Contacts of the helix formed by residues 354 - 365 (chain A) in PDB entry 2DFS
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 HIS 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A ASN 4.4 1.8 - - - -
338A VAL* 4.1 7.0 - - + -
339A GLU* 3.1 36.5 + - + -
350A ILE* 3.5 35.2 - - + -
351A PRO* 3.6 24.8 - - + +
352A PRO 4.5 0.4 - - - -
353A LYS* 1.3 73.3 - - - +
355A ASP* 1.3 54.7 + - - +
356A PRO* 3.4 29.7 - - + +
357A LEU* 3.2 9.7 + - + +
358A THR* 2.7 37.3 + - - -
368A TYR* 3.1 10.7 + - - +
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Residues in contact with ASP 355 (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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284A TYR* 5.9 2.7 - - - +
353A LYS* 2.6 35.0 + - - +
354A HIS* 1.3 70.7 + - - +
356A PRO* 1.3 70.0 - - + +
358A THR* 3.9 2.0 - - - -
359A ILE* 3.3 33.6 + - + +
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Residues in contact with PRO 356 (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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284A TYR* 6.0 2.2 - - - +
334A HIS* 3.6 38.9 - - - +
337A ASN* 3.3 35.7 - - + +
338A VAL* 4.1 1.3 - - - +
354A HIS* 3.4 26.5 - - + +
355A ASP* 1.3 94.5 - - + +
357A LEU* 1.3 55.1 + - - +
359A ILE* 3.5 0.7 + - - +
360A PHE* 3.0 26.9 + - - +
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Residues in contact with LEU 357 (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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335A LEU* 5.3 0.4 - - + -
338A VAL* 4.1 16.7 - - + +
350A ILE* 4.0 24.2 - - + -
354A HIS* 3.2 16.1 + - + +
356A PRO* 1.3 76.8 - - - +
358A THR* 1.4 60.1 + - - +
360A PHE* 3.2 23.8 + - + +
361A CYS* 3.0 37.8 + - - -
368A TYR* 3.6 29.8 - - + +
371A MET* 4.4 3.4 - - + -
372A ALA* 4.0 20.4 - - + +
375A LEU* 4.0 20.9 - - + -
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Residues in contact with THR 358 (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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353A LYS* 3.5 30.4 + - + +
354A HIS 2.7 28.2 + - - -
355A ASP* 3.9 5.4 - - - -
357A LEU* 1.4 70.7 - - - +
359A ILE* 1.4 63.7 + - + +
361A CYS* 3.6 1.9 + - - +
362A ASP* 3.1 26.1 + - + +
368A TYR* 3.7 20.1 - - + -
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Residues in contact with ILE 359 (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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277A LEU 4.5 0.2 - - - +
278A ARG* 4.1 36.8 - - + +
334A HIS* 3.5 49.1 - - + +
355A ASP* 3.3 17.5 + - + +
356A PRO* 3.8 0.7 - - + +
358A THR* 1.4 74.6 - - + +
360A PHE* 1.4 64.4 + - - +
362A ASP* 3.4 7.1 + - - +
363A LEU* 3.0 39.3 + - + +
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Residues in contact with PHE 360 (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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331A GLY* 3.2 32.8 - - - -
334A HIS* 4.3 10.3 - - + +
335A LEU* 3.8 43.1 - - + +
356A PRO 3.0 16.2 + - - +
357A LEU* 3.2 23.3 + - + +
359A ILE* 1.4 74.4 - - - +
361A CYS* 1.3 66.6 + - - +
363A LEU* 3.4 4.8 + - - +
364A MET* 3.2 62.1 + - + +
366A VAL* 5.6 0.9 - - + -
371A MET* 4.0 24.7 - - + -
403A LEU* 5.0 2.0 - - + -
407A ILE* 5.0 5.4 - - + -
580A LEU* 4.3 11.9 - - + -
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Residues in contact with CYS 361 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A LEU* 3.0 31.1 + - - +
358A THR 4.1 2.7 - - - +
360A PHE* 1.3 74.3 - - - +
362A ASP* 1.4 55.6 + - - +
364A MET 3.5 0.2 + - - -
365A GLY* 2.8 31.4 + - - -
366A VAL* 3.4 31.0 + - - +
367A ASP 3.7 16.8 - - - -
368A TYR* 3.8 24.0 - - + -
371A MET* 4.0 18.6 - - - -
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Residues in contact with ASP 362 (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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278A ARG* 2.6 48.3 + - - +
327A ARG* 3.9 7.3 + - - -
358A THR* 3.1 21.7 + - + +
359A ILE* 3.5 4.9 - - - +
361A CYS* 1.4 74.6 - - - +
363A LEU* 1.3 65.9 + - - +
364A MET 3.4 0.2 + - - -
365A GLY* 3.5 8.9 + - - -
585A LYS* 5.7 3.3 - - - +
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Residues in contact with LEU 363 (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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276A THR 3.1 28.7 - - - +
277A LEU* 4.3 3.6 - - - +
278A ARG* 3.4 17.0 - - - +
327A ARG* 3.0 44.9 + - + +
330A ALA* 3.6 21.1 - - + +
331A GLY* 3.6 29.6 - - - +
334A HIS* 4.8 0.2 - - + -
359A ILE* 3.0 32.4 + - + +
360A PHE* 3.8 4.7 - - - +
362A ASP* 1.3 76.8 - - - +
364A MET* 1.3 65.1 + - + +
585A LYS* 6.0 1.9 - - - +
586A PHE* 3.6 16.1 - - - -
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Residues in contact with MET 364 (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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327A ARG 5.0 2.7 - - - +
328A ILE* 4.5 22.9 - - + +
331A GLY* 5.1 3.4 - - - -
332A ILE* 5.8 0.4 - - + +
360A PHE* 3.2 51.6 + - + +
361A CYS 4.2 1.1 - - - +
363A LEU* 1.3 77.4 - - + +
365A GLY* 1.4 57.2 + - - +
366A VAL* 3.5 14.8 - - + -
407A ILE* 4.3 14.4 - - + -
580A LEU* 4.3 7.9 - - + -
583A SER* 2.9 23.2 + - - -
585A LYS* 5.0 0.8 - - - +
586A PHE* 3.8 26.7 - - - +
589A LEU* 3.6 40.6 - - + +
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Residues in contact with GLY 365 (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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361A CYS 2.8 13.7 + - - -
362A ASP* 3.5 8.4 + - - -
363A LEU 5.0 0.2 - - - -
364A MET* 1.4 73.4 - - - +
366A VAL* 1.3 63.4 + - - +
583A SER* 3.9 10.5 + - - -
584A LYS* 3.7 23.7 + - - +
585A LYS* 4.3 18.4 - - - +
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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