1 - - - -
360B PRO* 4.3 0.2 - - - -
371B LEU* 2.9 20.2 - - - +
372B LYS* 1.4 75.3 - - - +
374B SER* 1.4 60.4 + - - +
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 4.8 6.1 - - - -
273B ALA 4.5 0.9 - - - -
291B LEU* 3.8 7.5 - - - +
318B VAL 5.4 0.3 + - - -
319B PHE* 3.3 22.1 - - - +
320B ARG* 2.2 41.8 + - - +
321B GLY* 3.9 2.7 + - - -
360B PRO* 3.1 30.7 - - - -
371B LEU* 3.7 7.9 - - - -
373B MET* 1.4 73.2 - - - +
375B ALA* 1.3 61.2 + - - +
376B THR* 5.7 1.6 - - - -
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Residues in contact with ALA 375 (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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272B PHE* 3.4 12.2 - - - -
273B ALA* 3.3 36.0 + - + +
274B PRO* 4.5 0.6 - - - +
291B LEU* 3.9 17.9 - - + +
295B MET* 1.9 39.0 - - + -
318B VAL 3.3 2.9 - - - -
319B PHE* 4.3 0.4 - - + +
374B SER* 1.3 77.6 - - - +
376B THR* 1.3 62.8 + - - +
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Residues in contact with THR 376 (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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233B ALA 4.1 6.2 + - - -
234B THR* 4.4 18.8 - - + +
237B GLY* 3.4 32.4 + - - -
238B VAL* 4.6 8.1 - - + -
241B CYS* 4.9 1.7 - - - -
271B GLY 3.4 6.7 - - - +
272B PHE* 4.4 5.7 - - - -
295B MET* 3.5 6.7 - - - +
317B ALA* 3.3 2.3 - - - -
318B VAL* 2.3 66.5 + - + +
320B ARG* 5.6 1.2 + - - -
374B SER* 5.7 1.2 - - - -
375B ALA* 1.3 74.3 + - - +
377B PHE* 1.3 69.2 + - - +
378B ILE* 4.9 4.0 - - + -
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Residues in contact with PHE 377 (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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269B MET* 3.7 5.6 - - + -
270B PRO* 2.8 34.7 - - - +
271B GLY* 3.0 17.4 + - - +
295B MET* 3.3 37.9 - - + +
296B PHE* 3.8 12.1 - + - -
301B MET* 3.0 31.6 - - + -
312B TYR* 3.6 31.6 - + - -
315B VAL* 3.2 29.4 - - + -
316B ALA 3.5 4.5 - - - -
317B ALA* 4.5 6.7 - - + -
376B THR* 1.3 76.7 - - - +
378B ILE* 1.3 83.4 - - - +
379B GLY* 3.9 1.1 - - - -
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Residues in contact with ILE 378 (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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200B GLU* 5.4 1.8 - - - +
202B TYR* 3.6 30.7 - - + +
238B VAL* 4.3 16.4 - - + -
255B LEU* 5.3 8.7 - - + -
259B MET* 3.0 33.9 - - + -
268B PHE* 4.0 11.2 - - + -
269B MET 3.4 4.5 - - - +
270B PRO* 3.6 11.2 - - + -
315B VAL* 3.5 0.3 - - - -
316B ALA* 2.4 43.5 + - + +
318B VAL* 5.8 4.5 - - + -
376B THR* 4.9 4.5 - - + -
377B PHE* 1.3 106.5 - - - +
379B GLY* 1.3 71.2 + - - +
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Residues in contact with GLY 379 (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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259B MET* 2.3 30.1 - - - +
268B PHE* 2.9 13.3 - - - -
269B MET* 3.0 14.9 + - - +
312B TYR* 4.3 6.3 - - - -
314B THR 3.4 10.1 - - - -
315B VAL* 4.1 0.7 - - - -
377B PHE* 4.2 7.0 - - - -
378B ILE* 1.3 74.5 - - - +
380B ASN* 1.3 66.3 + - - +
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Residues in contact with ASN 380 (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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259B MET* 2.9 14.1 + - - +
266B HIS* 3.5 11.1 - - + +
267B PHE 1.2 39.4 + - - +
268B PHE* 2.0 52.0 - - - -
269B MET* 6.1 0.7 - - - -
312B TYR* 2.8 3.1 - - - +
313B LEU* 1.9 53.7 + - + +
314B THR 3.3 2.8 + - - -
379B GLY* 1.3 70.1 - - - +
381B SER* 1.0 52.7 - - - +
384B ILE* 5.7 2.6 - - - +
432B TYR* 3.6 15.3 - - + +
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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