Contacts of the helix formed by residues 288 - 295 (chain A) 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 VAL 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A LEU 3.2 0.4 + - - -
287A SER* 1.3 73.6 - - - +
289A ALA* 1.3 56.9 + - - +
291A ILE* 2.4 42.7 - - + +
292A THR* 5.0 0.5 - - - +
319A TYR* 5.3 4.4 - - + -
322A ASP 4.3 4.7 - - - +
323A VAL* 4.3 18.6 - - + -
324A VAL* 5.3 1.3 - - + -
327A ASP* 3.3 33.4 - - + +
373A ARG* 2.4 56.5 - - + +
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Residues in contact with ALA 289 (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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287A SER* 4.5 1.2 + - - -
288A VAL* 1.3 75.9 - - - +
290A GLU* 1.3 56.0 + - - +
291A ILE 2.7 7.2 + - - -
292A THR* 2.3 36.3 + - - -
293A ASN* 3.7 0.9 + - - +
319A TYR* 5.8 0.2 - - - -
327A ASP* 3.9 12.5 - - + +
331A ALA* 3.0 33.9 - - + +
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Residues in contact with GLU 290 (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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283A HIS* 5.6 2.5 + - - -
286A LEU* 3.5 24.1 - - + +
287A SER* 2.4 38.9 + - - +
288A VAL 3.1 1.0 - - - -
289A ALA* 1.3 75.4 - - - +
291A ILE* 1.4 60.6 - - - +
292A THR 3.1 0.2 - - - -
293A ASN* 3.2 16.4 + - + +
294A ALA* 2.8 30.7 + - - +
297A GLU* 5.1 5.9 - - - +
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Residues in contact with ILE 291 (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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273A ALA* 3.1 10.3 - - + +
274A PRO* 4.5 1.6 - - + -
286A LEU* 4.8 14.6 - - + +
287A SER 3.1 10.8 - - - +
288A VAL* 2.4 29.3 + - + +
290A GLU* 1.4 80.9 - - - +
292A THR* 1.3 58.2 + - - +
294A ALA* 2.9 26.9 - - - +
295A CYS 3.1 3.1 + - - -
319A TYR* 5.0 1.3 - - + -
371A VAL* 5.1 2.7 - - + -
373A ARG* 2.7 52.3 - - + +
374A ALA* 3.5 4.0 - - - +
375A VAL* 2.5 53.5 - - + +
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Residues in contact with THR 292 (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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289A ALA* 2.3 29.9 + - - +
291A ILE* 1.3 79.2 - - - +
293A ASN* 1.2 65.9 + - - +
295A CYS* 2.9 21.0 - - - +
296A PHE* 3.2 10.6 - - - -
319A TYR* 2.4 45.1 - - + +
327A ASP 5.0 1.3 - - - +
331A ALA* 3.9 27.4 + - + +
332A ILE* 4.6 5.6 - - + -
334A THR* 4.9 0.9 + - - -
335A ILE* 4.0 14.8 - - - +
375A VAL* 3.5 6.5 - - - -
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Residues in contact with ASN 293 (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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289A ALA 4.7 0.2 - - - +
290A GLU* 3.2 21.0 + - + +
292A THR* 1.2 80.7 + - - +
294A ALA* 1.4 66.8 - - - +
296A PHE* 2.8 14.7 + - - +
297A GLU* 2.8 37.5 + - - +
335A ILE* 5.0 4.3 - - + -
338A LYS* 3.5 28.6 + - - +
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Residues in contact with ALA 294 (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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273A ALA* 2.8 37.7 - - + +
286A LEU* 5.8 4.7 - - + -
290A GLU 2.8 13.5 + - - +
291A ILE* 2.9 7.9 - - - +
293A ASN* 1.4 71.2 - - - +
295A CYS* 1.3 63.5 + - - +
297A GLU* 3.0 25.1 + - - +
300A ASN* 2.0 34.3 + - - +
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Residues in contact with CYS 295 (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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271A THR* 3.4 40.9 - - - +
273A ALA* 3.9 1.5 - - - +
291A ILE 3.1 2.8 + - - -
292A THR 2.9 11.7 + - - +
293A ASN 2.9 0.2 - - - -
294A ALA* 1.3 83.4 - - - +
296A PHE* 1.2 72.5 + - + +
297A GLU 3.0 6.8 - - - +
300A ASN* 3.4 3.5 + - - +
317A LEU* 5.0 2.5 - - + -
375A VAL* 1.6 58.8 - - - -
376A CYS 4.2 0.2 - - - -
377A MET* 3.9 12.2 - - + +
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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