Contacts of the strand formed by residues 314 - 320 (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 THR 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ALA* 5.5 7.0 - - + -
404A PHE* 5.0 4.3 - - + -
258B ASN 2.7 29.4 - - - +
259B MET* 3.0 30.6 + - - +
260B VAL 4.8 0.4 - - - +
261B PRO* 3.5 26.7 - - + -
312B TYR* 3.6 1.6 - - - +
313B LEU* 1.3 84.0 + - - +
315B VAL* 1.3 71.2 + - - +
347B ILE* 3.9 14.0 - - + +
350B ASN* 3.9 9.2 + - - -
379B GLY* 3.4 0.2 - - - -
380B ASN 3.3 14.6 + - - +
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Residues in contact with VAL 315 (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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258B ASN* 5.7 0.7 - - - -
259B MET* 4.3 0.4 - - - -
296B PHE* 4.0 7.9 - - + -
312B TYR* 3.5 19.5 - - + -
314B THR* 1.3 81.3 - - - +
316B ALA* 1.4 60.5 + - - +
317B ALA* 4.9 0.4 - - + +
343B PHE* 3.2 33.0 - - + -
350B ASN 3.0 13.5 + - - +
351B VAL* 3.2 19.2 - - + -
352B LYS* 2.9 27.6 + - - +
377B PHE* 3.2 34.1 - - + -
378B ILE 3.5 3.6 - - - -
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Residues in contact with ALA 316 (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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255B LEU* 5.5 7.2 - - + -
258B ASN* 4.6 12.6 - - + -
259B MET* 3.3 27.9 - - + -
315B VAL* 1.4 70.8 - - - +
317B ALA* 1.3 57.2 + - - +
318B VAL* 5.1 4.0 - - + -
352B LYS* 3.8 14.1 - - + -
377B PHE* 3.4 0.5 - - - -
378B ILE* 2.4 54.6 + - + +
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Residues in contact with ALA 317 (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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295B MET* 4.8 3.4 - - - -
315B VAL* 3.9 1.7 + - + -
316B ALA* 1.3 72.8 - - - +
318B VAL* 1.3 65.7 + - - +
319B PHE* 4.3 9.0 - - + -
332B MET* 3.6 31.0 - - + -
351B VAL* 4.9 1.6 - - + -
352B LYS* 2.9 11.5 + - - +
353B THR* 3.2 7.3 - - - -
354B ALA 3.0 21.5 + - - -
376B THR 3.3 10.1 - - - +
377B PHE* 4.1 11.9 - - + +
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Residues in contact with VAL 318 (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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237B GLY 4.4 4.5 - - - +
238B VAL* 6.1 1.6 - - + -
241B CYS* 4.1 26.9 - - + -
242B LEU* 4.3 15.0 - - + -
255B LEU* 5.8 5.4 - - + -
316B ALA* 5.1 5.4 - - + -
317B ALA* 1.3 82.0 - - - +
319B PHE* 1.4 64.1 + - - +
320B ARG* 4.5 0.6 + - + +
352B LYS* 6.0 1.6 - - + -
354B ALA* 3.3 32.3 - - + +
355B VAL* 5.1 1.3 - - - -
356B CYS* 5.1 1.3 - - - -
374B SER* 5.4 0.2 + - - -
375B ALA* 3.2 1.0 - - - -
376B THR* 2.3 62.1 + - + +
378B ILE* 5.8 4.0 - - + -
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Residues in contact with PHE 319 (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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288B VAL* 5.0 2.7 - - + -
291B LEU* 5.0 10.5 - - + -
292B THR* 4.3 7.4 - - + -
295B MET* 3.9 26.7 - - + -
317B ALA* 4.2 7.9 - - + -
318B VAL* 1.4 72.1 - - - +
320B ARG* 1.3 62.7 - - - +
321B GLY 3.7 2.8 + - - +
328B VAL* 2.2 46.3 - - + +
332B MET* 3.0 39.0 - - + -
353B THR* 2.4 29.4 - - + -
354B ALA 3.0 9.3 + - - -
355B VAL* 3.0 33.9 - - + +
373B MET* 6.2 0.4 - - + -
374B SER 3.3 13.2 - - - +
375B ALA* 4.7 1.1 - - + -
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Residues in contact with ARG 320 (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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236B SER* 2.9 20.5 + - - -
237B GLY* 4.3 0.4 - - - -
240B THR* 3.8 14.1 - - - +
241B CYS* 2.2 53.9 - - + +
272B PHE* 4.9 2.1 - - - -
318B VAL* 4.3 1.8 - - + +
319B PHE* 1.3 74.1 - - - +
321B GLY* 1.3 58.8 + - - +
356B CYS* 3.2 33.0 - - + +
358B ILE 3.2 13.7 + - - +
359B PRO* 3.0 19.8 - - - +
360B PRO* 3.3 21.6 - - + +
374B SER* 2.2 42.8 + - - +
376B THR* 5.6 1.5 + - - -
501B TXL 2.8 40.6 - - - -
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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