Contacts of the helix formed by residues 375 - 385 (chain B) in PDB entry 2DB3
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 375 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324B VAL* 5.3 0.4 - - - -
325B SER 3.5 14.8 - - - +
327B THR 3.5 29.4 - - - +
328B ARG* 3.6 11.7 - - + +
331B ALA* 4.4 2.9 - - + -
352B VAL 3.2 2.0 + - - +
353B TYR* 3.2 20.1 - - + +
354B GLY 3.9 0.5 + - - -
374B ALA* 1.3 77.1 - - - +
376B PRO* 1.3 74.9 - - - +
377B GLY 3.3 0.5 + - - -
378B ARG 3.6 0.3 + - - -
379B LEU* 3.3 17.8 + - - +
5F U 3.5 20.6 - - - -
6F U 2.8 18.7 + - - -
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Residues in contact with PRO 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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324B VAL* 4.0 4.7 - - + -
325B SER 3.5 14.1 - - - +
375B THR* 1.3 85.3 - - - +
377B GLY* 1.3 63.5 + - - +
379B LEU* 3.3 5.6 + - + +
380B LEU* 2.9 28.9 + - - +
404B MET* 3.4 25.1 - - + -
409B PHE* 3.7 21.8 - - + -
412B ASP* 4.1 23.6 - - + +
413B MET* 3.7 13.2 - - + -
416B ILE* 4.5 7.4 - - + +
5F U 3.9 5.8 - - - +
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Residues in contact with GLY 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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375B THR 3.4 1.0 - - - -
376B PRO* 1.3 72.6 - - - +
378B ARG* 1.3 62.6 + - - +
380B LEU* 3.2 8.4 + - - +
381B ASP 3.0 16.5 + - - -
412B ASP* 4.6 6.5 + - - -
5F U 2.9 19.0 + - - -
6F U 2.9 37.7 - - - +
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Residues in contact with ARG 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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352B VAL* 3.8 7.4 - - + +
353B TYR* 3.4 23.8 - - - +
354B GLY* 3.7 3.4 - - - +
356B THR* 2.3 49.1 + - - -
357B SER 3.5 1.4 + - - -
358B PHE* 3.3 35.8 - - - +
361B GLN* 3.3 21.1 + - - +
375B THR* 3.6 0.6 + - - +
376B PRO 3.5 0.2 - - - -
377B GLY* 1.3 70.0 - - - +
379B LEU* 1.3 66.4 + - - +
381B ASP* 3.1 3.7 + - - +
382B PHE* 3.1 24.8 + - + -
6F U 2.9 46.6 + - - +
7F U 2.7 35.4 + - - -
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Residues in contact with LEU 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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322B VAL* 4.1 24.9 - - + -
324B VAL* 4.4 8.7 - - + -
352B VAL* 3.7 8.8 - - + +
372B VAL* 5.1 5.2 - - + -
374B ALA* 4.0 17.3 - - + -
375B THR 3.3 12.4 + - - +
376B PRO 3.3 7.8 + - - +
377B GLY 3.2 0.4 - - - -
378B ARG* 1.3 77.9 - - - +
380B LEU* 1.3 57.4 + - - +
382B PHE* 2.9 7.1 + - - +
383B VAL* 2.8 36.9 + - + +
388B ILE* 4.0 34.1 - - + -
390B PHE* 4.5 4.9 - - + -
416B ILE* 3.7 32.8 - - + -
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Residues in contact with LEU 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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376B PRO 2.9 19.5 + - - +
377B GLY* 3.2 5.8 + - - +
379B LEU* 1.3 76.4 - - - +
381B ASP* 1.3 57.9 + - - +
383B VAL* 3.7 19.1 - - + -
384B ASP* 2.8 38.1 + - - +
412B ASP* 3.4 50.7 - - + +
415B ARG* 3.5 37.9 - - + +
416B ILE* 3.5 26.9 - - + +
419B HIS* 6.0 0.2 - - - +
6F U 6.1 0.2 - - - -
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Residues in contact with ASP 381 (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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358B PHE* 3.4 17.8 - - + -
377B GLY 3.0 6.4 + - - +
378B ARG 3.3 9.9 - - - +
379B LEU 3.1 0.4 - - - -
380B LEU* 1.3 75.0 - - - +
382B PHE* 1.3 65.6 + - - +
384B ASP* 3.4 5.9 + - - +
385B ARG* 2.6 56.6 + - - +
6F U 2.9 47.3 + - - +
7F U 4.6 5.0 - - - +
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Residues in contact with PHE 382 (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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352B VAL* 3.1 31.9 - - + -
358B PHE* 3.5 34.1 - + - -
361B GLN* 3.9 6.3 - - + -
362B ASN* 3.2 50.0 - - + -
365B ILE* 4.2 9.2 - - + -
378B ARG* 3.1 28.9 + - + -
379B LEU 2.9 8.4 + - - +
381B ASP* 1.3 76.7 - - - +
383B VAL* 1.3 60.9 + - - +
385B ARG* 3.4 1.3 + - - +
386B THR 3.2 3.1 + - - -
387B PHE* 2.8 48.7 + - + +
388B ILE* 3.8 28.3 - - + -
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Residues in contact with VAL 383 (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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379B LEU* 2.8 25.7 + - + +
380B LEU* 3.7 17.5 - - + +
382B PHE* 1.3 78.6 - - - +
384B ASP* 1.3 67.4 + - - +
386B THR* 3.1 15.1 + - - -
388B ILE* 3.5 22.4 - - + +
390B PHE* 3.6 31.2 - - + -
415B ARG* 5.6 0.4 - - - +
419B HIS* 3.3 42.0 + - + +
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Residues in contact with ASP 384 (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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380B LEU 2.8 21.4 + - - +
381B ASP* 3.4 6.3 + - - +
382B PHE 3.3 0.2 - - - -
383B VAL* 1.3 83.6 - - - +
385B ARG* 1.3 60.3 + - + +
386B THR* 3.1 5.2 + - - -
415B ARG* 2.6 38.6 + - - -
419B HIS* 5.3 2.4 - - - -
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Residues in contact with ARG 385 (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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358B PHE* 3.2 42.6 - - - +
381B ASP* 2.6 55.7 + - - +
382B PHE 3.4 1.1 + - - +
383B VAL 3.3 0.2 - - - -
384B ASP* 1.3 75.7 - - + +
386B THR* 1.3 70.5 + - - +
387B PHE* 3.4 35.6 + - + -
6F U 5.3 0.2 + - - -
7F U 5.7 3.2 + - - -
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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